Starting phenix.real_space_refine on Thu Jul 2 16:46:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7a_73873/07_2026/9z7a_73873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7a_73873/07_2026/9z7a_73873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z7a_73873/07_2026/9z7a_73873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7a_73873/07_2026/9z7a_73873.map" model { file = "/net/cci-nas-00/data/ceres_data/9z7a_73873/07_2026/9z7a_73873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7a_73873/07_2026/9z7a_73873.cif" } resolution = 1.99 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= 0.021 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 5616 2.51 5 N 1546 2.21 5 O 1827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9014 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6163 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 19, 'TRANS': 810} Chain breaks: 6 Chain: "B" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1488 Classifications: {'peptide': 197} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 185} Chain breaks: 2 Chain: "C" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1363 Classifications: {'peptide': 177} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 165} Chain breaks: 3 Time building chain proxies: 2.28, per 1000 atoms: 0.25 Number of scatterers: 9014 At special positions: 0 Unit cell: (74.102, 133.196, 136.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1827 8.00 N 1546 7.00 C 5616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " 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: 0.72 Conformation dependent library (CDL) restraints added in 214.9 milliseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 19 sheets defined 3.7% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 removed outlier: 4.248A pdb=" N PHE A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 13 " --> pdb=" O TYR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 245 through 256 removed outlier: 4.200A pdb=" N GLN A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'B' and resid 63 through 66 removed outlier: 3.573A pdb=" N ARG B 66 " --> pdb=" O PRO B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.838A pdb=" N VAL C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.211A pdb=" N VAL A 3 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.744A pdb=" N ILE A 29 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 40 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 69 removed outlier: 6.746A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N THR A 109 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A 99 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG A 111 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 removed outlier: 4.433A pdb=" N GLU A 142 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 146 " --> pdb=" O PRO A 214 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 215 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASN A 240 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.599A pdb=" N ILE A 261 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU A 306 " --> pdb=" O GLN A 329 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 328 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 349 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A 369 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A 414 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN A 458 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 275 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 288 through 293 current: chain 'A' and resid 334 through 338 removed outlier: 4.247A pdb=" N ALA A 338 " --> pdb=" O GLN A 360 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 446 current: chain 'A' and resid 591 through 602 removed outlier: 5.608A pdb=" N VAL A 592 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLU A 635 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N LEU A 594 " --> pdb=" O GLU A 635 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N LEU A 637 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 13.534A pdb=" N GLU A 596 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 14.503A pdb=" N LEU A 639 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 13.629A pdb=" N SER A 598 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASP