Starting phenix.real_space_refine on Tue Mar 3 21:34:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stx_25438/03_2026/7stx_25438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stx_25438/03_2026/7stx_25438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stx_25438/03_2026/7stx_25438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stx_25438/03_2026/7stx_25438.map" model { file = "/net/cci-nas-00/data/ceres_data/7stx_25438/03_2026/7stx_25438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stx_25438/03_2026/7stx_25438.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 44 5.16 5 C 5508 2.51 5 N 1438 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8611 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1272 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7246 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 31, 'TRANS': 882} Chain breaks: 4 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 28, 'ARG:plan': 3, 'GLU:plan': 5, 'ASP:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.67, per 1000 atoms: 0.19 Number of scatterers: 8611 At special positions: 0 Unit cell: (94.62, 101.26, 114.54, 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 44 16.00 P 3 15.00 O 1618 8.00 N 1438 7.00 C 5508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 290.7 milliseconds 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 65.5% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 27 through 38 removed outlier: 4.295A pdb=" N PHE A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 103 Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.598A pdb=" N VAL A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.862A pdb=" N UNK B 18 " --> pdb=" O UNK B 14 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N UNK B 19 " --> pdb=" O UNK B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 24 No H-bonds generated for 'chain 'B' and resid 22 through 24' Processing helix chain 'B' and resid 27 through 35 removed outlier: 3.567A pdb=" N UNK B 32 " --> pdb=" O UNK B 28 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N UNK B 33 " --> pdb=" O UNK B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 61 through 72 removed outlier: 4.558A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.804A pdb=" N ILE B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.895A pdb=" N THR B 99 " --> pdb=" O PRO B 95 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 103' Processing helix chain 'B' and resid 113 through 127 Processing helix chain 'B' and resid 128 through 143 removed outlier: 3.870A pdb=" N GLN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLN B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 162 removed outlier: 3.884A pdb=" N SER B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 187 removed outlier: 4.202A pdb=" N MET B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 206 removed outlier: 3.694A pdb=" N GLU B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 removed outlier: 3.770A pdb=" N ASP B 214 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.699A pdb=" N LYS B 223 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.909A pdb=" N ALA B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 260 removed outlier: 3.956A pdb=" N LEU B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 279 removed outlier: 3.911A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 4.302A pdb=" N PHE B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 336 removed outlier: 3.732A pdb=" N LEU B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 335 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 372 through 376 removed outlier: 3.597A pdb=" N LEU B 375 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 376 " --> pdb=" O VAL B 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 376' Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.676A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 449 removed outlier: 4.174A pdb=" N VAL B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.704A pdb=" N GLU B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 502 Processing helix chain 'B' and resid 505 through 520 removed outlier: 3.955A pdb=" N LYS B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 543 through 551 removed outlier: 4.210A pdb=" N TYR B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 583 Processing helix chain 'B' and resid 592 through 605 Processing helix chain 'B' and resid 606 through 624 removed outlier: 3.628A pdb=" N ALA B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 