Starting phenix.real_space_refine on Sun Sep 13 06:04:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rop_54127/09_2026/9rop_54127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rop_54127/09_2026/9rop_54127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rop_54127/09_2026/9rop_54127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rop_54127/09_2026/9rop_54127.map" model { file = "/net/cci-nas-00/data/ceres_data/9rop_54127/09_2026/9rop_54127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rop_54127/09_2026/9rop_54127.cif" } resolution = 3.24 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= 0.001 sd= 0.013 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 S 58 5.16 5 C 6574 2.51 5 N 1715 2.21 5 O 1922 1.98 5 H 10307 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20576 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 15477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 15477 Classifications: {'peptide': 994} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 950} Chain: "B" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 4556 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 260} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Time building chain proxies: 3.18, per 1000 atoms: 0.15 Number of scatterers: 20576 At special positions: 0 Unit cell: (82.071, 81.242, 176.577, 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 58 16.00 O 1922 8.00 N 1715 7.00 C 6574 6.00 H 10307 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 450.0 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 12 sheets defined 50.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 99 through 122 removed outlier: 4.485A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 159 removed outlier: 4.360A pdb=" N LEU A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.916A pdb=" N THR A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 369 removed outlier: 3.724A pdb=" N GLU A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 473 removed outlier: 3.635A pdb=" N MET A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 597 through 609 removed outlier: 4.485A pdb=" N ASP A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 656 through 660 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.870A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 708 removed outlier: 3.629A pdb=" N GLN A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 755 through 782 removed outlier: 4.026A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 796 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 814 Processing helix chain 'A' and resid 816 through 824 removed outlier: 4.146A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 857 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 3.668A pdb=" N LEU A 884 " --> pdb=" O ILE A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 938 removed outlier: 3.913A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.621A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 987 through 990 Processing helix chain 'A' and resid 991 through 1012 Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 94 through 110 removed outlier: 3.781A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'C' and resid 33 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 173 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.974A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 243 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 199 removed outlier: 4.185A pdb=" N THR A 247 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 213 Processing sheet with id=AA5, first strand: chain 'A' and resid 663 through 666 removed outlier: 7.109A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY A 731 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU A 750 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA A 733 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 396 through 399 removed outlier: 7.189A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE A 393 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 10.875A pdb=" N VAL A 586 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LEU A 583 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N PHE A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 587 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 589 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 553 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 502 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 495 " --> pdb=" O GLN A 502 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS A 476 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 396 through 399 removed outlier: 7.189A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N PHE A 393 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 10.875A pdb=" N VAL A 586 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N CYS A 518 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE A 585 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 520 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLY A 587 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N LEU A 522 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 11.999A pdb=" N ILE A 589 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 88 removed outlier: 6.438A pdb=" N ARG B 273 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS B 216 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B 275 " --> pdb=" O THR B 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 210 523 hydrogen bonds defined for protein. 