A 655 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 636 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN A 657 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A 638 " --> pdb=" O ASN A 657 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR A 659 " --> pdb=" O LYS A 638 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 640 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY A 650 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER A 702 " --> pdb=" O GLY A 650 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET A 652 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ASN A 704 " --> pdb=" O MET A 652 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N GLY A 654 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR A 706 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 656 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLU A 708 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A 658 " --> pdb=" O GLU A 708 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 703 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 12.808A pdb=" N PHE A 719 " --> pdb=" O ASP A 740 " (cutoff:3.500A) removed outlier: 11.936A pdb=" N VAL A 742 " --> pdb=" O PHE A 719 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY A 721 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N SER A 744 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 723 " --> pdb=" O SER A 744 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 746 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 725 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA A 737 " --> pdb=" O THR A 759 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 757 through 760 current: chain 'A' and resid 809 through 813 removed outlier: 8.823A pdb=" N GLU A 884 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N GLU A 910 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY A 886 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N SER A 912 " --> pdb=" O GLY A 886 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 888 " --> pdb=" O SER A 912 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.200A pdb=" N VAL A 321 " --> pdb=" O MET A 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 565 removed outlier: 6.677A pdb=" N VAL A 664 " --> pdb=" O GLN A 714 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU A 713 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 750 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 802 " --> pdb=" O HIS A 823 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY A 825 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N LEU A 804 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A 822 " --> pdb=" O THR A 864 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 611 through 612 Processing sheet with id=AB1, first strand: chain 'A' and resid 670 through 674 Processing sheet with id=AB2, first strand: chain 'A' and resid 795 through 797 removed outlier: 6.285A pdb=" N VAL A 795 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY A 816 " --> pdb=" O VAL A 858 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ARG A 860 " --> pdb=" O GLY A 816 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 818 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 857 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TYR A 878 " --> pdb=" O ALA A 857 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU A 859 " --> pdb=" O TYR A 878 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA A 875 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU A 896 " --> pdb=" O ALA A 875 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP A 877 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'B' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 11 through 12 current: chain 'B' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 61 current: chain 'B' and resid 109 through 110 Processing sheet with id=AB5, first strand: chain 'B' and resid 127 through 130 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 145 through 152 current: chain 'B' and resid 183 through 189 Processing sheet with id=AB6, first strand: chain 'B' and resid 158 through 161 Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 13 current: chain 'C' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 53 through 54 current: chain 'C' and