Starting phenix.real_space_refine on Fri Sep 11 06:59:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vp9_21307/09_2026/6vp9_21307_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vp9_21307/09_2026/6vp9_21307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vp9_21307/09_2026/6vp9_21307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vp9_21307/09_2026/6vp9_21307.map" model { file = "/net/cci-nas-00/data/ceres_data/6vp9_21307/09_2026/6vp9_21307_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vp9_21307/09_2026/6vp9_21307_neut.cif" } resolution = 3.46 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 ------------------------------------------------------------------------------- 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= 0.005 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 5507 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 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8610 Number of models: 1 Model: "" Number of chains: 4 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: 7245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7245 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 32, 'TRANS': 881} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 6, 'TYR:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 6, 'GLN:plan1': 3, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 113 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CMC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CMC:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.88, per 1000 atoms: 0.22 Number of scatterers: 8610 At special positions: 0 Unit cell: (107.07, 99.6, 100.43, 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 5507 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 304.0 milliseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 2 sheets defined 65.7% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 27 through 38 removed outlier: 4.137A pdb=" N PHE A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.513A pdb=" N LYS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.661A pdb=" N VAL A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 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 30 through 35 Processing helix chain 'B' and resid 47 through 55 removed outlier: 4.071A pdb=" N LEU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 72 removed outlier: 4.329A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.537A pdb=" N ILE B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 removed outlier: 3.883A pdb=" N THR B 99 " --> pdb=" O PRO B 95 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 Processing helix chain 'B' and resid 128 through 143 removed outlier: 3.575A pdb=" N GLN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLN B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 162 removed outlier: 3.949A pdb=" N TYR B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.537A pdb=" N LYS B 170 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 4.139A pdb=" N MET B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 207 removed outlier: 3.690A pdb=" N GLY B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 removed outlier: 4.069A pdb=" N ASP B 214 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.731A pdb=" N THR B 225 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.974A pdb=" N ALA B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 260 removed outlier: 3.966A pdb=" N LEU B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 280 removed outlier: 3.733A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 315 removed outlier: 3.945A pdb=" N PHE B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 336 removed outlier: 3.713A pdb=" N LEU B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) removed outlier: 3.605A 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 Processing helix chain 'B' and resid 379 through 382 removed outlier: 4.370A pdb=" N THR B 382 " --> pdb=" O THR B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.745A pdb=" N HIS B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 449 removed outlier: 4.294A pdb=" N VAL B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.646A pdb=" N LEU B 470 " --> pdb=" O TYR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.705A pdb=" N VAL B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 502 Processing helix chain 'B' and resid 505 through 520 removed outlier: 3.693A 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 537 through 542 removed outlier: 3.717A pdb=" N THR B 541 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 removed outlier: 4.071A pdb=" N TYR B 549 " --> pdb=" O LEU B 545 " (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 625 removed outlier: 3.582A pdb=" N ALA B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.569A