636 Processing helix chain 'B' and resid 672 through 698 removed outlier: 3.539A pdb=" N LYS B 676 " --> pdb=" O SER B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 728 Processing helix chain 'B' and resid 728 through 746 removed outlier: 3.712A pdb=" N GLN B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 739 " --> pdb=" O GLU B 735 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 767 removed outlier: 3.750A pdb=" N ASN B 766 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 790 removed outlier: 4.172A pdb=" N SER B 776 " --> pdb=" O CYS B 772 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 781 " --> pdb=" O PHE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 820 removed outlier: 3.790A pdb=" N GLU B 799 " --> pdb=" O MET B 795 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 810 " --> pdb=" O LYS B 806 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 814 " --> pdb=" O ASP B 810 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 830 Processing helix chain 'B' and resid 835 through 868 removed outlier: 3.965A pdb=" N LEU B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 847 " --> pdb=" O PHE B 843 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 860 " --> pdb=" O SER B 856 " (cutoff:3.500A) Proline residue: B 864 - end of helix Processing helix chain 'B' and resid 883 through 905 removed outlier: 3.921A pdb=" N SER B 889 " --> pdb=" O PRO B 885 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 895 " --> pdb=" O GLN B 891 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 896 " --> pdb=" O ASP B 892 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 900 " --> pdb=" O GLY B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 933 through 964 removed outlier: 3.540A pdb=" N SER B 938 " --> pdb=" O GLU B 934 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 969 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.782A pdb=" N ALA A 46 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A 53 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 113 removed outlier: 7.570A pdb=" N GLU A 147 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 135 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA A 149 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR A 133 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 151 " --> pdb=" O TYR A 131 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1191 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: 1.33 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1439 1.31 - 1.44: 2318 1.44 - 1.57: 4951 1.57 - 1.70: 6 1.70 - 1.83: 72 Bond restraints: 8786 Sorted by residual: bond pdb=" C1B COA A 201 " pdb=" O4B COA A 201 " ideal model delta sigma weight residual 1.418 1.641 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1B COA A 201 " pdb=" C2B COA A 201 " ideal model delta sigma weight residual 1.533 1.320 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C9P COA A 201 " pdb=" N8P COA A 201 " ideal model delta sigma weight residual 1.340 1.509 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" C4B COA A 201 " pdb=" O4B COA A 201 " ideal model delta sigma weight residual 1.453 1.298 0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" C3B COA A 201 " pdb=" O3B COA A 201 " ideal model delta sigma weight residual 1.419 1.335 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.22: 11808 6.22 - 12.45: 60 12.45 - 18.67: 13 18.67 - 24.90: 5 24.90 - 31.12: 3 Bond angle restraints: 11889 Sorted by residual: angle pdb=" N GLN B 462 " pdb=" CA GLN B 462 " pdb=" C GLN B 462 " ideal model delta sigma weight residual 110.41 79.86 30.55 1.23e+00 6.61e-01 6.17e+02 angle pdb=" N PRO B 701 " pdb=" CA PRO B 701 " pdb=" C PRO B 701 " ideal model delta sigma weight residual 111.77 80.65 31.12 1.67e+00 3.59e-01 3.47e+02 angle pdb=" N LEU B 640 " pdb=" CA LEU B 640 " pdb=" C LEU B 640 " ideal model delta sigma weight residual 109.07 81.03 28.04 1.61e+00 3.86e-01 3.03e+02 angle pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" C LYS B 145 " ideal model delta sigma weight residual 110.36 86.51 23.85 1.55e+00 4.16e-01 2.37e+02 angle pdb=" C LYS B 667 " pdb=" CA LYS B 667 " pdb=" CB LYS B 667 " ideal model delta sigma weight residual 111.23 86.82 24.41 1.63e+00 3.76e-01 2.24e+02 ... (remaining 11884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4591 18.00 - 35.99: 568 35.99 - 53.99: 132 53.99 - 71.99: 33 71.99 - 89.98: 14 Dihedral angle restraints: 5338 sinusoidal: 2165 harmonic: 3173 Sorted by residual: dihedral pdb=" C LYS B 145 " pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" CB LYS B 145 " ideal model delta harmonic sigma weight residual -122.60 -93.42 -29.18 0 2.50e+00 1.60e-01 1.36e+02 dihedral pdb=" C GLN B 462 " pdb=" N GLN B 462 " pdb=" CA GLN B 462 " pdb=" CB GLN B 462 " ideal model delta harmonic sigma weight residual -122.60 -95.16 -27.44 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C LYS B 667 " pdb=" N LYS B 667 " pdb=" CA LYS B 667 " pdb=" CB LYS B 667 " ideal model delta harmonic sigma weight residual -122.60 -98.27 -24.33 0 2.50e+00 1.60e-01 9.47e+01 ... (remaining 5335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1284 0.145 - 0.291: 36 0.291 - 0.436: 10 0.436 - 0.581: 3 0.581 - 0.727: 2 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CA LYS B 145 " pdb=" N LYS B 145 " pdb=" C LYS B 145 " pdb=" CB LYS B 145 " both_signs ideal model delta sigma weight residual False 2.51 3.24 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA GLN B 462 " pdb=" N GLN B 462 " pdb=" C GLN B 462 " pdb=" CB GLN B 462 " both_signs ideal model delta sigma weight residual False 2.51 3.21 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA LEU B 640 " pdb=" N LEU B 640 " pdb=" C LEU B 640 " pdb=" CB LEU B 640 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 6.95e+00 ... (remaining 1332 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 43 " -0.032 2.00e-02 2.50e+03 3.72e-02 2.42e+01 pdb=" CG PHE A 43 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE A 43 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 43 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 43 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE A 43 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 43 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 666 " -0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C PRO B 666 " 0.082 2.00e-02 2.50e+03 pdb=" O PRO B 666 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS B 667 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 757 " -0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO B 758 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 758 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 758 " -0.048 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 5 2.07 - 2.78: 2064 2.78 - 3.48: 10706 3.48 - 4.19: 19909 4.19 - 4.90: 35969 Nonbonded interactions: 68653 Sorted by model distance: nonbonded pdb=" CG2 ILE B 277 " pdb=" OG SER B 298 " model vdw 1.362 3.460 nonbonded pdb=" OD1 ASN A 16 " pdb=" NE2 GLN B 538 " model vdw 1.673 3.120 nonbonded pdb=" N GLN B 462 " pdb=" O GLN B 462 " model vdw 1.881 2.496 nonbonded pdb=" N PRO B 701 " pdb=" O PRO B 701 " model vdw 1.986 2.496 nonbonded pdb=" N LYS B 145 " pdb=" O LYS B 145 " model vdw 2.061 2.496 ... (remaining 68648 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: 1.920 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.630 Find NCS groups from input model: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 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 : 0.012 0.296 8790 Z= 0.618 Angle : 1.480 31.120 11889 Z= 0.854 Chirality : 0.079 0.727 1335 Planarity : 0.009 0.092 1508 Dihedral : 17.437 89.984 3280 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.66 % Favored : 89.95 % Rotamer: Outliers : 2.09 % Allowed : 11.31 % Favored : 86.61 % Cbeta Deviations : 1.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.56 (0.18), residues: 1035 helix: -3.42 (0.12), residues: 673 sheet: -4.64 (0.68), residues: 35 loop : -3.70 (0.27), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 616 TYR 0.027 0.003 TYR A 42 PHE 0.079 0.004 PHE A 43 TRP 0.020 0.002 TRP B 686 HIS 0.013 0.002 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.01185 ( 8786) covalent geometry : angle 1.47991 (11889) hydrogen bonds : bond 0.18272 ( 405) hydrogen bonds : angle 7.32970 ( 1191) Misc. bond : bond 0.14819 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 670 ASP cc_start: 0.4363 (OUTLIER) cc_final: 0.3952 (t70) REVERT: B 906 ASP cc_start: 0.4825 (m-30) cc_final: 0.4400 (m-30) outliers start: 19 outliers final: 5 residues processed: 225 average time/residue: 0.1106 time to fit residues: 32.6138 Evaluate side-chains 115 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0770 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 ASN B 387 GLN B 428 HIS ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 573 ASN B 605 ASN B 608 HIS B 766 ASN B 868 ASN B 898 GLN B 914 HIS B 951 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.204961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.167495 