resid 98 through 99 Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 119 removed outlier: 5.712A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 146 through 148 208 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2924 1.34 - 1.46: 1805 1.46 - 1.58: 4407 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 9177 Sorted by residual: bond pdb=" CB ASN A 856 " pdb=" CG ASN A 856 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 4.97e+00 bond pdb=" CA ASN A 856 " pdb=" CB ASN A 856 " ideal model delta sigma weight residual 1.528 1.555 -0.027 1.59e-02 3.96e+03 2.84e+00 bond pdb=" C HIS C 38 " pdb=" N LYS C 39 " ideal model delta sigma weight residual 1.331 1.283 0.048 2.83e-02 1.25e+03 2.84e+00 bond pdb=" CA ASN A 747 " pdb=" CB ASN A 747 " ideal model delta sigma weight residual 1.529 1.554 -0.025 1.58e-02 4.01e+03 2.59e+00 bond pdb=" CB GLN B 112 " pdb=" CG GLN B 112 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.54e+00 ... (remaining 9172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 12204 2.24 - 4.47: 226 4.47 - 6.71: 23 6.71 - 8.94: 9 8.94 - 11.18: 2 Bond angle restraints: 12464 Sorted by residual: angle pdb=" CA LYS A 636 " pdb=" CB LYS A 636 " pdb=" CG LYS A 636 " ideal model delta sigma weight residual 114.10 125.28 -11.18 2.00e+00 2.50e-01 3.12e+01 angle pdb=" C ASN C 50 " pdb=" N THR C 51 " pdb=" CA THR C 51 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C ALA A 417 " pdb=" N SER A 418 " pdb=" CA SER A 418 " ideal model delta sigma weight residual 126.45 134.77 -8.32 1.77e+00 3.19e-01 2.21e+01 angle pdb=" CA ASN A 856 " pdb=" CB ASN A 856 " pdb=" CG ASN A 856 " ideal model delta sigma weight residual 112.60 117.10 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N ASP B 74 " pdb=" CA ASP B 74 " pdb=" C ASP B 74 " ideal model delta sigma weight residual 107.23 100.60 6.63 1.67e+00 3.59e-01 1.58e+01 ... (remaining 12459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4842 17.57 - 35.15: 380 35.15 - 52.72: 117 52.72 - 70.30: 30 70.30 - 87.87: 16 Dihedral angle restraints: 5385 sinusoidal: 2001 harmonic: 3384 Sorted by residual: dihedral pdb=" CB CYS B 147 " pdb=" SG CYS B 147 " pdb=" SG CYS B 203 " pdb=" CB CYS B 203 " ideal model delta sinusoidal sigma weight residual 93.00 159.71 -66.71 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 43.13 49.87 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CA ARG A 420 " pdb=" C ARG A 420 " pdb=" N PRO A 421 " pdb=" CA PRO A 421 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 5382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 858 0.036 - 0.072: 363 0.072 - 0.109: 135 0.109 - 0.145: 58 0.145 - 0.181: 14 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA VAL B 39 " pdb=" N VAL B 39 " pdb=" C VAL B 39 " pdb=" CB VAL B 39 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA ILE A 723 " pdb=" N ILE A 723 " pdb=" C ILE A 723 " pdb=" CB ILE A 723 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA GLN A 252 " pdb=" N GLN A 252 " pdb=" C GLN A 252 " pdb=" CB GLN A 252 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1425 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 69 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO A 70 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 51 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C THR C 51 " -0.038 2.00e-02 2.50e+03 pdb=" O THR C 51 " 0.014 2.00e-02 2.50e+03 pdb=" N SER C 52 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 155 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 156 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " -0.024 5.00e-02 4.00e+02 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.02: 4710 3.02 - 3.49: 8797 3.49 - 3.96: 16426 3.96 - 4.43: 18603 4.43 - 4.90: 29875 Nonbonded interactions: 78411 Sorted by model distance: nonbonded pdb=" N SER A 69 " pdb=" O SER A 69 " model vdw 2.544 2.496 nonbonded pdb=" C SER A 418 " pdb=" OG SER A 418 " model vdw 2.588 2.616 nonbonded pdb=" N TYR B 54 " pdb=" O TYR B 54 " model vdw 2.593 2.496 nonbonded pdb=" N SER A 647 " pdb=" OG SER A 647 " model vdw 2.606 2.496 nonbonded pdb=" N MET A 852 " pdb=" N LYS A 853 " model vdw 2.612 2.560 ... (remaining 78406 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.960 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.005 0.056 9181 Z= 0.228 Angle : 0.751 11.178 12472 Z= 