Starting phenix.real_space_refine on Sat Jul 26 20:26:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stx_25438/07_2025/7stx_25438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stx_25438/07_2025/7stx_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_25438/07_2025/7stx_25438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stx_25438/07_2025/7stx_25438.map" model { file = "/net/cci-nas-00/data/ceres_data/7stx_25438/07_2025/7stx_25438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stx_25438/07_2025/7stx_25438.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TYR:plan': 1, 'UNK:plan-1': 28, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} 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: 5.54, per 1000 atoms: 0.64 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.85 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: 2.37 Time building geometry restraints manager: 2.97 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: 1.510 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.470 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.590 ------------------------------------------------------------------------------- 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 : 8.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP B 686 HIS 0.013 0.002 HIS B 473 PHE 0.079 0.004 PHE A 43 TYR 0.027 0.003 TYR A 42 ARG 0.006 0.001 ARG B 616 Details of bonding type rmsd hydrogen bonds : bond 0.18272 ( 405) hydrogen bonds : angle 7.32970 ( 1191) covalent geometry : bond 0.01185 ( 8786) covalent geometry : angle 1.47991 (11889) 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 : 1.092 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: 0.3630 time to fit residues: 106.8859 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 : 1.163 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.0470 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.4531 r_free = 0.4531 target = 0.203274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.170586 restraints weight = 8868.852| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 1.76 r_work: 0.4091 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8790 Z= 0.143 Angle : 0.658 9.298 11889 Z= 0.343 Chirality : 0.041 0.175 1335 Planarity : 0.006 0.072 1508 Dihedral : 9.541 59.871 1240 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.92 % Favored : 91.88 % Rotamer: Outliers : 2.63 % Allowed : 15.81 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.23), residues: 1035 helix: -1.59 (0.18), residues: 660 sheet: -4.29 (0.77), residues: 32 loop : -3.29 (0.28), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 686 HIS 0.003 0.001 HIS B 414 PHE 0.027 0.002 PHE A 107 TYR 0.017 0.001 TYR B 297 ARG 0.004 0.001 ARG B 613 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 405) hydrogen bonds : angle 4.37339 ( 1191) covalent geometry : bond 0.00319 ( 8786) covalent geometry : angle 0.65816 (11889) Misc. bond : bond 0.00109 ( 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 171 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8070 (tt0) REVERT: B 172 MET cc_start: 0.7006 (mmt) cc_final: 0.6754 (mmt) REVERT: B 236 MET cc_start: 0.7724 (mmm) cc_final: 0.7516 (tpt) REVERT: B 279 GLU cc_start: 0.5213 (OUTLIER) cc_final: 0.4717 (pt0) REVERT: B 315 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7484 (pttt) REVERT: B 653 ARG cc_start: 0.6185 (mmp80) cc_final: 0.5672 (mmm-85) REVERT: B 795 MET cc_start: 0.5900 (mmp) cc_final: 0.5187 (ppp) REVERT: B 799 GLU cc_start: 0.6792 (pp20) cc_final: 0.6316 (pt0) REVERT: B 883 MET cc_start: 0.7028 (tpp) cc_final: 0.6791 (tpp) REVERT: B 961 LYS cc_start: 0.6593 (mttt) cc_final: 0.6356 (mptt) outliers start: 24 outliers final: 14 residues processed: 167 average time/residue: 0.2513 time to fit residues: 55.5496 Evaluate side-chains 122 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 740 THR Chi-restraints excluded: chain B residue 817 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 13 optimal weight: 2.9990 chunk 78 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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 = 0.4424 r_free = 0.4424 target = 0.191671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.157346 restraints weight = 8982.685| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.69 r_work: 0.3861 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8790 Z= 0.205 Angle : 0.749 11.812 11889 Z= 0.382 Chirality : 0.045 0.212 1335 Planarity : 0.006 0.067 1508 Dihedral : 8.983 56.636 1233 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.70 % Favored : 91.21 % Rotamer: Outliers : 3.18 % Allowed : 19.43 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.24), residues: 1035 helix: -1.05 (0.19), residues: 663 sheet: -3.92 (0.71), residues: 42 loop : -3.17 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 281 HIS 0.033 0.002 HIS B 914 PHE 0.026 0.003 PHE A 107 TYR 0.038 0.002 TYR A 42 ARG 0.006 0.001 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.05214 ( 405) hydrogen bonds : angle 4.35758 ( 1191) covalent geometry : bond 0.00476 ( 8786) covalent geometry : angle 0.74886 (11889) Misc. bond : bond 0.00100 ( 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 171 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8127 (tt0) REVERT: B 172 MET cc_start: 0.7415 (mmt) cc_final: 0.7209 (mmt) REVERT: B 184 MET cc_start: 0.7027 (mtt) cc_final: 0.6792 (mtt) REVERT: B 748 ASP cc_start: 0.7140 (t0) cc_final: 0.6463 (p0) REVERT: B 795 MET cc_start: 0.6058 (mmp) cc_final: 0.5449 (ppp) REVERT: B 914 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.5954 (t-90) outliers start: 29 outliers final: 22 residues processed: 166 average time/residue: 0.2084 time to fit residues: 47.7681 Evaluate side-chains 144 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 729 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 0.0010 chunk 37 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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 538 GLN B 771 GLN B 898 GLN B 914 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.194044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.161141 restraints weight = 8894.521| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.75 r_work: 0.3894 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8790 Z= 0.132 Angle : 0.633 9.923 11889 Z= 0.325 Chirality : 0.041 0.249 1335 Planarity : 0.005 0.065 1508 Dihedral : 7.907 59.156 1231 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.31 % Favored : 91.59 % Rotamer: Outliers : 2.85 % Allowed : 21.41 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.26), residues: 1035 helix: -0.41 (0.20), residues: 668 sheet: -3.99 (0.78), residues: 37 loop : -2.94 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 686 HIS 0.006 0.001 HIS B 914 PHE 0.025 0.002 PHE A 107 TYR 0.026 0.002 TYR B 239 ARG 0.006 0.000 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 405) hydrogen bonds : angle 3.90491 ( 1191) covalent geometry : bond 0.00298 ( 8786) covalent geometry : angle 0.63321 (11889) Misc. bond : bond 0.00052 ( 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 153 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8243 (tt0) REVERT: B 81 SER cc_start: 0.7874 (t) cc_final: 0.7568 (p) REVERT: B 142 ILE cc_start: 0.8161 (mp) cc_final: 0.7945 (mt) REVERT: B 211 GLU cc_start: 0.7747 (tp30) cc_final: 0.7546 (tp30) REVERT: B 653 ARG cc_start: 0.6354 (mmp80) cc_final: 0.5812 (mmm-85) REVERT: B 795 MET cc_start: 0.6242 (mmp) cc_final: 0.5594 (ptm) REVERT: B 799 GLU cc_start: 0.7010 (pp20) cc_final: 0.6243 (pt0) outliers start: 26 outliers final: 15 residues processed: 142 average time/residue: 0.2072 time to fit residues: 41.9433 Evaluate side-chains 135 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 729 LEU Chi-restraints excluded: chain B residue 817 SER 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 1 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 66 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 914 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.193683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.161240 restraints weight = 8846.448| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 1.63 r_work: 0.3884 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8790 Z= 0.125 Angle : 0.608 8.977 11889 Z= 0.310 Chirality : 0.041 0.191 1335 Planarity : 0.005 0.064 1508 Dihedral : 7.292 59.707 1231 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.60 % Favored : 91.21 % Rotamer: Outliers : 3.40 % Allowed : 22.06 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.26), residues: 1035 helix: 0.03 (0.20), residues: 660 sheet: -4.36 (0.69), residues: 37 loop : -2.96 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 686 HIS 0.010 0.001 HIS B 914 PHE 0.024 0.002 PHE A 107 TYR 0.015 0.001 TYR A 42 ARG 0.005 0.000 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 405) hydrogen bonds : angle 3.76486 ( 1191) covalent geometry : bond 0.00283 ( 8786) covalent geometry : angle 0.60753 (11889) Misc. bond : bond 0.00045 ( 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 159 