restraints weight = 9022.690| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 1.66 r_work: 0.4139 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4000 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8790 Z= 0.140 Angle : 0.654 8.894 11889 Z= 0.340 Chirality : 0.041 0.178 1335 Planarity : 0.006 0.072 1508 Dihedral : 9.510 59.399 1240 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.88 % Rotamer: Outliers : 2.41 % Allowed : 15.70 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -3.48 (0.23), residues: 1035 helix: -1.61 (0.18), residues: 660 sheet: -4.28 (0.77), residues: 32 loop : -3.29 (0.28), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 613 TYR 0.015 0.001 TYR B 297 PHE 0.028 0.002 PHE A 107 TRP 0.011 0.002 TRP B 686 HIS 0.003 0.001 HIS B 501 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8786) covalent geometry : angle 0.65383 (11889) hydrogen bonds : bond 0.03974 ( 405) hydrogen bonds : angle 4.38779 ( 1191) Misc. bond : bond 0.00108 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8032 (tt0) REVERT: B 172 MET cc_start: 0.6919 (mmt) cc_final: 0.6646 (mmt) REVERT: B 236 MET cc_start: 0.7671 (mmm) cc_final: 0.7454 (tpt) REVERT: B 279 GLU cc_start: 0.5172 (OUTLIER) cc_final: 0.4633 (pt0) REVERT: B 289 HIS cc_start: 0.4258 (OUTLIER) cc_final: 0.3809 (m-70) REVERT: B 315 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7493 (pttt) REVERT: B 352 MET cc_start: 0.6634 (mmm) cc_final: 0.6427 (mmm) REVERT: B 653 ARG cc_start: 0.6177 (mmp80) cc_final: 0.5651 (mmm-85) REVERT: B 795 MET cc_start: 0.5761 (mmp) cc_final: 0.5107 (ppp) REVERT: B 799 GLU cc_start: 0.6737 (pp20) cc_final: 0.6273 (pt0) REVERT: B 883 MET cc_start: 0.6989 (tpp) cc_final: 0.6730 (tpp) outliers start: 22 outliers final: 12 residues processed: 160 average time/residue: 0.1044 time to fit residues: 22.0131 Evaluate side-chains 119 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain C residue 5 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN B 413 GLN B 473 HIS B 501 HIS B 538 GLN B 611 GLN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.185216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.148941 restraints weight = 9066.527| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.84 r_work: 0.3874 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8790 Z= 0.204 Angle : 0.740 11.127 11889 Z= 0.379 Chirality : 0.045 0.217 1335 Planarity : 0.006 0.067 1508 Dihedral : 8.932 56.238 1233 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.50 % Favored : 91.40 % Rotamer: Outliers : 3.29 % Allowed : 18.66 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -2.84 (0.24), residues: 1035 helix: -1.04 (0.19), residues: 661 sheet: -3.92 (0.71), residues: 42 loop : -3.17 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 5 TYR 0.039 0.002 TYR A 42 PHE 0.028 0.003 PHE A 107 TRP 0.021 0.002 TRP B 281 HIS 0.025 0.002 HIS B 914 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8786) covalent geometry : angle 0.73980 (11889) hydrogen bonds : bond 0.05228 ( 405) hydrogen bonds : angle 4.35871 ( 1191) Misc. bond : bond 0.00094 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.328 Fit side-chains REVERT: A 125 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8064 (tt0) REVERT: B 172 MET cc_start: 0.7520 (mmt) cc_final: 0.7297 (mmt) REVERT: B 184 MET cc_start: 0.6942 (mtt) cc_final: 0.6701 (mtt) REVERT: B 748 ASP cc_start: 0.7218 (t0) cc_final: 0.6437 (p0) REVERT: B 795 MET cc_start: 0.6063 (mmp) cc_final: 0.5406 (ppp) REVERT: B 883 MET cc_start: 0.7433 (tpp) cc_final: 0.6982 (tpp) outliers start: 30 outliers final: 20 residues processed: 169 average time/residue: 0.0884 time to fit residues: 20.7210 Evaluate side-chains 140 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 894 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN B 771 GLN B 898 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.194294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.161309 restraints weight = 9006.319| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 1.68 r_work: 0.3854 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8790 Z= 0.151 Angle : 0.655 10.022 11889 Z= 0.335 Chirality : 0.043 0.247 1335 Planarity : 0.005 0.065 1508 Dihedral : 7.998 59.046 1231 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.41 % Favored : 91.50 % Rotamer: Outliers : 3.40 % Allowed : 21.08 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -2.12 (0.26), residues: 1035 helix: -0.47 (0.20), residues: 666 sheet: -3.99 (0.77), residues: 37 