Starting phenix.real_space_refine on Sun Sep 13 06:18:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9roq_54128/09_2026/9roq_54128.cif Found real_map, /net/cci-nas-00/data/ceres_data/9roq_54128/09_2026/9roq_54128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9roq_54128/09_2026/9roq_54128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9roq_54128/09_2026/9roq_54128.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9roq_54128/09_2026/9roq_54128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9roq_54128/09_2026/9roq_54128.map" } resolution = 3.33 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 6598 2.51 5 N 1721 2.21 5 O 1928 1.98 5 H 10345 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 20650 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 15476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 15476 Classifications: {'peptide': 994} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 950} Chain: "B" Number of atoms: 4663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4663 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 266} Chain: "C" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 511 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Time building chain proxies: 3.82, per 1000 atoms: 0.18 Number of scatterers: 20650 At special positions: 0 Unit cell: (78.755, 89.532, 170.774, 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 1928 8.00 N 1721 7.00 C 6598 6.00 H 10345 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=2.04 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 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: 2.05 Conformation dependent library (CDL) restraints added in 559.9 milliseconds 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 49.8% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 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 removed outlier: 3.529A pdb=" N ARG A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 93 through 98 removed outlier: 3.546A pdb=" N PHE A 97 " --> pdb=" O CYS A 93 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 98' Processing helix chain 'A' and resid 99 through 120 removed outlier: 3.529A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 160 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 261 through 264 removed outlier: 4.176A pdb=" N ARG A 264 " --> pdb=" O THR A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 282 through 315 removed outlier: 3.523A pdb=" N GLU A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.772A pdb=" N VAL A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.518A pdb=" N LYS A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 Processing helix chain 'A' and resid 441 through 445 removed outlier: 4.204A pdb=" N ARG A 445 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 465 Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.544A pdb=" N ALA A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 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 667 through 673 Processing helix chain 'A' and resid 674 through 684 Processing helix chain 'A' and resid 694 through 708 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 756 through 796 removed outlier: 3.807A pdb=" N THR A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE A 784 " --> pdb=" O LEU A 780 " (cutoff:3.500A) Proline residue: A 785 - end of helix Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 814 Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.598A pdb=" N LYS A 833 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 834' Processing helix chain 'A' and resid 846 through 854 Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 879 through 883 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 938 removed outlier: 3.941A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 removed outlier: 3.525A pdb=" N GLN A 947 " --> pdb=" O SER A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 971 Processing helix chain 'A' and resid 973 through 978 removed outlier: 3.561A pdb=" N LEU A 978 " --> pdb=" O MET A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.654A pdb=" N TRP A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 984 through 989' Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.669A pdb=" N ASP A1002 " --> pdb=" O ILE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 31 through 58 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 94 through 111 removed outlier: 