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: B 142 ILE cc_start: 0.8235 (mp) cc_final: 0.8033 (mt) REVERT: B 653 ARG cc_start: 0.6343 (mmp80) cc_final: 0.5793 (mmm-85) REVERT: B 795 MET cc_start: 0.6185 (mmp) cc_final: 0.5582 (ptm) REVERT: B 802 GLU cc_start: 0.7310 (tt0) cc_final: 0.6863 (tt0) outliers start: 31 outliers final: 20 residues processed: 153 average time/residue: 0.2228 time to fit residues: 47.3480 Evaluate side-chains 138 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 36 LEU 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 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 817 SER 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 66 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 914 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.174791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138628 restraints weight = 9131.221| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.85 r_work: 0.3672 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8790 Z= 0.255 Angle : 0.780 11.270 11889 Z= 0.396 Chirality : 0.048 0.229 1335 Planarity : 0.006 0.067 1508 Dihedral : 7.891 53.169 1231 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.86 % Favored : 90.05 % Rotamer: Outliers : 3.95 % Allowed : 21.73 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.25), residues: 1035 helix: -0.43 (0.19), residues: 684 sheet: -4.07 (0.59), residues: 44 loop : -3.18 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 281 HIS 0.016 0.002 HIS B 914 PHE 0.026 0.003 PHE A 107 TYR 0.040 0.002 TYR A 42 ARG 0.005 0.001 ARG B 690 Details of bonding type rmsd hydrogen bonds : bond 0.05496 ( 405) hydrogen bonds : angle 4.36475 ( 1191) covalent geometry : bond 0.00613 ( 8786) covalent geometry : angle 0.78017 (11889) Misc. bond : bond 0.00125 ( 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 157 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: B 157 ILE cc_start: 0.7712 (mt) cc_final: 0.7353 (mt) REVERT: B 236 MET cc_start: 0.7545 (tpt) cc_final: 0.7342 (tpt) REVERT: B 289 HIS cc_start: 0.4703 (OUTLIER) cc_final: 0.4372 (t-90) REVERT: B 297 TYR cc_start: 0.5558 (OUTLIER) cc_final: 0.3903 (m-80) REVERT: B 729 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6791 (tt) REVERT: B 795 MET cc_start: 0.6321 (mmp) cc_final: 0.5528 (ptm) REVERT: B 802 GLU cc_start: 0.7234 (tt0) cc_final: 0.6754 (tt0) REVERT: B 883 MET cc_start: 0.6890 (tpp) cc_final: 0.6600 (tpp) outliers start: 36 outliers final: 26 residues processed: 149 average time/residue: 0.2227 time to fit residues: 45.3368 Evaluate side-chains 141 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 156 LEU 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 297 TYR 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 882 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 899 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 81 optimal weight: 0.4980 chunk 20 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 47 optimal weight: 0.0040 chunk 89 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 380 GLN B 914 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.191858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.158530 restraints weight = 8993.755| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.70 r_work: 0.3967 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8790 Z= 0.125 Angle : 0.622 9.167 11889 Z= 0.319 Chirality : 0.041 0.234 1335 Planarity : 0.005 0.065 1508 Dihedral : 7.129 58.076 1231 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.41 % Favored : 91.50 % Rotamer: Outliers : 2.96 % Allowed : 23.16 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.26), residues: 1035 helix: 0.22 (0.20), residues: 670 sheet: -4.48 (0.64), residues: 35 loop : -3.11 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 489 HIS 0.002 0.001 HIS B 448 PHE 0.025 0.001 PHE A 107 TYR 0.012 0.001 TYR A 128 ARG 0.005 0.000 ARG A 5 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 405) hydrogen bonds : angle 3.88230 ( 1191) covalent geometry : bond 0.00280 ( 8786) covalent geometry : angle 0.62214 (11889) Misc. bond : bond 0.00040 ( 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 149 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: B 97 LEU cc_start: 0.8272 (mt) cc_final: 0.8058 (mp) REVERT: B 101 LEU cc_start: 0.8119 (mt) cc_final: 0.7878 (tp) REVERT: B 142 ILE cc_start: 0.8142 (mp) cc_final: 0.7940 (mt) REVERT: B 157 ILE cc_start: 0.7511 (mt) cc_final: 0.7152 (mt) REVERT: B 216 ILE cc_start: 0.7403 (mt) cc_final: 0.7168 (pt) REVERT: B 641 