0.423 Chirality : 0.050 0.181 1428 Planarity : 0.006 0.061 1616 Dihedral : 15.685 87.871 3225 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.01 % Allowed : 16.57 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -1.02 (0.23), residues: 1176 helix: -2.53 (0.74), residues: 28 sheet: -0.73 (0.21), residues: 528 loop : -0.38 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 145 TYR 0.025 0.003 TYR A 205 PHE 0.027 0.002 PHE A 169 TRP 0.012 0.002 TRP A 438 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 ( 9177) covalent geometry : angle 0.75059 / 0.42 (12464) SS BOND : bond 0.00580 / 0.18 ( 4) SS BOND : angle 1.00686 / 0.60 ( 8) hydrogen bonds : bond 0.15851 / 10.62 ( 208) hydrogen bonds : angle 8.15170 / 5.63 ( 534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 208 MET cc_start: 0.7530 (mmp) cc_final: 0.6845 (tmt) REVERT: A 634 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8069 (pp) REVERT: A 638 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7917 (mmtm) REVERT: A 657 ASN cc_start: 0.8630 (m110) cc_final: 0.8342 (m-40) REVERT: A 691 THR cc_start: 0.8469 (m) cc_final: 0.8114 (t) REVERT: A 783 MET cc_start: 0.7140 (mmm) cc_final: 0.6726 (tpp) REVERT: A 864 THR cc_start: 0.8133 (m) cc_final: 0.7259 (p) REVERT: A 884 GLU cc_start: 0.6670 (mp0) cc_final: 0.6050 (tm-30) REVERT: A 891 LYS cc_start: 0.6878 (tttt) cc_final: 0.6581 (mtpp) REVERT: B 158 THR cc_start: 0.8222 (m) cc_final: 0.7900 (t) REVERT: C 17 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 24 ARG cc_start: 0.7367 (tpp-160) cc_final: 0.7129 (tpp-160) REVERT: C 32 ASP cc_start: 0.7637 (m-30) cc_final: 0.7397 (m-30) outliers start: 10 outliers final: 6 residues processed: 135 average time/residue: 0.5267 time to fit residues: 75.3810 Evaluate side-chains 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 636 LYS Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 93 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 ASN A 204 ASN A 246 GLN A 254 GLN A 747 ASN A 761 GLN A 867 GLN B 5 GLN B 162 ASN C 125 GLN C 159 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106087 restraints weight = 8770.314| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.51 r_work: 0.3158 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9181 Z= 0.216 Angle : 0.559 6.046 12472 Z= 0.305 Chirality : 0.045 0.139 1428 Planarity : 0.004 0.045 1616 Dihedral : 5.918 58.679 1280 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.12 % Allowed : 14.55 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.41 (0.24), residues: 1176 helix: -1.82 (0.86), residues: 28 sheet: -0.35 (0.22), residues: 538 loop : 0.06 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 675 TYR 0.017 0.002 TYR A 701 PHE 0.017 0.002 PHE B 80 TRP 0.014 0.002 TRP A 438 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 ( 9177) covalent geometry : angle 0.55800 / 0.31 (12464) SS BOND : bond 0.00726 / 0.23 ( 4) SS BOND : angle 1.17128 / 0.67 ( 8) hydrogen bonds : bond 0.03850 / 2.51 ( 208) hydrogen bonds : angle 6.28436 / 4.34 ( 534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.232 Fit side-chains REVERT: A 208 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.6859 (tmt) REVERT: A 267 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7710 (mm-30) REVERT: A 596 GLU cc_start: 0.7907 (mp0) cc_final: 0.7586 (mp0) REVERT: A 638 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8166 (mmtm) REVERT: A 657 ASN cc_start: 0.8717 (m110) cc_final: 0.8302 (m110) REVERT: A 783 MET cc_start: 0.7169 (mmm) cc_final: 0.6775 (tpp) REVERT: A 856 ASN cc_start: 0.8190 (t0) cc_final: 0.7844 (t0) REVERT: A 864 THR cc_start: 0.8229 (m) cc_final: 0.7893 (m) REVERT: A 884 GLU cc_start: 0.6786 (mp0) cc_final: 0.6143 (tm-30) REVERT: C 24 ARG cc_start: 0.7301 (tpp-160) cc_final: 0.7036 (tpp-160) outliers start: 21 outliers final: 6 residues processed: 139 average time/residue: 0.4835 time to fit residues: 71.4833 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 251 GLN A 747 ASN B 5 GLN C 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.153152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107738 restraints weight = 8787.222| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.51 r_work: 0.3176 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9181 Z= 0.128 Angle : 0.482 5.650 12472 Z= 0.263 Chirality : 0.043 