1473 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: 4.66 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10283 1.03 - 1.23: 143 1.23 - 1.43: 4180 1.43 - 1.62: 6097 1.62 - 1.82: 86 Bond restraints: 20789 Sorted by residual: bond pdb=" CB TRP A 906 " pdb=" CG TRP A 906 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.57e-01 bond pdb=" CA PHE B 24 " pdb=" CB PHE B 24 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.85e-01 bond pdb=" CG PRO B 244 " pdb=" CD PRO B 244 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.61e-01 bond pdb=" CG MET A 832 " pdb=" SD MET A 832 " ideal model delta sigma weight residual 1.803 1.822 -0.019 2.50e-02 1.60e+03 5.60e-01 bond pdb=" CB ASP B 218 " pdb=" CG ASP B 218 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.54e-01 ... (remaining 20784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 36964 1.52 - 3.04: 646 3.04 - 4.56: 65 4.56 - 6.08: 9 6.08 - 7.60: 3 Bond angle restraints: 37687 Sorted by residual: angle pdb=" CB MET A 591 " pdb=" CG MET A 591 " pdb=" SD MET A 591 " ideal model delta sigma weight residual 112.70 120.30 -7.60 3.00e+00 1.11e-01 6.43e+00 angle pdb=" CG MET A 832 " pdb=" SD MET A 832 " pdb=" CE MET A 832 " ideal model delta sigma weight residual 100.90 106.40 -5.50 2.20e+00 2.07e-01 6.25e+00 angle pdb=" C ASP C 32 " pdb=" CA ASP C 32 " pdb=" CB ASP C 32 " ideal model delta sigma weight residual 110.16 113.73 -3.57 1.44e+00 4.82e-01 6.16e+00 angle pdb=" CB MET A 816 " pdb=" CG MET A 816 " pdb=" SD MET A 816 " ideal model delta sigma weight residual 112.70 120.14 -7.44 3.00e+00 1.11e-01 6.15e+00 angle pdb=" CA MET A 591 " pdb=" CB MET A 591 " pdb=" CG MET A 591 " ideal model delta sigma weight residual 114.10 118.98 -4.88 2.00e+00 2.50e-01 5.96e+00 ... (remaining 37682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8605 17.92 - 35.85: 808 35.85 - 53.77: 268 53.77 - 71.70: 75 71.70 - 89.62: 13 Dihedral angle restraints: 9769 sinusoidal: 5370 harmonic: 4399 Sorted by residual: dihedral pdb=" CA GLU B 219 " pdb=" C GLU B 219 " pdb=" N ASP B 220 " pdb=" CA ASP B 220 " ideal model delta harmonic sigma weight residual 180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS B 221 " pdb=" C LYS B 221 " pdb=" N ASP B 222 " pdb=" CA ASP B 222 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA MET A 980 " pdb=" C MET A 980 " pdb=" N TYR A 981 " pdb=" CA TYR A 981 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 9766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 936 0.027 - 0.055: 435 0.055 - 0.082: 137 0.082 - 0.109: 70 0.109 - 0.137: 30 Chirality restraints: 1608 Sorted by residual: chirality pdb=" CA VAL B 148 " pdb=" N VAL B 148 " pdb=" C VAL B 148 " pdb=" CB VAL B 148 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE A 711 " pdb=" N ILE A 711 " pdb=" C ILE A 711 " pdb=" CB ILE A 711 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 492 " pdb=" N ILE A 492 " pdb=" C ILE A 492 " pdb=" CB ILE A 492 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1605 not shown) Planarity restraints: 3077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 32 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C ASP C 32 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP C 32 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR C 33 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 169 " -0.018 2.00e-02 2.50e+03 8.50e-03 2.17e+00 pdb=" CG TYR B 169 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 169 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 169 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 169 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 169 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 169 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TYR B 169 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR B 169 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR B 169 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR B 169 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 599 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO A 600 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " 0.020 5.00e-02 4.00e+02 ... (remaining 3074 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 579 2.10 - 2.72: 36718 2.72 - 3.35: 62650 3.35 - 3.97: 77405 3.97 - 4.60: 120634 Nonbonded interactions: 297986 Sorted by model distance: nonbonded pdb=" OE1 GLU A 334 " pdb=" H GLU A 334 " model vdw 1.471 2.450 nonbonded pdb=" O ILE A 784 " pdb=" HG1 THR A 788 " model vdw 1.551 2.450 nonbonded pdb=" O SER B 286 " pdb="HH22 ARG B 294 " model vdw 1.556 2.450 nonbonded pdb=" O SER A 739 " pdb=" HG SER A 742 " model vdw 1.588 2.450 nonbonded pdb=" O ASP B 94 " pdb=" HG SER B 97 " model vdw 1.600 2.450 ... (remaining 297981 