4.067A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 5.927A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'C' and resid 32 through 56 removed outlier: 3.529A pdb=" N LEU C 56 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.922A pdb=" N ASN A 248 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS A 212 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 252 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY A 210 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 254 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 208 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 256 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE A 206 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL A 258 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG A 204 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.922A pdb=" N ASN A 248 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS A 212 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 252 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY A 210 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 254 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 208 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 256 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE A 206 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL A 258 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG A 204 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'A' and resid 662 through 666 removed outlier: 6.529A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 715 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.888A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE A 393 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N VAL A 586 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N LEU A 583 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N PHE A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 587 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 553 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.888A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE A 393 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 11.041A pdb=" N VAL A 586 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N CYS A 518 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 585 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER A 520 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLY A 587 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N LEU A 522 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 11.951A pdb=" N ILE A 589 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.090A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 513 hydrogen bonds defined for protein. 1452 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: 5.09 Time building geometry restraints manager: 2.80 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: 10321 1.03 - 1.23: 58 1.23 - 1.43: 4274 1.43 - 1.62: 6125 1.62 - 1.82: 86 Bond restraints: 20864 Sorted by residual: bond pdb=" CA THR B 60 " pdb=" C THR B 60 " ideal model delta sigma weight residual 1.522 1.504 0.018 1.38e-02 5.25e+03 1.76e+00 bond pdb=" N VAL B 301 " pdb=" CA VAL B 301 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.01e+00 bond pdb=" N ASP B 164 " pdb=" CA ASP B 164 " ideal model delta sigma weight residual 1.468 1.456 0.012 1.24e-02 6.50e+03 9.04e-01 bond pdb=" CA GLU B 300 " pdb=" C GLU B 300 " ideal model delta sigma weight residual 1.526 1.517 0.009 1.03e-02 9.43e+03 7.87e-01 bond pdb=" CB CYS A 918 " pdb=" SG CYS A 918 " ideal model delta sigma weight residual 1.808 1.780 0.028 3.30e-02 9.18e+02 6.99e-01 ... (remaining 20859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.50: 37816 7.50 - 15.00: 0 15.00 - 22.51: 0 22.51 - 30.01: 0 30.01 - 37.51: 9 Bond angle restraints: 37825 Sorted by residual: angle pdb=" C ASN B 158 " pdb=" CA ASN B 158 " pdb=" HA ASN B 158 " ideal model delta sigma weight residual 109.00 71.49 37.51 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C GLU B 23 " pdb=" CA GLU B 23 " pdb=" HA GLU B 23 " ideal model delta sigma weight residual 109.00 74.00 35.00 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N GLU B 23 " pdb=" CA GLU B 23 " pdb=" HA GLU B 23 " ideal model delta sigma weight residual 110.00 75.24 34.76 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C LYS B 22 " pdb=" CA LYS B 22 " pdb=" HA LYS B 22 " ideal model delta sigma weight residual 109.00 74.36 34.64 3.00e+00 