pdb=" N SER B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 698 removed outlier: 3.878A 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 747 removed outlier: 3.829A pdb=" N GLN B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 739 " --> pdb=" O GLU B 735 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 747 " --> pdb=" O ARG B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 767 removed outlier: 3.971A pdb=" N ASN B 766 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 790 removed outlier: 4.239A pdb=" N SER B 776 " --> pdb=" O CYS B 772 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 781 " --> pdb=" O PHE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 820 removed outlier: 3.764A pdb=" N GLU B 799 " --> pdb=" O MET B 795 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 810 " --> pdb=" O LYS B 806 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 830 Processing helix chain 'B' and resid 835 through 869 removed outlier: 3.707A pdb=" N LEU B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) Proline residue: B 864 - end of helix Processing helix chain 'B' and resid 883 through 904 removed outlier: 3.847A pdb=" N SER B 889 " --> pdb=" O PRO B 885 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 896 " --> pdb=" O ASP B 892 " (cutoff:3.500A) removed outlier: 3.527A 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 965 removed outlier: 3.745A pdb=" N SER B 938 " --> pdb=" O GLU B 934 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 969 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 7.087A pdb=" N ILE A 44 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR A 56 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 46 " --> pdb=" O MET A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 113 427 hydrogen bonds defined for protein. 1254 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: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2775 1.34 - 1.46: 1589 1.46 - 1.58: 4344 1.58 - 1.70: 5 1.70 - 1.82: 73 Bond restraints: 8786 Sorted by residual: bond pdb=" O3B CMC A 201 " pdb=" P3B CMC A 201 " ideal model delta sigma weight residual 1.728 1.614 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" O3A CMC A 201 " pdb=" P2A CMC A 201 " ideal model delta sigma weight residual 1.658 1.603 0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" O5B CMC A 201 " pdb=" P1A CMC A 201 " ideal model delta sigma weight residual 1.652 1.604 0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" CCP CMC A 201 " pdb=" O6A CMC A 201 " ideal model delta sigma weight residual 1.413 1.454 -0.041 2.00e-02 2.50e+03 4.29e+00 bond pdb=" C5B CMC A 201 " pdb=" O5B CMC A 201 " ideal model delta sigma weight residual 1.412 1.450 -0.038 2.00e-02 2.50e+03 3.64e+00 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 11409 1.46 - 2.92: 393 2.92 - 4.37: 66 4.37 - 5.83: 17 5.83 - 7.29: 4 Bond angle restraints: 11889 Sorted by residual: angle pdb=" N PRO B 17 " pdb=" CA PRO B 17 " pdb=" CB PRO B 17 " ideal model delta sigma weight residual 103.25 110.05 -6.80 1.05e+00 9.07e-01 4.19e+01 angle pdb=" N LYS B 458 " pdb=" CA LYS B 458 " pdb=" CB LYS B 458 " ideal model delta sigma weight residual 114.17 110.15 4.02 1.14e+00 7.69e-01 1.24e+01 angle pdb=" N SER A 115 " pdb=" CA SER A 115 " pdb=" C SER A 115 " ideal model delta sigma weight residual 113.18 108.98 4.20 1.33e+00 5.65e-01 9.99e+00 angle pdb=" N HIS B 536 " pdb=" CA HIS B 536 " pdb=" C HIS B 536 " ideal model delta sigma weight residual 110.80 116.62 -5.82 2.13e+00 2.20e-01 7.46e+00 angle pdb=" C ARG A 14 " pdb=" N PHE A 15 " pdb=" CA PHE A 15 " ideal model delta sigma weight residual 122.61 117.62 4.99 1.94e+00 2.66e-01 6.62e+00 ... (remaining 11884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.87: 5067 27.87 - 55.74: 243 55.74 - 83.61: 23 83.61 - 111.48: 5 111.48 - 139.35: 1 Dihedral angle restraints: 5339 sinusoidal: 2168 harmonic: 3171 Sorted by residual: dihedral pdb=" CA LYS B 535 " pdb=" C LYS B 535 " pdb=" N HIS B 536 " pdb=" CA HIS B 536 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CDP CMC A 201 " pdb=" CBP CMC A 201 " pdb=" CCP CMC A 201 " pdb=" O6A CMC A 201 " ideal model delta sinusoidal sigma weight residual 191.32 51.97 139.35 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" CA LEU B 652 " pdb=" C LEU B 652 " pdb=" N ARG B 653 " pdb=" CA ARG B 653 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 941 0.043 - 0.087: 330 0.087 - 0.130: 59 0.130 - 0.173: 3 0.173 - 0.217: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA PRO B 17 " pdb=" N PRO B 17 " pdb=" C PRO B 17 " pdb=" CB PRO B 17 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR B 225 " pdb=" CA THR B 225 " pdb=" OG1 THR B 225 " pdb=" CG2 THR B 225 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA PRO B 756 " pdb=" N PRO B 756 " pdb=" C PRO B 756 " pdb=" CB PRO B 756 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1331 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CMC A 201 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C9P CMC A 201 " -0.089 2.00e-02 2.50e+03 pdb=" CAP CMC A 201 " 0.113 2.00e-02 2.50e+03 pdb=" N8P CMC A 201 " -0.535 2.00e-02 2.50e+03 pdb=" O9P CMC A 201 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P CMC A 201 " -0.338 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C5P CMC A 201 " 0.087 2.00e-02 2.50e+03 pdb=" C6P CMC A 201 " -0.163 2.00e-02 2.50e+03 pdb=" N4P CMC A 201 " 0.509 2.00e-02 2.50e+03 pdb=" O5P CMC A 201 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 755 " 0.039 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO B 756 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 756 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 756 " 0.033 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 73 2.61 - 3.18: 7748 3.18 - 3.75: 12556 3.75 - 4.33: 18572 4.33 - 4.90: 30416 Nonbonded interactions: 69365 Sorted by model distance: nonbonded pdb=" OD1 ASN A 16 " pdb=" NE2 GLN B 538 " model vdw 2.032 3.120 nonbonded pdb=" O ASN B 167 " pdb=" OG1 THR B 171 " model vdw 2.139 3.040 nonbonded pdb=" OE1 GLU B 735 " pdb=" OH TYR B 778 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR B 149 " pdb=" O MET B 180 " model vdw 2.219 3.040 nonbonded pdb=" O ASN B 27 " pdb=" N ILE B 31 " model vdw 2.220 3.120 ... (remaining 69360 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: 0.750 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.290 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 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 : 0.007 0.377 8787 Z= 0.475 Angle : 0.648 7.288 11889 Z= 0.367 Chirality : 0.043 0.217 1334 Planarity : 0.012 0.302 1508 Dihedral : 15.773 139.346 3283 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Cbeta Deviations : 0.00 % 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: -3.63 (0.22), residues: 1061 helix: -1.76 (0.17), residues: 668 sheet: -3.84 (0.67), residues: 40 loop : -3.28 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 445 TYR 0.015 0.001 TYR A 42 PHE 0.033 0.002 PHE A 43 TRP 0.012 0.001 TRP B 686 HIS 0.010 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 ( 8786) covalent geometry : angle 0.64810 / 0.37 (11889) hydrogen bonds : bond 0.14339 / 9.40 ( 427) hydrogen bonds : angle 5.60223 / 3.76 ( 1254) Misc. bond : bond 0.37727 / 19.86 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.358 Fit side-chains REVERT: B 115 TYR cc_start: 0.8039 (m-80) cc_final: 0.7780 (m-10) REVERT: B 195 GLU cc_start: 0.7720 (mp0) cc_final: 0.7298 (mp0) REVERT: B 219 LYS cc_start: 0.8566 (tmtt) cc_final: 0.8311 (tptm) REVERT: B 297 TYR cc_start: 0.7233 (m-80) cc_final: 0.6206 (m-80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1091 time to fit residues: 18.6735 Evaluate side-chains 103 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN B 116 HIS B 159 GLN B 249 ASN B 387 GLN B 413 GLN B 447 GLN B 462 GLN B 490 GLN B 605 ASN B 608 HIS B 659 ASN B 750 GLN B 766 ASN B 868 ASN B 891 GLN B 898 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.163280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135697 restraints weight = 10164.125| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.32 r_work: 0.3313 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8787 Z= 0.140 Angle : 0.571 7.636 11889 Z= 0.294 Chirality : 0.040 0.166 1334 Planarity : 0.004 0.055 1508 Dihedral : 8.566 139.652 1230 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.99 % Allowed : 12.40 % Favored : 86.61 % Cbeta Deviations : 0.00 % 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: -2.46 (0.25), residues: 1061 helix: -0.80 (0.19), residues: 683 sheet: -3.83 (0.74), residues: 39 loop : -2.93 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.021 0.002 TYR B 239 PHE 0.026 0.002 PHE A 15 TRP 0.007 0.001 TRP B 686 HIS 0.006 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8786) covalent geometry : angle 0.57089 / 0.29 (11889) hydrogen bonds : bond 0.03822 / 2.36 ( 427) hydrogen bonds : angle 4.15233 / 2.80 ( 1254) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 146 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: B 115 TYR cc_start: 0.8371 (m-80) cc_final: 0.8093 (m-10) REVERT: B 219 LYS cc_start: 0.8689 (tmtt) cc_final: 0.8376 (tptm) REVERT: B 297 TYR cc_start: 0.7882 (m-80) cc_final: 0.7125 (m-10) REVERT: B 883 MET cc_start: 0.7355 (tmm) cc_final: 0.7127 (tmm) outliers start: 9 outliers final: 8 residues processed: 126 average time/residue: 0.0979 time to fit residues: 17.2833 Evaluate side-chains 116 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain B residue 891 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 36 