loop : -2.91 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 5 TYR 0.027 0.002 TYR B 239 PHE 0.025 0.002 PHE A 107 TRP 0.012 0.002 TRP B 686 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8786) covalent geometry : angle 0.65503 (11889) hydrogen bonds : bond 0.04095 ( 405) hydrogen bonds : angle 4.01838 ( 1191) Misc. bond : bond 0.00066 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.341 Fit side-chains REVERT: A 125 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8253 (tt0) REVERT: B 142 ILE cc_start: 0.8156 (mp) cc_final: 0.7930 (mt) REVERT: B 216 ILE cc_start: 0.7373 (mt) cc_final: 0.7120 (pt) REVERT: B 795 MET cc_start: 0.6338 (mmp) cc_final: 0.5635 (ptm) REVERT: B 799 GLU cc_start: 0.7032 (pp20) cc_final: 0.6193 (pt0) outliers start: 31 outliers final: 21 residues processed: 150 average time/residue: 0.0856 time to fit residues: 18.1424 Evaluate side-chains 141 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 0.0170 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.189613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.155457 restraints weight = 9005.316| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.75 r_work: 0.3876 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8790 Z= 0.152 Angle : 0.644 7.872 11889 Z= 0.329 Chirality : 0.042 0.195 1335 Planarity : 0.005 0.065 1508 Dihedral : 7.422 59.744 1231 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.41 % Favored : 91.40 % Rotamer: Outliers : 3.73 % Allowed : 20.97 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.83 (0.26), residues: 1035 helix: -0.11 (0.20), residues: 662 sheet: -4.04 (0.66), residues: 42 loop : -3.05 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 5 TYR 0.021 0.001 TYR A 42 PHE 0.025 0.002 PHE A 107 TRP 0.012 0.002 TRP B 281 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8786) covalent geometry : angle 0.64445 (11889) hydrogen bonds : bond 0.04107 ( 405) hydrogen bonds : angle 3.93441 ( 1191) Misc. bond : bond 0.00060 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.334 Fit side-chains REVERT: A 125 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8275 (tt0) REVERT: B 81 SER cc_start: 0.7900 (t) cc_final: 0.7605 (p) REVERT: B 142 ILE cc_start: 0.8220 (mp) cc_final: 0.7992 (mt) REVERT: B 157 ILE cc_start: 0.7481 (mt) cc_final: 0.7154 (mt) REVERT: B 795 MET cc_start: 0.6149 (mmp) cc_final: 0.5596 (ptm) outliers start: 34 outliers final: 24 residues processed: 158 average time/residue: 0.0839 time to fit residues: 18.8723 Evaluate side-chains 140 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 0.0670 chunk 88 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.196474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.159123 restraints weight = 8946.280| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.63 r_work: 0.3889 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8790 Z= 0.123 Angle : 0.607 10.636 11889 Z= 0.308 Chirality : 0.041 0.257 1335 Planarity : 0.005 0.064 1508 Dihedral : 6.988 58.436 1231 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.02 % Favored : 91.79 % Rotamer: Outliers : 2.96 % Allowed : 21.62 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.50 (0.26), residues: 1035 helix: 0.20 (0.21), residues: 670 sheet: -4.32 (0.69), residues: 35 loop : -3.13 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 5 TYR 0.015 0.001 TYR B 140 PHE 0.024 0.001 PHE A 107 TRP 0.010 0.001 TRP B 686 HIS 0.002 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8786) covalent geometry : angle 0.60669 (11889) hydrogen bonds : bond 0.03507 ( 405) hydrogen bonds : angle 3.73515 ( 1191) Misc. bond : bond 0.00042 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.296 Fit side-chains REVERT: A 151 ASP cc_start: 0.7517 (t0) cc_final: 0.7138 (t70) REVERT: B 216 ILE cc_start: 0.7395 (mt) cc_final: 0.7051 (pt) REVERT: B 289 HIS cc_start: 0.3908 (OUTLIER) cc_final: 0.3630 (t-90) REVERT: B 653 ARG cc_start: 0.6292 (mmp80) cc_final: 0.5703 (mmm-85) REVERT: B 747 LYS cc_start: 0.6454 (pttt) cc_final: 0.5632 (ttmt) REVERT: B 795 MET cc_start: 0.6043 (mmp) cc_final: 0.5469 (ptm) REVERT: B 912 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7673 (mt-10) outliers start: 27 outliers final: 20 residues processed: 149 average time/residue: 0.0850 time to fit residues: 17.7247 Evaluate side-chains 136 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.190752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.156782 restraints weight = 9035.161| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 1.70 