1.11e-01 1.33e+02 angle pdb=" CB LYS B 22 " pdb=" CA LYS B 22 " pdb=" HA LYS B 22 " ideal model delta sigma weight residual 109.00 74.97 34.03 3.00e+00 1.11e-01 1.29e+02 ... (remaining 37820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8604 17.86 - 35.71: 870 35.71 - 53.57: 238 53.57 - 71.43: 65 71.43 - 89.29: 24 Dihedral angle restraints: 9801 sinusoidal: 5388 harmonic: 4413 Sorted by residual: dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 177.16 -84.16 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual -86.00 -37.23 -48.77 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CA GLY B 161 " pdb=" C GLY B 161 " pdb=" N LEU B 162 " pdb=" CA LEU B 162 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 9798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1510 0.085 - 0.171: 99 0.171 - 0.256: 0 0.256 - 0.341: 0 0.341 - 0.427: 3 Chirality restraints: 1612 Sorted by residual: chirality pdb=" CA ASN B 158 " pdb=" N ASN B 158 " pdb=" C ASN B 158 " pdb=" CB ASN B 158 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA LYS B 22 " pdb=" N LYS B 22 " pdb=" C LYS B 22 " pdb=" CB LYS B 22 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA GLU B 23 " pdb=" N GLU B 23 " pdb=" C GLU B 23 " pdb=" CB GLU B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 1609 not shown) Planarity restraints: 3086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 36 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C LEU B 36 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU B 36 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 37 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 190 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 191 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 191 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 191 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 38 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C PHE B 38 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE B 38 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR B 39 " -0.009 2.00e-02 2.50e+03 ... (remaining 3083 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 636 2.10 - 2.73: 37361 2.73 - 3.35: 62558 3.35 - 3.98: 76895 3.98 - 4.60: 120110 Nonbonded interactions: 297560 Sorted by model distance: nonbonded pdb=" O ASP B 164 " pdb=" H TYR B 167 " model vdw 1.481 2.450 nonbonded pdb=" OE1 GLN A 856 " pdb=" HH TYR A1001 " model vdw 1.571 2.450 nonbonded pdb=" H CYS B 213 " pdb=" OH TYR B 229 " model vdw 1.577 2.450 nonbonded pdb=" O LYS A 36 " pdb="HE22 GLN A 696 " model vdw 1.580 2.450 nonbonded pdb=" OE1 GLU A 287 " pdb=" H LEU A 844 " model vdw 1.580 2.450 ... (remaining 297555 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: 1.710 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: 0.140 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.450 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.003 0.030 10522 Z= 0.135 Angle : 0.615 7.496 14264 Z= 0.340 Chirality : 0.044 0.427 1612 Planarity : 0.004 0.041 1840 Dihedral : 15.785 89.286 3908 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.50 % Rotamer: Outliers : 0.18 % Allowed : 16.74 % Favored : 83.08 % 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: -1.49 (0.23), residues: 1307 helix: -0.35 (0.21), residues: 568 sheet: -1.22 (0.40), residues: 173 loop : -1.48 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 107 TYR 0.011 0.001 TYR A 315 PHE 0.013 0.001 PHE A 100 TRP 0.009 0.001 TRP A 894 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (10519) covalent geometry : angle 0.61396 / 0.34 (14258) SS BOND : bond 0.00506 / 0.27 ( 3) SS BOND : angle 1.93106 / 1.04 ( 6) hydrogen bonds : bond 0.15795 / 10.44 ( 500) hydrogen bonds : angle 7.16503 / 5.17 ( 1452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.574 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: C 32 ASP cc_start: 0.9280 (m-30) cc_final: 0.9039 (p0) outliers start: 2 outliers final: 1 residues processed: 119 average time/residue: 0.1930 time to fit residues: 34.7444 Evaluate side-chains 116 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** 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 = 0.4238 r_free = 0.4238 target = 0.130108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.088614 restraints weight = 86359.250| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 6.13 r_work: 0.3321 rms_B_bonded: 5.42 restraints_weight: 