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 ========== 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=0.00 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: 1.070 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: 0.120 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 0.036 10485 Z= 0.163 Angle : 0.552 7.604 14215 Z= 0.286 Chirality : 0.040 0.137 1608 Planarity : 0.003 0.035 1835 Dihedral : 16.164 89.625 3893 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.27 % Allowed : 15.82 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.80 (0.23), residues: 1303 helix: 0.48 (0.21), residues: 576 sheet: -0.88 (0.48), residues: 124 loop : -1.45 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 58 TYR 0.022 0.001 TYR B 169 PHE 0.016 0.001 PHE B 24 TRP 0.008 0.001 TRP A 894 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (10482) covalent geometry : angle 0.55176 / 0.29 (14209) SS BOND : bond 0.00376 / 0.18 ( 3) SS BOND : angle 1.37510 / 0.76 ( 6) hydrogen bonds : bond 0.15914 / 10.70 ( 516) hydrogen bonds : angle 6.99257 / 5.18 ( 1473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 102 average time/residue: 0.1647 time to fit residues: 26.3470 Evaluate side-chains 102 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.137037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082523 restraints weight = 77274.091| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 5.82 r_work: 0.3142 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10485 Z= 0.125 Angle : 0.550 6.124 14215 Z= 0.291 Chirality : 0.040 0.159 1608 Planarity : 0.004 0.053 1835 Dihedral : 4.872 55.034 1417 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.53 % Allowed : 16.18 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.59 (0.23), residues: 1303 helix: 0.85 (0.22), residues: 571 sheet: -0.83 (0.45), residues: 134 loop : -1.52 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 182 TYR 0.017 0.001 TYR B 169 PHE 0.020 0.001 PHE B 24 TRP 0.010 0.001 TRP A 890 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10482) covalent geometry : angle 0.54924 / 0.29 (14209) SS BOND : bond 0.00520 / 0.26 ( 3) SS BOND : angle 1.19091 / 0.67 ( 6) hydrogen bonds : bond 0.04206 / 2.92 ( 516) hydrogen bonds : angle 5.03892 / 3.71 ( 1473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 110 average time/residue: 0.1666 time to fit residues: 29.4705 Evaluate side-chains 105 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 50.0000 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 chunk 116 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.137000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.083403 restraints weight = 77362.603| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 5.39 r_work: 0.3147 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10485 Z= 0.123 Angle : 0.518 6.562 14215 Z= 0.273 Chirality : 0.040 0.154 1608 Planarity : 0.004 0.038 1835 Dihedral : 4.551 57.025 1415 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.16 % Allowed : 16.09 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.50 (0.23), residues: 1303 helix: 0.97 (0.22), residues: 572 sheet: -0.85 (0.45), residues: 133 loop : -1.52 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 911 TYR 0.016 0.001 TYR B 169 PHE 0.018 0.001 PHE B 24 TRP 0.007 0.001 TRP A 890 HIS 0.007 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10482) covalent geometry : angle 0.51748 / 0.27 (14209) SS BOND : bond 0.00259 / 0.13 ( 3) SS BOND : angle 1.08632 / 0.61 ( 6) hydrogen bonds : bond 0.03695 / 2.56 ( 516) hydrogen bonds : angle 4.71910 / 3.46 ( 1473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.9249 (mmtp) cc_final: 0.8725 (mmtt) outliers start: 13 outliers final: 8 residues processed: 122 average time/residue: 0.1667 time to fit residues: 31.7927 Evaluate side-chains 116 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 1 optimal weight: 40.0000 chunk 3 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.137052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082063 restraints weight = 78203.556| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 5.61 r_work: 0.3151 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10485 Z= 0.124 Angle : 0.511 6.175 14215 Z= 0.268 Chirality : 0.040 0.151 1608 Planarity : 0.003 0.038 1835 Dihedral : 4.482 58.448 1415 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.07 % Allowed : 16.62 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.43 (0.23), residues: 1303 helix: 1.04 (0.22), residues: 573 sheet: -0.81 (0.45), residues: 132 loop : -1.50 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 911 TYR 0.015 0.001 TYR B 169 PHE 0.017 0.001 PHE B 24 TRP 0.006 0.001 TRP A 890 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10482) covalent geometry : angle 0.51041 / 0.27 (14209) SS BOND : bond 0.00268 / 0.13 ( 3) SS BOND : angle 1.11318 / 0.63 ( 6) hydrogen bonds : bond 0.03348 / 2.33 ( 516) hydrogen bonds : angle 4.53708 / 3.34 ( 1473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8392 (m) REVERT: A 359 LYS cc_start: 0.9290 (mmtp) cc_final: 0.8796 (mmtt) outliers start: 12 outliers final: 9 