r_work: 0.3911 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8790 Z= 0.144 Angle : 0.637 9.018 11889 Z= 0.322 Chirality : 0.042 0.260 1335 Planarity : 0.005 0.063 1508 Dihedral : 6.854 57.804 1231 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.41 % Favored : 91.50 % Rotamer: Outliers : 3.95 % Allowed : 21.08 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.42 (0.26), residues: 1035 helix: 0.29 (0.20), residues: 676 sheet: -4.12 (0.60), residues: 42 loop : -3.19 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 743 TYR 0.019 0.002 TYR A 42 PHE 0.023 0.002 PHE A 107 TRP 0.011 0.002 TRP B 686 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8786) covalent geometry : angle 0.63664 (11889) hydrogen bonds : bond 0.03903 ( 405) hydrogen bonds : angle 3.82039 ( 1191) Misc. bond : bond 0.00066 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.351 Fit side-chains REVERT: B 81 SER cc_start: 0.7890 (t) cc_final: 0.7585 (p) REVERT: B 157 ILE cc_start: 0.7497 (mt) cc_final: 0.7149 (mt) REVERT: B 216 ILE cc_start: 0.7429 (mt) cc_final: 0.7129 (pt) REVERT: B 289 HIS cc_start: 0.4118 (OUTLIER) cc_final: 0.3795 (t-90) REVERT: B 407 ASP cc_start: 0.6582 (p0) cc_final: 0.6312 (t0) REVERT: B 641 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7658 (mpp-170) REVERT: B 653 ARG cc_start: 0.6395 (mmp80) cc_final: 0.5908 (mmm-85) REVERT: B 747 LYS cc_start: 0.6450 (pttt) cc_final: 0.5654 (ttmt) REVERT: B 748 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6602 (p0) REVERT: B 795 MET cc_start: 0.5881 (mmp) cc_final: 0.5410 (ptm) outliers start: 36 outliers final: 28 residues processed: 145 average time/residue: 0.0837 time to fit residues: 17.0765 Evaluate side-chains 145 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain C residue 2 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.189964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.153460 restraints weight = 8951.920| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.11 r_work: 0.3802 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8790 Z= 0.182 Angle : 0.692 11.283 11889 Z= 0.348 Chirality : 0.044 0.253 1335 Planarity : 0.005 0.064 1508 Dihedral : 6.937 59.514 1231 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.99 % Favored : 90.92 % Rotamer: Outliers : 4.06 % Allowed : 21.51 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.50 (0.26), residues: 1035 helix: 0.20 (0.20), residues: 676 sheet: -4.21 (0.56), residues: 42 loop : -3.15 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 743 TYR 0.026 0.002 TYR A 42 PHE 0.024 0.002 PHE A 107 TRP 0.013 0.002 TRP B 686 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 8786) covalent geometry : angle 0.69176 (11889) hydrogen bonds : bond 0.04468 ( 405) hydrogen bonds : angle 4.00761 ( 1191) Misc. bond : bond 0.00087 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.240 Fit side-chains REVERT: A 151 ASP cc_start: 0.7639 (t0) cc_final: 0.7271 (t0) REVERT: B 81 SER cc_start: 0.7871 (t) cc_final: 0.7564 (p) REVERT: B 157 ILE cc_start: 0.7558 (mt) cc_final: 0.7215 (mt) REVERT: B 216 ILE cc_start: 0.7322 (mt) cc_final: 0.6975 (pt) REVERT: B 289 HIS cc_start: 0.4514 (OUTLIER) cc_final: 0.3921 (t-90) REVERT: B 407 ASP cc_start: 0.6722 (p0) cc_final: 0.6491 (t0) REVERT: B 641 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7613 (mpp-170) REVERT: B 748 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6603 (p0) REVERT: B 795 MET cc_start: 0.6002 (mmp) cc_final: 0.5434 (ppp) outliers start: 37 outliers final: 30 residues processed: 145 average time/residue: 0.0904 time to fit residues: 18.2226 Evaluate side-chains 140 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain C residue 2 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.190947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.157395 restraints weight = 8906.771| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.62 r_work: 0.3931 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.6425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8790 Z= 0.140 Angle : 0.648 10.783 11889 Z= 0.327 Chirality : 0.042 0.228 1335 Planarity : 0.005 0.063 1508 Dihedral : 7.005 55.212 1231 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.08 % Favored : 90.82 % Rotamer: Outliers : 3.29 % Allowed : 23.05 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.27 (0.26), residues: 1035 helix: 0.44 (0.20), residues: 675 sheet: -4.10 (0.57), residues: 42 loop : -3.20 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 743 TYR 0.015 0.001 TYR A 42 PHE 0.023 0.002 