2.0000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.0677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10522 Z= 0.151 Angle : 0.572 5.725 14264 Z= 0.305 Chirality : 0.044 0.433 1612 Planarity : 0.004 0.053 1840 Dihedral : 4.625 31.664 1417 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.50 % Rotamer: Outliers : 1.24 % Allowed : 16.47 % Favored : 82.29 % Cbeta Deviations : 0.08 % 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: -1.20 (0.23), residues: 1307 helix: 0.08 (0.21), residues: 574 sheet: -1.16 (0.42), residues: 163 loop : -1.54 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 911 TYR 0.011 0.001 TYR A 778 PHE 0.017 0.001 PHE A 307 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 0.00330 / 0.15 (10519) covalent geometry : angle 0.57026 / 0.30 (14258) SS BOND : bond 0.00273 / 0.14 ( 3) SS BOND : angle 1.94814 / 1.08 ( 6) hydrogen bonds : bond 0.04580 / 3.09 ( 500) hydrogen bonds : angle 5.35761 / 3.85 ( 1452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.566 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: A 184 GLU cc_start: 0.9576 (mt-10) cc_final: 0.9183 (mp0) REVERT: A 391 MET cc_start: 0.4596 (OUTLIER) cc_final: 0.4152 (mmp) outliers start: 14 outliers final: 9 residues processed: 136 average time/residue: 0.1973 time to fit residues: 41.1569 Evaluate side-chains 132 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 50.0000 chunk 22 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 905 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** 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 = 0.4211 r_free = 0.4211 target = 0.128294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.087138 restraints weight = 87281.134| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 6.00 r_work: 0.3294 rms_B_bonded: 5.32 restraints_weight: 2.0000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10522 Z= 0.209 Angle : 0.580 6.644 14264 Z= 0.312 Chirality : 0.044 0.428 1612 Planarity : 0.004 0.049 1840 Dihedral : 4.532 20.823 1415 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.03 % Favored : 91.89 % Rotamer: Outliers : 1.86 % Allowed : 16.83 % Favored : 81.31 % Cbeta Deviations : 0.16 % 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: -1.29 (0.23), residues: 1307 helix: 0.13 (0.21), residues: 576 sheet: -1.23 (0.42), residues: 163 loop : -1.74 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 911 TYR 0.013 0.001 TYR B 243 PHE 0.015 0.001 PHE A 923 TRP 0.008 0.001 TRP A 418 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (10519) covalent geometry : angle 0.57939 / 0.31 (14258) SS BOND : bond 0.00375 / 0.19 ( 3) SS BOND : angle 1.59328 / 0.87 ( 6) hydrogen bonds : bond 0.04129 / 2.72 ( 500) hydrogen bonds : angle 5.24922 / 3.75 ( 1452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.593 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: A 184 GLU cc_start: 0.9567 (mt-10) cc_final: 0.9098 (mp0) REVERT: A 386 MET cc_start: 0.6509 (tpt) cc_final: 0.6085 (tpt) REVERT: A 391 MET cc_start: 0.4712 (OUTLIER) cc_final: 0.4217 (mmp) outliers start: 21 outliers final: 18 residues processed: 133 average time/residue: 0.1891 time to fit residues: 39.0771 Evaluate side-chains 140 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 110 optimal weight: 0.0050 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 GLN A 930 GLN B 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.130578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.089549 restraints weight = 85580.335| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 5.98 r_work: 0.3336 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10522 Z= 0.116 Angle : 0.545 6.382 14264 Z= 0.284 Chirality : 0.044 0.429 1612 Planarity : 0.004 0.040 1840 Dihedral : 4.386 20.814 1415 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 2.13 % Allowed : 16.83 % Favored : 81.05 % Cbeta Deviations : 0.08 % 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: -0.85 (0.23), residues: 1307 helix: 0.53 (0.22), residues: 576 sheet: -1.19 (0.42), residues: 163 loop : -1.47 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.011 0.001 TYR A 869 PHE 0.013 0.001 PHE A 307 TRP 0.007 0.001 TRP A 418 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10519) covalent geometry : angle 0.54331 / 0.28 (14258) SS BOND : bond 0.00261 / 0.13 ( 3) SS BOND : angle 1.85387 / 0.97 ( 6) hydrogen bonds : bond 0.03749 / 2.50 ( 500) hydrogen bonds : angle 4.91266 / 3.51 ( 1452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.575 