0.134 1428 Planarity : 0.003 0.046 1616 Dihedral : 4.966 28.799 1271 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.02 % Allowed : 14.24 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.15 (0.24), residues: 1176 helix: -1.42 (0.93), residues: 28 sheet: -0.17 (0.21), residues: 549 loop : 0.22 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 675 TYR 0.012 0.001 TYR A 327 PHE 0.014 0.001 PHE B 80 TRP 0.011 0.002 TRP A 438 HIS 0.002 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 9177) covalent geometry : angle 0.48139 / 0.26 (12464) SS BOND : bond 0.00482 / 0.16 ( 4) SS BOND : angle 0.82650 / 0.49 ( 8) hydrogen bonds : bond 0.03215 / 2.09 ( 208) hydrogen bonds : angle 5.82672 / 4.02 ( 534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.205 Fit side-chains REVERT: A 208 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6962 (tmt) REVERT: A 267 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: A 596 GLU cc_start: 0.7874 (mp0) cc_final: 0.7549 (mp0) REVERT: A 638 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8091 (mmtm) REVERT: A 783 MET cc_start: 0.7135 (mmm) cc_final: 0.6766 (tpp) REVERT: A 856 ASN cc_start: 0.8205 (t0) cc_final: 0.7848 (t0) REVERT: A 864 THR cc_start: 0.8198 (m) cc_final: 0.7895 (m) REVERT: A 884 GLU cc_start: 0.6773 (mp0) cc_final: 0.6132 (tm-30) REVERT: C 106 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7964 (tt0) outliers start: 20 outliers final: 7 residues processed: 134 average time/residue: 0.5106 time to fit residues: 72.7815 Evaluate side-chains 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 251 GLN A 318 GLN A 747 ASN B 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107247 restraints weight = 8947.208| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.54 r_work: 0.3178 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9181 Z= 0.129 Angle : 0.474 5.544 12472 Z= 0.258 Chirality : 0.043 0.132 1428 Planarity : 0.003 0.045 1616 Dihedral : 4.760 21.110 1269 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.22 % Allowed : 13.84 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.09 (0.24), residues: 1176 helix: -1.34 (0.93), residues: 28 sheet: -0.12 (0.22), residues: 549 loop : 0.26 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 145 TYR 0.013 0.001 TYR A 327 PHE 0.016 0.001 PHE B 80 TRP 0.010 0.002 TRP A 438 HIS 0.002 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 9177) covalent geometry : angle 0.47358 / 0.26 (12464) SS BOND : bond 0.00466 / 0.15 ( 4) SS BOND : angle 0.78881 / 0.46 ( 8) hydrogen bonds : bond 0.03063 / 1.99 ( 208) hydrogen bonds : angle 5.62777 / 3.88 ( 534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.222 Fit side-chains REVERT: A 208 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7017 (tmt) REVERT: A 596 GLU cc_start: 0.7881 (mp0) cc_final: 0.7555 (mp0) REVERT: A 634 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 636 LYS cc_start: 0.8494 (ptmt) cc_final: 0.8044 (ttmt) REVERT: A 638 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8072 (mmtm) REVERT: A 657 ASN cc_start: 0.8652 (m110) cc_final: 0.8150 (m110) REVERT: A 783 MET cc_start: 0.7146 (mmm) cc_final: 0.6741 (tpp) REVERT: A 807 ASN cc_start: 0.7086 (OUTLIER) cc_final: 0.6620 (t0) REVERT: A 856 ASN cc_start: 0.8198 (t0) cc_final: 0.7805 (t0) REVERT: A 884 GLU cc_start: 0.6780 (mp0) cc_final: 0.6145 (tm-30) REVERT: C 10 THR cc_start: 0.8450 (m) cc_final: 0.8246 (t) REVERT: C 106 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7952 (tt0) outliers start: 22 outliers final: 10 residues processed: 137 average time/residue: 0.5137 time to fit residues: 75.0889 Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 807 ASN Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 7 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 83 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.0470 overall best weight: 0.5490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 251 GLN A 576 ASN A 747 ASN B 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.154007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108558 restraints weight = 8848.683| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.52 r_work: 0.3200 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9181 Z= 0.105 Angle : 0.449 5.449 12472 Z= 0.245 Chirality : 0.042 0.133 1428 Planarity : 0.003 0.045 1616 