PHE A 107 TRP 0.013 0.001 TRP B 686 HIS 0.003 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8786) covalent geometry : angle 0.64769 (11889) hydrogen bonds : bond 0.03845 ( 405) hydrogen bonds : angle 3.85154 ( 1191) Misc. bond : bond 0.00086 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.260 Fit side-chains REVERT: A 43 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6201 (m-80) REVERT: A 151 ASP cc_start: 0.7445 (t0) cc_final: 0.6975 (t70) REVERT: B 81 SER cc_start: 0.7896 (t) cc_final: 0.7582 (p) REVERT: B 157 ILE cc_start: 0.7528 (mt) cc_final: 0.7172 (mt) REVERT: B 289 HIS cc_start: 0.4333 (OUTLIER) cc_final: 0.3796 (t-90) REVERT: B 641 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7620 (mpp-170) REVERT: B 653 ARG cc_start: 0.6370 (mmp80) cc_final: 0.5830 (mmm-85) REVERT: B 747 LYS cc_start: 0.6507 (pttt) cc_final: 0.5759 (ttmt) REVERT: B 795 MET cc_start: 0.5787 (mmp) cc_final: 0.5397 (ppp) outliers start: 30 outliers final: 25 residues processed: 139 average time/residue: 0.0819 time to fit residues: 16.1013 Evaluate side-chains 136 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain C residue 2 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 0.0370 chunk 99 optimal weight: 0.0980 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.195762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.160630 restraints weight = 8882.241| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.06 r_work: 0.3911 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.6539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8790 Z= 0.122 Angle : 0.626 10.281 11889 Z= 0.316 Chirality : 0.041 0.232 1335 Planarity : 0.005 0.062 1508 Dihedral : 6.473 53.438 1231 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.89 % Favored : 91.01 % Rotamer: Outliers : 3.18 % Allowed : 23.16 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.98 (0.27), residues: 1035 helix: 0.68 (0.20), residues: 676 sheet: -4.26 (0.63), residues: 35 loop : -3.17 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 5 TYR 0.014 0.001 TYR B 123 PHE 0.022 0.001 PHE A 107 TRP 0.014 0.001 TRP B 489 HIS 0.002 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8786) covalent geometry : angle 0.62595 (11889) hydrogen bonds : bond 0.03409 ( 405) hydrogen bonds : angle 3.69496 ( 1191) Misc. bond : bond 0.00080 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.316 Fit side-chains REVERT: A 43 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6205 (m-80) REVERT: B 81 SER cc_start: 0.7961 (t) cc_final: 0.7620 (p) REVERT: B 157 ILE cc_start: 0.7506 (mt) cc_final: 0.7139 (mt) REVERT: B 238 MET cc_start: 0.7659 (mmm) cc_final: 0.7402 (mmt) REVERT: B 289 HIS cc_start: 0.4218 (OUTLIER) cc_final: 0.3792 (t-90) REVERT: B 641 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7567 (mpp-170) REVERT: B 653 ARG cc_start: 0.6263 (mmp80) cc_final: 0.5736 (mmm-85) REVERT: B 747 LYS cc_start: 0.6503 (pttt) cc_final: 0.5785 (ttmt) REVERT: B 795 MET cc_start: 0.5885 (mmp) cc_final: 0.5358 (ppp) outliers start: 29 outliers final: 20 residues processed: 138 average time/residue: 0.0930 time to fit residues: 18.0188 Evaluate side-chains 133 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 905 VAL Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain C residue 2 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 0.0070 chunk 60 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.194194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.159040 restraints weight = 8846.085| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.03 r_work: 0.3925 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8790 Z= 0.129 Angle : 0.632 10.032 11889 Z= 0.318 Chirality : 0.042 0.258 1335 Planarity : 0.005 0.061 1508 Dihedral : 6.406 56.686 1231 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.60 % Favored : 91.30 % Rotamer: Outliers : 3.18 % Allowed : 24.04 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.89 (0.27), residues: 1035 helix: 0.76 (0.20), residues: 676 sheet: -4.18 (0.61), residues: 37 loop : -3.13 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 743 TYR 0.014 0.001 TYR A 42 PHE 0.021 0.002 PHE A 107 TRP 0.012 0.001 TRP B 686 HIS 0.002 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8786) covalent geometry : angle 0.63201 (11889) hydrogen bonds : bond 0.03608 ( 405) hydrogen bonds : angle 3.69832 ( 1191) Misc. bond : bond 0.00073 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3117.46 seconds wall clock time: 53 minutes 43.25 seconds (3223.25 seconds total)