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: A 184 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9115 (mp0) REVERT: A 391 MET cc_start: 0.4673 (OUTLIER) cc_final: 0.4139 (mmp) REVERT: A 974 MET cc_start: 0.9154 (mmm) cc_final: 0.8878 (mmp) REVERT: C 32 ASP cc_start: 0.8905 (p0) cc_final: 0.8584 (p0) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 0.1870 time to fit residues: 41.3799 Evaluate side-chains 141 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 50.0000 chunk 100 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.129560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.088247 restraints weight = 86168.137| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 5.99 r_work: 0.3304 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10522 Z= 0.172 Angle : 0.549 5.840 14264 Z= 0.293 Chirality : 0.044 0.424 1612 Planarity : 0.004 0.048 1840 Dihedral : 4.369 21.227 1415 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.43 % Rotamer: Outliers : 1.95 % Allowed : 17.63 % Favored : 80.43 % 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: -0.84 (0.23), residues: 1307 helix: 0.51 (0.22), residues: 577 sheet: -1.11 (0.42), residues: 160 loop : -1.48 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 107 TYR 0.011 0.001 TYR A 869 PHE 0.012 0.001 PHE A 923 TRP 0.007 0.001 TRP A 418 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (10519) covalent geometry : angle 0.54804 / 0.29 (14258) SS BOND : bond 0.00327 / 0.17 ( 3) SS BOND : angle 1.65204 / 0.87 ( 6) hydrogen bonds : bond 0.03701 / 2.44 ( 500) hydrogen bonds : angle 4.92894 / 3.51 ( 1452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 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: A 184 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9041 (mp0) REVERT: A 391 MET cc_start: 0.4712 (OUTLIER) cc_final: 0.4169 (mmp) REVERT: A 708 GLN cc_start: 0.8982 (tt0) cc_final: 0.8296 (tm-30) REVERT: A 974 MET cc_start: 0.9222 (mmm) cc_final: 0.8891 (mmp) REVERT: C 32 ASP cc_start: 0.8917 (p0) cc_final: 0.8665 (p0) outliers start: 22 outliers final: 20 residues processed: 134 average time/residue: 0.1942 time to fit residues: 39.9082 Evaluate side-chains 140 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.130216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.089249 restraints weight = 85600.871| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 6.03 r_work: 0.3329 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10522 Z= 0.129 Angle : 0.537 7.257 14264 Z= 0.282 Chirality : 0.044 0.430 1612 Planarity : 0.004 0.041 1840 Dihedral : 4.280 20.321 1415 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.50 % Rotamer: Outliers : 2.39 % Allowed : 18.16 % Favored : 79.45 % Cbeta Deviations : 0.08 % 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: -0.64 (0.24), residues: 1307 helix: 0.67 (0.22), residues: 579 sheet: -1.14 (0.42), residues: 161 loop : -1.32 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.009 0.001 TYR A 869 PHE 0.021 0.001 PHE A 307 TRP 0.007 0.001 TRP A 418 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10519) covalent geometry : angle 0.53652 / 0.28 (14258) SS BOND : bond 0.00241 / 0.12 ( 3) SS BOND : angle 1.55628 / 0.83 ( 6) hydrogen bonds : bond 0.03605 / 2.39 ( 500) hydrogen bonds : angle 4.76419 / 3.39 ( 1452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.617 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: A 184 GLU cc_start: 0.9527 (mt-10) cc_final: 0.9040 (mp0) REVERT: A 386 MET cc_start: 0.6647 (tpt) cc_final: 0.6443 (tpt) REVERT: A 391 MET cc_start: 0.4751 (OUTLIER) cc_final: 0.4197 (mmp) REVERT: A 708 GLN cc_start: 0.8914 (tt0) cc_final: 0.8281 (tm-30) REVERT: A 958 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9212 (mt) REVERT: A 974 MET cc_start: 0.9179 (mmm) cc_final: 0.8905 (mmp) REVERT: C 32 ASP cc_start: 0.8882 (p0) cc_final: 0.8643 (p0) outliers start: 27 outliers final: 21 residues processed: 144 average time/residue: 0.2008 time to fit residues: 44.4876 Evaluate side-chains 144 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 22 optimal weight: 30.0000 chunk 53 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.131408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.090676 restraints weight = 84790.025| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 5.94 r_work: 0.3344 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10522 Z= 0.105 Angle : 0.529 5.867 14264 Z= 0.273 Chirality : 