residues processed: 118 average time/residue: 0.1711 time to fit residues: 31.8206 Evaluate side-chains 116 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 1 optimal weight: 40.0000 chunk 123 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.082839 restraints weight = 77791.982| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 5.55 r_work: 0.3134 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10485 Z= 0.152 Angle : 0.516 7.231 14215 Z= 0.272 Chirality : 0.040 0.148 1608 Planarity : 0.003 0.038 1835 Dihedral : 4.473 59.645 1415 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.89 % Allowed : 16.80 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.40 (0.23), residues: 1303 helix: 1.09 (0.22), residues: 574 sheet: -0.89 (0.44), residues: 133 loop : -1.49 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 911 TYR 0.016 0.001 TYR A 869 PHE 0.016 0.001 PHE B 24 TRP 0.007 0.001 TRP A 890 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10482) covalent geometry : angle 0.51537 / 0.27 (14209) SS BOND : bond 0.00301 / 0.15 ( 3) SS BOND : angle 1.14856 / 0.64 ( 6) hydrogen bonds : bond 0.03396 / 2.36 ( 516) hydrogen bonds : angle 4.49363 / 3.31 ( 1473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.9263 (mmtp) cc_final: 0.8747 (mmtt) outliers start: 10 outliers final: 9 residues processed: 116 average time/residue: 0.1584 time to fit residues: 29.1214 Evaluate side-chains 120 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 53 optimal weight: 50.0000 chunk 97 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.082801 restraints weight = 77863.411| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 5.56 r_work: 0.3144 rms_B_bonded: 5.06 restraints_weight: 2.0000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10485 Z= 0.142 Angle : 0.515 7.499 14215 Z= 0.269 Chirality : 0.039 0.146 1608 Planarity : 0.003 0.038 1835 Dihedral : 4.423 59.452 1415 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.16 % Allowed : 17.16 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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 (0.23), residues: 1303 helix: 1.15 (0.22), residues: 574 sheet: -0.89 (0.44), residues: 133 loop : -1.44 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 911 TYR 0.015 0.001 TYR A 869 PHE 0.015 0.001 PHE B 24 TRP 0.007 0.001 TRP A 894 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10482) covalent geometry : angle 0.51494 / 0.27 (14209) SS BOND : bond 0.00297 / 0.15 ( 3) SS BOND : angle 1.13194 / 0.63 ( 6) hydrogen bonds : bond 0.03265 / 2.29 ( 516) hydrogen bonds : angle 4.40506 / 3.25 ( 1473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.9293 (mmtp) cc_final: 0.8784 (mmtt) outliers start: 13 outliers final: 12 residues processed: 122 average time/residue: 0.1802 time to fit residues: 34.3469 Evaluate side-chains 124 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 43 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.134995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081071 restraints weight = 78268.219| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 5.71 r_work: 0.3110 rms_B_bonded: 5.16 restraints_weight: 2.0000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10485 Z= 0.219 Angle : 0.547 7.518 14215 Z= 0.290 Chirality : 0.040 0.175 1608 Planarity : 0.003 0.039 1835 Dihedral : 4.508 58.336 1415 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.60 % Allowed : 17.60 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.45 (0.23), residues: 1303 helix: 1.04 (0.22), residues: 575 sheet: -1.00 (0.44), residues: 133 loop : -1.49 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.020 0.001 TYR A 869 PHE 0.015 0.001 PHE B 24 TRP 0.008 0.001 TRP A 890 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (10482) covalent geometry : angle 0.54673 / 0.29 (14209) SS BOND : bond 0.00380 / 0.19 ( 3) SS BOND : angle 1.24159 / 0.69 ( 6) hydrogen bonds : bond 0.03420 / 2.39 ( 516) hydrogen bonds : angle 4.50513 / 3.32 ( 1473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.9320 (mmtp) cc_final: 0.8798 (mmtt) outliers start: 18 outliers final: 16 residues processed: 116 average time/residue: 0.1827 time to fit residues: 33.4307 Evaluate side-chains 122 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 97 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 50.0000 chunk 1 optimal weight: 40.0000 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.135553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.081723 restraints weight = 78200.969| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 5.54 r_work: 0.3117 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10485 Z= 0.175 Angle : 0.528 7.812 14215 Z= 0.278 Chirality : 0.040 0.145 1608 Planarity : 0.003 0.038 1835 Dihedral : 4.468 57.908 1415 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.16 % Allowed : 18.31 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.40 (0.23), residues: 1303 helix: 1.04 (0.22), residues: 578 sheet: -1.04 (0.44), residues: 133 loop : -1.41 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 911 TYR 0.016 0.001 TYR A 869 PHE 0.015 0.001 PHE B 50 TRP 0.008 0.001 