Dihedral : 4.546 20.675 1269 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.02 % Allowed : 14.34 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.24), residues: 1176 helix: -1.20 (0.92), residues: 28 sheet: -0.04 (0.21), residues: 550 loop : 0.29 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 24 TYR 0.012 0.001 TYR B 54 PHE 0.014 0.001 PHE B 80 TRP 0.009 0.001 TRP A 438 HIS 0.002 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 9177) covalent geometry : angle 0.44873 / 0.24 (12464) SS BOND : bond 0.00433 / 0.14 ( 4) SS BOND : angle 0.73896 / 0.44 ( 8) hydrogen bonds : bond 0.02836 / 1.84 ( 208) hydrogen bonds : angle 5.39860 / 3.72 ( 534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.280 Fit side-chains REVERT: A 208 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6993 (tmt) REVERT: A 596 GLU cc_start: 0.7808 (mp0) cc_final: 0.7518 (mp0) REVERT: A 636 LYS cc_start: 0.8492 (ptmt) cc_final: 0.8085 (ttmt) REVERT: A 638 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8088 (mmtm) REVERT: A 657 ASN cc_start: 0.8652 (m110) cc_final: 0.8138 (m110) REVERT: A 783 MET cc_start: 0.7138 (mmm) cc_final: 0.6727 (tpp) REVERT: A 884 GLU cc_start: 0.6798 (mp0) cc_final: 0.6166 (tm-30) REVERT: B 122 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8335 (p) REVERT: C 106 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7962 (tt0) outliers start: 20 outliers final: 8 residues processed: 137 average time/residue: 0.4611 time to fit residues: 67.5123 Evaluate side-chains 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 251 GLN A 318 GLN A 576 ASN A 747 ASN B 5 GLN B 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105084 restraints weight = 8818.644| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.52 r_work: 0.3143 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9181 Z= 0.210 Angle : 0.540 6.212 12472 Z= 0.295 Chirality : 0.045 0.149 1428 Planarity : 0.004 0.043 1616 Dihedral : 5.086 21.911 1269 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.12 % Allowed : 14.14 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1176 helix: -1.62 (0.88), residues: 28 sheet: -0.06 (0.22), residues: 539 loop : 0.30 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 24 TYR 0.016 0.002 TYR A 205 PHE 0.019 0.002 PHE B 80 TRP 0.014 0.002 TRP B 103 HIS 0.003 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 ( 9177) covalent geometry : angle 0.53983 / 0.29 (12464) SS BOND : bond 0.00717 / 0.23 ( 4) SS BOND : angle 0.99729 / 0.56 ( 8) hydrogen bonds : bond 0.03557 / 2.30 ( 208) hydrogen bonds : angle 5.79747 / 3.99 ( 534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.430 Fit side-chains REVERT: A 208 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.6958 (tmt) REVERT: A 596 GLU cc_start: 0.7838 (mp0) cc_final: 0.7545 (mp0) REVERT: A 636 LYS cc_start: 0.8537 (ptmt) cc_final: 0.8120 (ttmt) REVERT: A 638 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8112 (mptt) REVERT: A 657 ASN cc_start: 0.8677 (m110) cc_final: 0.8122 (m110) REVERT: A 783 MET cc_start: 0.7164 (mmm) cc_final: 0.6784 (tpp) REVERT: A 807 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6679 (t0) REVERT: A 819 SER cc_start: 0.7619 (t) cc_final: 0.7399 (m) REVERT: A 874 ASN cc_start: 0.6666 (t0) cc_final: 0.6264 (m-40) REVERT: A 884 GLU cc_start: 0.6786 (mp0) cc_final: 0.6198 (tm-30) REVERT: B 122 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8315 (p) REVERT: C 106 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8108 (tt0) outliers start: 21 outliers final: 11 residues processed: 133 average time/residue: 0.4962 time to fit residues: 70.4270 Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 807 ASN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 57 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 251 GLN A 576 ASN A 747 ASN B 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106400 restraints weight = 8918.148| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.53 r_work: 0.3167 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9181 Z= 0.145 Angle : 0.488 5.567 12472 Z= 0.266 Chirality : 0.043 0.147 1428 Planarity : 0.003 0.044 1616 Dihedral : 4.847 21.345 1269 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.02 % Allowed : 14.44 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.06 (0.24), residues: 1176 helix: -1.52 (0.89), residues: 28 sheet: -0.01 (0.21), residues: 551 loop : 0.35 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.012 0.002 TYR A 327 PHE 0.017 0.002 PHE B 80 TRP 0.012 0.002 TRP A 438 HIS 0.002 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 9177) covalent geometry : angle 0.48765 / 0.27 (12464) SS BOND : bond 0.00540 / 0.17 ( 4) SS BOND : angle 0.81885 / 0.48 ( 8) hydrogen bonds : bond 0.03172 / 2.06 ( 208) hydrogen bonds : angle 5.56547 / 3.83 ( 534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.328 Fit side-chains REVERT: A 208 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7005 (tmt) REVERT: A 596 GLU cc_start: 0.7818 (mp0) cc_final: 0.7529 (mp0) REVERT: A 634 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8148 (pp) REVERT: A 636 LYS cc_start: 0.8519 (ptmt) cc_final: 0.8095 (ttmt) REVERT: A 638 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8115 (mptt) REVERT: A 657 ASN cc_start: 0.8671 (m110) cc_final: 0.8129 (m110) REVERT: A 783 MET cc_start: 0.7171 (mmm) cc_final: 0.6775 (tpp) REVERT: A 819 SER cc_start: 0.7588 (t) cc_final: 0.7369 (m) REVERT: A 874 ASN cc_start: 0.6566 (t0) cc_final: 0.6210 (m-40) REVERT: A 884 GLU cc_start: 0.6817 (mp0) cc_final: 0.6169 (tm-30) REVERT: B 122 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8351 (p) REVERT: C 24 ARG cc_start: 0.7237 (tpp-160) cc_final: 0.6830 (tpp-160) outliers start: 20 outliers final: 10 residues processed: 137 average time/residue: 0.4981 time to fit residues: 72.8708 Evaluate side-chains 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 251 GLN A 318 GLN A 576 ASN A 747 ASN B 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.152827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107153 restraints weight = 8855.421| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.53 r_work: 0.3179 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9181 Z= 0.127 Angle : 0.473 5.516 12472 Z= 0.258 Chirality : 0.043 0.144 1428 Planarity : 0.003 0.045 1616 Dihedral : 4.715 21.109 1269 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.52 % Allowed : 14.75 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.12 (0.24), residues: 1176 helix: -1.45 (0.90), residues: 28 sheet: 0.05 (0.22), residues: 548 loop : 0.38 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.011 0.001 TYR A 327 PHE 0.016 0.001 PHE B 80 TRP 0.010 0.001 TRP A 438 HIS 0.002 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9177) covalent geometry : angle 0.47285 / 0.26 (12464) SS BOND : bond 0.00474 / 0.15 ( 4) SS BOND : angle 0.76255 / 0.45 ( 8) hydrogen bonds : bond 0.03016 / 1.96 ( 208) hydrogen bonds : angle 5.42674 / 3.73 ( 534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.318 Fit side-chains REVERT: A 208 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7021 (tmt) REVERT: A 596 GLU cc_start: 0.7798 (mp0) cc_final: 0.7506 (mp0) REVERT: A 636 LYS cc_start: 0.8503 (ptmt) cc_final: 0.8091 (ttmt) REVERT: A 638 LYS cc_start: 0.8439 (mmtt) cc_final: 0.8102 (mmtm) REVERT: A 657 ASN cc_start: 0.8660 (m110) cc_final: 0.8126 (m110) REVERT: A 762 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7513 (m) REVERT: A 819 SER cc_start: 0.7564 (t) cc_final: 0.7352 (m) REVERT: A 864 THR cc_start: 0.8142 (m) cc_final: 0.7785 (m) REVERT: A 884 GLU cc_start: 0.6797 (mp0) cc_final: 0.6153 (tm-30) outliers start: 15 outliers final: 10 residues processed: 131 average time/residue: 0.4891 time to fit residues: 68.2955 Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 251 GLN A 576 ASN A 747 ASN B 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108703 restraints weight = 8787.445| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.50 r_work: 0.3207 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9181 Z= 0.127 Angle : 0.474 5.483 12472 Z= 0.258 Chirality : 0.043 0.139 1428 Planarity : 0.003 0.045 1616 Dihedral : 4.682 21.020 1269 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.31 % Allowed : 15.05 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: 0.16 (0.24), residues: 1176 helix: -1.41 (0.90), residues: 28 sheet: 0.07 (0.21), residues: 553 loop : 0.41 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 24 TYR 0.011 0.001 TYR A 327 PHE 0.016 0.001 PHE B 80 TRP 0.010 0.001 TRP A 438 HIS 0.002 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9177) covalent geometry : angle 0.47369 / 0.26 (12464) SS BOND : bond 0.00531 / 0.17 ( 4) SS BOND : angle 0.79976 / 0.47 ( 8) hydrogen bonds : bond 0.03017 / 1.97 ( 208) hydrogen bonds : angle 5.38647 / 3.70 ( 534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 208 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7239 (tmt) REVERT: A 596 GLU cc_start: 0.7910 (mp0) cc_final: 0.7675 (mp0) REVERT: A 762 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7645 (m) REVERT: A 783 MET cc_start: 0.7339 (mmm) cc_final: 0.6937 (tpp) REVERT: A 864 THR cc_start: 0.8307 (m) cc_final: 0.7953 (m) REVERT: A 884 GLU cc_start: 0.6868 (mp0) cc_final: 0.6303 (tm-30) REVERT: C 24 ARG cc_start: 0.7451 (tpp-160) cc_final: 0.7157 (tpp-160) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.4988 time to fit residues: 68.7372 Evaluate side-chains 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 32 optimal weight: 0.0170 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 251 GLN A 576 ASN A 747 ASN B 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.150178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104052 restraints weight = 8766.310| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.52 r_work: 0.3124 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9181 Z= 0.285 Angle : 0.609 6.467 12472 Z= 0.332 Chirality : 0.047 0.157 1428 Planarity : 0.004 0.043 1616 Dihedral : 5.356 21.143 1269 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.82 % Allowed : 14.95 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % 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: -0.05 (0.24), residues: 1176 helix: -1.72 (0.91), residues: 28 sheet: 0.01 (0.22), residues: 519 loop : 0.16 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 24 TYR 0.019 0.003 TYR A 701 PHE 0.021 0.003 PHE B 80 TRP 0.018 0.003 TRP B 103 HIS 0.005 0.002 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.28 ( 9177) covalent geometry : angle 0.60816 / 0.33 (12464) SS BOND : bond 0.00844 / 0.27 ( 4) SS BOND : angle 1.14015 / 0.63 ( 8) hydrogen bonds : bond 0.03976 / 2.58 ( 208) hydrogen bonds : angle 5.98559 / 4.12 ( 534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.346 Fit side-chains REVERT: A 208 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7008 (tmm) REVERT: A 267 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: A 473 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8499 (ttmm) REVERT: A 596 GLU cc_start: 0.7900 (mp0) cc_final: 0.7570 (mp0) REVERT: A 723 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7499 (mm) REVERT: A 762 SER cc_start: 0.7590 (OUTLIER) cc_final: 0.7262 (m) REVERT: A 783 MET cc_start: 0.7199 (mmm) cc_final: 0.6850 (tpp) REVERT: A 874 ASN cc_start: 0.6632 (t0) cc_final: 0.6246 (m-40) REVERT: A 884 GLU cc_start: 0.6835 (mp0) cc_final: 0.6290 (tm-30) REVERT: C 24 ARG cc_start: 0.7301 (tpp-160) cc_final: 0.6940 (tpp-160) outliers start: 18 outliers final: 11 residues processed: 135 average time/residue: 0.5379 time to fit residues: 77.3722 Evaluate side-chains 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 78 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 246 GLN A 251 GLN A 576 ASN A 747 ASN B 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.153337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108324 restraints weight = 8649.721| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.49 r_work: 0.3206 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9181 Z= 0.124 Angle : 0.484 5.727 12472 Z= 0.263 Chirality : 0.043 0.141 1428 Planarity : 0.003 0.045 1616 Dihedral : 4.812 20.167 1269 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.31 % Allowed : 15.35 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.24), residues: 1176 helix: -1.38 (0.95), residues: 28 sheet: 0.04 (0.21), residues: 538 loop : 0.32 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 24 TYR 0.012 0.001 TYR A 327 PHE 0.014 0.001 PHE B 80 TRP 0.011 0.002 TRP A 438 HIS 0.002 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9177) covalent geometry : angle 0.48380 / 0.26 (12464) SS BOND : bond 0.00454 / 0.15 ( 4) SS BOND : angle 0.74528 / 0.44 ( 8) hydrogen bonds : bond 0.03080 / 2.00 ( 208) hydrogen bonds : angle 5.49575 / 3.77 ( 534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.61 seconds wall clock time: 74 minutes 44.65 seconds (4484.65 seconds total)