0.044 0.427 1612 Planarity : 0.004 0.041 1840 Dihedral : 4.184 20.815 1415 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.50 % Rotamer: Outliers : 2.30 % Allowed : 17.80 % Favored : 79.89 % Cbeta Deviations : 0.08 % 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 (0.24), residues: 1307 helix: 0.94 (0.22), residues: 572 sheet: -1.13 (0.44), residues: 141 loop : -1.19 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.009 0.001 TYR A 869 PHE 0.011 0.001 PHE A 923 TRP 0.007 0.001 TRP A 418 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (10519) covalent geometry : angle 0.52838 / 0.27 (14258) SS BOND : bond 0.00198 / 0.10 ( 3) SS BOND : angle 1.51854 / 0.81 ( 6) hydrogen bonds : bond 0.03441 / 2.28 ( 500) hydrogen bonds : angle 4.61549 / 3.29 ( 1452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 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: A 184 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9044 (mp0) REVERT: A 391 MET cc_start: 0.4663 (OUTLIER) cc_final: 0.4100 (mmp) REVERT: A 708 GLN cc_start: 0.8855 (tt0) cc_final: 0.8214 (tm-30) REVERT: A 974 MET cc_start: 0.9122 (mmm) cc_final: 0.8869 (mmp) REVERT: C 32 ASP cc_start: 0.8854 (p0) cc_final: 0.8634 (p0) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.1935 time to fit residues: 43.9093 Evaluate side-chains 146 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 52 optimal weight: 40.0000 chunk 12 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 50.0000 chunk 14 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 54 optimal weight: 0.0060 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 685 HIS ** 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 = 0.4229 r_free = 0.4229 target = 0.129828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.089442 restraints weight = 86126.582| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 5.69 r_work: 0.3317 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10522 Z= 0.167 Angle : 0.552 8.224 14264 Z= 0.291 Chirality : 0.044 0.428 1612 Planarity : 0.004 0.041 1840 Dihedral : 4.181 20.987 1415 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.81 % Favored : 93.11 % Rotamer: Outliers : 2.21 % Allowed : 18.33 % Favored : 79.45 % Cbeta Deviations : 0.08 % 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: -0.53 (0.24), residues: 1307 helix: 0.81 (0.22), residues: 581 sheet: -1.22 (0.41), residues: 166 loop : -1.28 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.014 0.001 TYR A 869 PHE 0.019 0.001 PHE A 307 TRP 0.008 0.001 TRP A 418 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (10519) covalent geometry : angle 0.55164 / 0.29 (14258) SS BOND : bond 0.00288 / 0.15 ( 3) SS BOND : angle 1.41806 / 0.76 ( 6) hydrogen bonds : bond 0.03546 / 2.33 ( 500) hydrogen bonds : angle 4.71862 / 3.36 ( 1452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.580 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: A 184 GLU cc_start: 0.9471 (mt-10) cc_final: 0.8990 (mp0) REVERT: A 391 MET cc_start: 0.4733 (OUTLIER) cc_final: 0.4102 (mmp) REVERT: A 708 GLN cc_start: 0.8839 (tt0) cc_final: 0.8226 (tm-30) REVERT: A 974 MET cc_start: 0.9171 (mmm) cc_final: 0.8902 (mmp) REVERT: B 228 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7861 (mp0) REVERT: C 32 ASP cc_start: 0.8917 (p0) cc_final: 0.8694 (p0) outliers start: 25 outliers final: 22 residues processed: 137 average time/residue: 0.1912 time to fit residues: 41.1572 Evaluate side-chains 146 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 267 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 685 HIS ** 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 = 0.4227 r_free = 0.4227 target = 0.129784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.089070 restraints weight = 86725.117| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 5.78 r_work: 0.3313 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10522 Z= 0.158 Angle : 0.552 8.587 14264 Z= 0.289 Chirality : 0.044 0.427 1612 Planarity : 0.004 0.043 1840 Dihedral : 4.185 20.714 1415 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 2.04 % Allowed : 18.60 % Favored : 79.36 % Cbeta Deviations : 0.08 % 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: -0.53 (0.24), residues: 1307 helix: 0.81 (0.22), residues: 580 sheet: -1.24 (0.44), residues: 146 loop : -1.29 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.011 0.001 TYR B 243 PHE 0.018 0.001 PHE A 923 TRP 0.008 0.001 TRP A 418 