TRP A 890 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (10482) covalent geometry : angle 0.52779 / 0.28 (14209) SS BOND : bond 0.00366 / 0.18 ( 3) SS BOND : angle 1.20791 / 0.66 ( 6) hydrogen bonds : bond 0.03282 / 2.30 ( 516) hydrogen bonds : angle 4.41711 / 3.26 ( 1473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.4249 (mmp) cc_final: 0.3801 (mmp) REVERT: A 359 LYS cc_start: 0.9296 (mmtp) cc_final: 0.8780 (mmmm) outliers start: 13 outliers final: 12 residues processed: 117 average time/residue: 0.1762 time to fit residues: 31.8281 Evaluate side-chains 120 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 107 optimal weight: 0.0570 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 21 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 overall best weight: 1.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.136892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082822 restraints weight = 77656.968| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 5.70 r_work: 0.3145 rms_B_bonded: 5.13 restraints_weight: 2.0000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10485 Z= 0.116 Angle : 0.514 7.766 14215 Z= 0.266 Chirality : 0.040 0.145 1608 Planarity : 0.003 0.037 1835 Dihedral : 4.378 57.369 1415 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.89 % Allowed : 18.49 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.23 (0.23), residues: 1303 helix: 1.19 (0.22), residues: 581 sheet: -0.96 (0.44), residues: 133 loop : -1.33 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 911 TYR 0.013 0.001 TYR A 869 PHE 0.012 0.001 PHE B 24 TRP 0.007 0.001 TRP A 894 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10482) covalent geometry : angle 0.51405 / 0.27 (14209) SS BOND : bond 0.00275 / 0.13 ( 3) SS BOND : angle 1.14315 / 0.63 ( 6) hydrogen bonds : bond 0.03093 / 2.17 ( 516) hydrogen bonds : angle 4.27316 / 3.15 ( 1473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.4119 (mmp) cc_final: 0.3699 (mmp) REVERT: A 359 LYS cc_start: 0.9274 (mmtp) cc_final: 0.8774 (mmmm) outliers start: 10 outliers final: 9 residues processed: 121 average time/residue: 0.1760 time to fit residues: 33.8389 Evaluate side-chains 121 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 108 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 50.0000 chunk 48 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.135113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080618 restraints weight = 77983.682| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 5.61 r_work: 0.3114 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10485 Z= 0.215 Angle : 0.540 7.495 14215 Z= 0.286 Chirality : 0.040 0.173 1608 Planarity : 0.003 0.039 1835 Dihedral : 4.423 56.655 1415 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.07 % Allowed : 18.22 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.37 (0.23), residues: 1303 helix: 1.09 (0.22), residues: 578 sheet: -1.07 (0.44), residues: 133 loop : -1.40 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.020 0.001 TYR A 869 PHE 0.014 0.001 PHE B 50 TRP 0.008 0.001 TRP A 890 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (10482) covalent geometry : angle 0.53905 / 0.29 (14209) SS BOND : bond 0.00430 / 0.21 ( 3) SS BOND : angle 1.28164 / 0.70 ( 6) hydrogen bonds : bond 0.03269 / 2.29 ( 516) hydrogen bonds : angle 4.40617 / 3.25 ( 1473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.4136 (mmp) cc_final: 0.3722 (mmp) REVERT: A 359 LYS cc_start: 0.9302 (mmtp) cc_final: 0.8779 (mmmm) outliers start: 12 outliers final: 11 residues processed: 115 average time/residue: 0.1833 time to fit residues: 33.1002 Evaluate side-chains 121 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 729 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain B residue 24 PHE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 56 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 70 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 40.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.134330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.079681 restraints weight = 77930.917| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 5.47 r_work: 0.3105 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10485 Z= 0.228 Angle : 0.556 7.911 14215 Z= 0.295 Chirality : 0.040 0.176 1608 Planarity : 0.004 0.039 1835 Dihedral : 4.511 56.083 1415 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 1.07 % Allowed : 18.31 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.46 (0.23), residues: 1303 helix: 0.98 (0.21), residues: 578 sheet: -1.17 (0.44), residues: 134 loop : -1.40 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.019 0.001 TYR A 869 PHE 0.016 0.001 PHE B 50 TRP 0.008 0.001 TRP A 890 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 (10482) covalent geometry : angle 0.55511 / 0.29 (14209) SS BOND : bond 0.00405 / 0.20 ( 3) SS BOND : angle 1.24443 / 0.69 ( 6) hydrogen bonds : bond 0.03347 / 2.35 ( 516) hydrogen bonds : angle 4.45087 / 3.28 ( 1473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5562.16 seconds wall clock time: 95 minutes 40.76 seconds (5740.76 seconds total)