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 0.0040 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 733 GLN B 834 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.168383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139160 restraints weight = 10103.521| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.46 r_work: 0.3313 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8787 Z= 0.128 Angle : 0.529 6.631 11889 Z= 0.272 Chirality : 0.039 0.132 1334 Planarity : 0.004 0.044 1508 Dihedral : 8.400 141.223 1230 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.65 % Allowed : 14.49 % Favored : 83.86 % Cbeta Deviations : 0.00 % 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: -1.79 (0.25), residues: 1061 helix: -0.19 (0.20), residues: 675 sheet: -3.69 (0.77), residues: 39 loop : -2.82 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 67 TYR 0.026 0.001 TYR B 239 PHE 0.028 0.001 PHE A 15 TRP 0.007 0.001 TRP B 686 HIS 0.005 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8786) covalent geometry : angle 0.52922 / 0.27 (11889) hydrogen bonds : bond 0.03478 / 2.13 ( 427) hydrogen bonds : angle 3.92448 / 2.65 ( 1254) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.350 Fit side-chains REVERT: B 115 TYR cc_start: 0.8387 (m-80) cc_final: 0.8111 (m-10) REVERT: B 137 MET cc_start: 0.8201 (mmm) cc_final: 0.7966 (mmm) REVERT: B 217 ARG cc_start: 0.8677 (mmm-85) cc_final: 0.8131 (ttt-90) REVERT: B 219 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8368 (tptm) REVERT: B 297 TYR cc_start: 0.7934 (m-80) cc_final: 0.7101 (m-80) outliers start: 15 outliers final: 11 residues processed: 128 average time/residue: 0.1091 time to fit residues: 19.1119 Evaluate side-chains 122 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 781 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 76 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN B 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.140924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.111102 restraints weight = 9929.732| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.51 r_work: 0.2939 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8787 Z= 0.168 Angle : 0.548 6.606 11889 Z= 0.281 Chirality : 0.041 0.194 1334 Planarity : 0.004 0.052 1508 Dihedral : 8.333 144.808 1230 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.41 % Allowed : 15.59 % Favored : 82.00 % Cbeta Deviations : 0.00 % 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: -1.52 (0.26), residues: 1061 helix: -0.00 (0.20), residues: 674 sheet: -3.43 (0.80), residues: 38 loop : -2.66 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 67 TYR 0.019 0.001 TYR B 239 PHE 0.027 0.002 PHE A 15 TRP 0.008 0.001 TRP B 686 HIS 0.006 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 8786) covalent geometry : angle 0.54788 / 0.28 (11889) hydrogen bonds : bond 0.03638 / 2.24 ( 427) hydrogen bonds : angle 3.90533 / 2.65 ( 1254) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.339 Fit side-chains REVERT: A 146 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: B 115 TYR cc_start: 0.8286 (m-80) cc_final: 0.8025 (m-10) REVERT: B 195 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: B 219 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8347 (tptm) REVERT: B 297 TYR cc_start: 0.8076 (m-80) cc_final: 0.7400 (m-80) outliers start: 22 outliers final: 15 residues processed: 125 average time/residue: 0.1011 time to fit residues: 17.6040 Evaluate side-chains 119 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 65 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 899 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 63 optimal weight: 0.0770 chunk 8 optimal weight: 0.0470 chunk 77 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN B 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.144541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.117086 restraints weight = 9795.477| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.39 r_work: 0.3022 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8787 Z= 0.107 Angle : 0.502 6.115 11889 Z= 0.259 Chirality : 0.039 0.192 1334 Planarity : 0.004 0.042 1508 Dihedral : 8.121 141.832 1230 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.09 % Allowed : 16.68 % Favored : 81.23 % Cbeta Deviations : 0.00 % 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: -1.09 (0.26), residues: 1061 helix: 0.36 (0.21), residues: 673 sheet: -3.46 (0.77), residues: 39 loop : -2.53 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 67 TYR 0.017 0.001 TYR B 239 PHE 0.021 0.001 PHE A 15 TRP 0.007 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8786) covalent geometry : angle 0.50174 / 0.26 (11889) hydrogen bonds : bond 0.03187 / 1.95 ( 427) hydrogen bonds : angle 3.72710 / 2.53 ( 1254) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.404 