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (10519) covalent geometry : angle 0.55162 / 0.29 (14258) SS BOND : bond 0.00279 / 0.14 ( 3) SS BOND : angle 1.40790 / 0.76 ( 6) hydrogen bonds : bond 0.03519 / 2.31 ( 500) hydrogen bonds : angle 4.68522 / 3.33 ( 1452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.593 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: A 184 GLU cc_start: 0.9476 (mt-10) cc_final: 0.8990 (mp0) REVERT: A 391 MET cc_start: 0.4732 (OUTLIER) cc_final: 0.4074 (mmp) REVERT: A 708 GLN cc_start: 0.8805 (tt0) cc_final: 0.8208 (tm-30) REVERT: A 974 MET cc_start: 0.9211 (mmm) cc_final: 0.8871 (mmp) REVERT: B 228 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7830 (mp0) REVERT: C 32 ASP cc_start: 0.8925 (p0) cc_final: 0.8700 (p0) outliers start: 23 outliers final: 21 residues processed: 135 average time/residue: 0.1926 time to fit residues: 40.4082 Evaluate side-chains 143 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 80 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 685 HIS ** 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 = 0.4214 r_free = 0.4214 target = 0.128953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.088433 restraints weight = 86703.525| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 5.64 r_work: 0.3295 rms_B_bonded: 5.07 restraints_weight: 2.0000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10522 Z= 0.193 Angle : 0.569 6.650 14264 Z= 0.303 Chirality : 0.044 0.427 1612 Planarity : 0.004 0.044 1840 Dihedral : 4.236 20.778 1415 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.88 % Favored : 92.04 % Rotamer: Outliers : 2.13 % Allowed : 18.78 % Favored : 79.10 % Cbeta Deviations : 0.08 % 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: -0.65 (0.23), residues: 1307 helix: 0.70 (0.22), residues: 580 sheet: -1.24 (0.44), residues: 146 loop : -1.35 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.013 0.001 TYR B 243 PHE 0.018 0.001 PHE A 923 TRP 0.008 0.001 TRP A 418 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (10519) covalent geometry : angle 0.56851 / 0.30 (14258) SS BOND : bond 0.00327 / 0.17 ( 3) SS BOND : angle 1.41047 / 0.75 ( 6) hydrogen bonds : bond 0.03629 / 2.38 ( 500) hydrogen bonds : angle 4.80925 / 3.41 ( 1452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.567 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: A 184 GLU cc_start: 0.9490 (mt-10) cc_final: 0.9014 (mp0) REVERT: A 391 MET cc_start: 0.4751 (OUTLIER) cc_final: 0.4062 (mmp) REVERT: A 708 GLN cc_start: 0.8805 (tt0) cc_final: 0.8202 (tm-30) REVERT: A 974 MET cc_start: 0.9247 (mmm) cc_final: 0.8906 (mmp) REVERT: B 57 MET cc_start: 0.8004 (tpt) cc_final: 0.7665 (mmt) REVERT: C 32 ASP cc_start: 0.8979 (p0) cc_final: 0.8746 (p0) outliers start: 24 outliers final: 21 residues processed: 129 average time/residue: 0.1848 time to fit residues: 37.4096 Evaluate side-chains 140 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 744 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 40.0000 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 112 optimal weight: 0.1980 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 685 HIS ** 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 = 0.4218 r_free = 0.4218 target = 0.129321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.088230 restraints weight = 86535.990| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 5.86 r_work: 0.3300 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10522 Z= 0.168 Angle : 0.559 7.515 14264 Z= 0.294 Chirality : 0.044 0.429 1612 Planarity : 0.004 0.043 1840 Dihedral : 4.245 20.328 1415 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.27 % Favored : 92.65 % Rotamer: Outliers : 2.13 % Allowed : 19.13 % Favored : 78.74 % Cbeta Deviations : 0.08 % 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: -0.61 (0.23), residues: 1307 helix: 0.72 (0.22), residues: 580 sheet: -1.16 (0.45), residues: 146 loop : -1.34 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.012 0.001 TYR B 243 PHE 0.018 0.001 PHE A 923 TRP 0.008 0.001 TRP A 418 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (10519) covalent geometry : angle 0.55820 / 0.29 (14258) SS BOND : bond 0.00310 / 0.16 ( 3) SS BOND : angle 1.41207 / 0.75 ( 6) hydrogen bonds : bond 0.03551 / 2.33 ( 500) hydrogen bonds : angle 4.76268 / 3.37 ( 1452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5598.89 seconds wall clock time: 95 minutes 48.82 seconds (5748.82 seconds total)