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7623 (mpp-170) REVERT: B 748 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6696 (p0) REVERT: B 795 MET cc_start: 0.5980 (mmp) cc_final: 0.5463 (ptm) REVERT: B 802 GLU cc_start: 0.7360 (tt0) cc_final: 0.6889 (tt0) outliers start: 27 outliers final: 19 residues processed: 144 average time/residue: 0.2171 time to fit residues: 43.4370 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 : 0.958 ------------------------------------------------------------------------------- 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 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 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 640 LEU 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 894 VAL Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 914 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.191090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.157798 restraints weight = 9048.515| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 1.68 r_work: 0.3847 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.6370 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= 0.148 Angle : 0.649 11.642 11889 Z= 0.330 Chirality : 0.043 0.254 1335 Planarity : 0.005 0.064 1508 Dihedral : 6.978 59.626 1231 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.89 % Favored : 91.01 % Rotamer: Outliers : 3.18 % Allowed : 23.27 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.26), residues: 1035 helix: 0.35 (0.20), residues: 675 sheet: -4.14 (0.57), residues: 42 loop : -3.19 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 686 HIS 0.006 0.001 HIS B 914 PHE 0.023 0.002 PHE A 107 TYR 0.036 0.002 TYR B 239 ARG 0.004 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 405) hydrogen bonds : angle 3.88566 ( 1191) covalent geometry : bond 0.00344 ( 8786) covalent geometry : angle 0.64874 (11889) Misc. bond : bond 0.00063 ( 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 145 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: B 81 SER cc_start: 0.7882 (t) cc_final: 0.7575 (p) REVERT: B 101 LEU cc_start: 0.8131 (mt) cc_final: 0.7927 (tp) REVERT: B 142 ILE cc_start: 0.8226 (mp) cc_final: 0.8004 (mt) REVERT: B 157 ILE cc_start: 0.7556 (mt) cc_final: 0.7217 (mt) REVERT: B 216 ILE cc_start: 0.7477 (mt) cc_final: 0.7164 (pt) REVERT: B 641 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7671 (mpp-170) REVERT: B 748 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6712 (p0) REVERT: B 795 MET cc_start: 0.5952 (mmp) cc_final: 0.5409 (ptm) REVERT: B 802 GLU cc_start: 0.7344 (tt0) cc_final: 0.6877 (tt0) outliers start: 29 outliers final: 22 residues processed: 138 average time/residue: 0.2155 time to fit residues: 41.2633 Evaluate side-chains 132 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 315 LYS 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 640 LEU 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 894 VAL Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 95 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.194461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.158143 restraints weight = 8985.294| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.11 r_work: 0.3883 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.6494 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= 0.127 Angle : 0.652 15.362 11889 Z= 0.324 Chirality : 0.042 0.266 1335 Planarity : 0.005 0.064 1508 Dihedral : 7.007 59.564 1231 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.99 % Favored : 90.92 % Rotamer: Outliers : 3.18 % Allowed : 23.05 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1035 helix: 0.51 (0.20), residues: 674 sheet: -4.37 (0.62), residues: 35 loop : -3.06 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 686 HIS 0.008 0.001 HIS B 914 PHE 0.023 0.002 PHE A 107 TYR 0.039 0.001 TYR B 239 ARG 0.004 0.000 ARG B 743 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 405) hydrogen bonds : angle 3.79181 ( 1191) covalent geometry : bond 0.00289 ( 8786) covalent geometry : angle 0.65157 (11889) Misc. bond : bond 0.00107 ( 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 141 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6204 (m-80) REVERT: B 142 ILE cc_start: 0.8149 (mp) cc_final: 0.7939 (mt) REVERT: B 157 ILE cc_start: 0.7545 (mt) cc_final: 0.7222 (mt) REVERT: B 216 ILE cc_start: 0.7325 (mt) cc_final: 0.6991 (pt) REVERT: B 289 HIS cc_start: 0.4005 (OUTLIER) cc_final: 0.3443 (t-90) REVERT: B 407 ASP cc_start: 0.6599 (p0) cc_final: 0.6373 (t0) REVERT: B 641 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7580 (mpp-170) REVERT: B 747 LYS cc_start: 0.6365 (pttm) cc_final: 0.5578 (ttpt) REVERT: B 748 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6566 (p0) REVERT: B 795 MET cc_start: 0.5911 (mmp) cc_final: 0.5384 (ppp) REVERT: B 802 GLU cc_start: 0.7225 (tt0) cc_final: 0.6773 (tt0) outliers start: 29 outliers final: 23 residues processed: 134 average time/residue: 0.2086 time to fit residues: 38.5837 Evaluate side-chains 131 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 47 GLU Chi-restraints excluded: chain A residue 94 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 267 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 315 LYS 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 640 LEU 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 894 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.0060 chunk 63 optimal weight: 0.1980 chunk 43 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.192266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.157467 restraints weight = 8975.561| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.79 r_work: 0.3919 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.6563 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= 0.131 Angle : 0.651 14.890 11889 Z= 0.324 Chirality : 0.042 0.259 1335 Planarity : 0.005 0.062 1508 Dihedral : 6.926 57.212 1231 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.18 % Favored : 90.72 % Rotamer: Outliers : 3.07 % Allowed : 23.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.26), residues: 1035 helix: 0.61 (0.20), residues: 672 sheet: -3.92 (0.60), residues: 42 loop : -3.08 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 686 HIS 0.003 0.001 HIS B 907 PHE 0.022 0.002 PHE A 107 TYR 0.024 0.001 TYR A 32 ARG 0.004 0.000 ARG B 743 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 405) hydrogen bonds : angle 3.75567 ( 1191) covalent geometry : bond 0.00303 ( 8786) covalent geometry : angle 0.65078 (11889) Misc. bond : bond 0.00073 ( 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 142 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: B 81 SER cc_start: 0.7938 (t) cc_final: 0.7611 (p) REVERT: B 142 ILE cc_start: 0.8205 (mp) cc_final: 0.7993 (mt) REVERT: B 157 ILE cc_start: 0.7497 (mt) cc_final: 0.7147 (mt) REVERT: B 289 HIS cc_start: 0.4149 (OUTLIER) cc_final: 0.3594 (t-90) REVERT: B 743 ARG cc_start: 0.7242 (mtm110) cc_final: 0.6972 (ptt90) REVERT: B 747 LYS cc_start: 0.6121 (pttm) cc_final: 0.5536 (ttpt) REVERT: B 748 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6491 (p0) REVERT: B 795 MET cc_start: 0.5791 (mmp) cc_final: 0.5345 (ppp) REVERT: B 802 GLU cc_start: 0.7390 (tt0) cc_final: 0.6903 (tt0) outliers start: 28 outliers final: 24 residues processed: 135 average time/residue: 0.2010 time to fit residues: 38.1573 Evaluate side-chains 135 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 47 GLU Chi-restraints excluded: chain A residue 94 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 267 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 315 LYS 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 640 LEU 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 761 MET Chi-restraints excluded: chain B residue 894 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 16 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 0.0980 chunk 104 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.192245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.156299 restraints weight = 9002.587| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.91 r_work: 0.3893 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8790 Z= 0.139 Angle : 0.667 14.529 11889 Z= 0.331 Chirality : 0.043 0.297 1335 Planarity : 0.005 0.063 1508 Dihedral : 6.815 59.532 1231 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.47 % Favored : 90.43 % Rotamer: Outliers : 3.40 % Allowed : 23.16 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.26), residues: 1035 helix: 0.64 (0.20), residues: 678 sheet: -3.85 (0.61), residues: 42 loop : -3.16 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 686 HIS 0.004 0.001 HIS B 907 PHE 0.022 0.002 PHE A 107 TYR 0.023 0.001 TYR A 32 ARG 0.005 0.000 ARG B 743 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 405) hydrogen bonds : angle 3.76844 ( 1191) covalent geometry : bond 0.00326 ( 8786) covalent geometry : angle 0.66747 (11889) Misc. bond : bond 0.00074 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7442.04 seconds wall clock time: 129 minutes 40.07 seconds (7780.07 seconds total)