Fit side-chains REVERT: B 109 VAL cc_start: 0.7441 (OUTLIER) cc_final: 0.7027 (m) REVERT: B 115 TYR cc_start: 0.8263 (m-80) cc_final: 0.7982 (m-10) REVERT: B 195 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: B 219 LYS cc_start: 0.8647 (tmtt) cc_final: 0.8302 (tptm) REVERT: B 297 TYR cc_start: 0.8066 (m-80) cc_final: 0.7464 (m-80) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.0980 time to fit residues: 18.1431 Evaluate side-chains 124 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 899 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 0.0010 chunk 102 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 72 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.143863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116214 restraints weight = 9773.927| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.40 r_work: 0.3020 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8787 Z= 0.119 Angle : 0.505 5.795 11889 Z= 0.259 Chirality : 0.039 0.166 1334 Planarity : 0.004 0.043 1508 Dihedral : 8.029 143.366 1230 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.31 % Allowed : 17.34 % Favored : 80.35 % Cbeta Deviations : 0.00 % 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: -0.88 (0.26), residues: 1061 helix: 0.56 (0.21), residues: 671 sheet: -3.28 (0.76), residues: 38 loop : -2.51 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 67 TYR 0.015 0.001 TYR B 239 PHE 0.022 0.001 PHE A 15 TRP 0.007 0.001 TRP B 686 HIS 0.005 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 8786) covalent geometry : angle 0.50545 / 0.26 (11889) hydrogen bonds : bond 0.03198 / 1.97 ( 427) hydrogen bonds : angle 3.66198 / 2.49 ( 1254) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.296 Fit side-chains REVERT: B 109 VAL cc_start: 0.7438 (OUTLIER) cc_final: 0.7055 (m) REVERT: B 115 TYR cc_start: 0.8285 (m-80) cc_final: 0.8001 (m-10) REVERT: B 195 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: B 211 GLU cc_start: 0.7931 (mp0) cc_final: 0.7114 (tp30) REVERT: B 219 LYS cc_start: 0.8659 (tmtt) cc_final: 0.8298 (tptm) REVERT: B 297 TYR cc_start: 0.8014 (m-80) cc_final: 0.7386 (m-80) outliers start: 21 outliers final: 13 residues processed: 126 average time/residue: 0.0980 time to fit residues: 17.5042 Evaluate side-chains 125 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 899 THR 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 76 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 GLN ** 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 = 0.3548 r_free = 0.3548 target = 0.142850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112337 restraints weight = 9931.762| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.44 r_work: 0.2993 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8787 Z= 0.147 Angle : 0.530 7.057 11889 Z= 0.270 Chirality : 0.040 0.160 1334 Planarity : 0.004 0.041 1508 Dihedral : 8.005 145.921 1230 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.85 % Allowed : 17.01 % Favored : 80.13 % Cbeta Deviations : 0.00 % 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: -0.83 (0.26), residues: 1061 helix: 0.59 (0.21), residues: 671 sheet: -3.37 (0.75), residues: 39 loop : -2.46 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 67 TYR 0.014 0.001 TYR B 239 PHE 0.025 0.002 PHE A 15 TRP 0.008 0.001 TRP B 686 HIS 0.005 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8786) covalent geometry : angle 0.53027 / 0.27 (11889) hydrogen bonds : bond 0.03421 / 2.10 ( 427) hydrogen bonds : angle 3.71779 / 2.52 ( 1254) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.325 Fit side-chains REVERT: B 109 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7058 (m) REVERT: B 115 TYR cc_start: 0.8263 (m-80) cc_final: 0.8018 (m-80) REVERT: B 211 GLU cc_start: 0.7930 (mp0) cc_final: 0.7149 (tp30) REVERT: B 219 LYS cc_start: 0.8683 (tmtt) cc_final: 0.8311 (tptm) REVERT: B 297 TYR cc_start: 0.8002 (m-80) cc_final: 0.7529 (m-80) REVERT: B 652 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8201 (mp) outliers start: 26 outliers final: 18 residues processed: 129 average time/residue: 0.0969 time to fit residues: 17.6094 Evaluate side-chains 126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 65 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 899 THR 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 23 optimal weight: 10.0000 chunk 53 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 GLN ** 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 = 0.3553 r_free = 0.3553 target = 0.143524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114698 restraints weight = 9764.401| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.42 r_work: 0.3023 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8787 Z= 0.126 Angle : 0.541 13.991 11889 Z= 0.269 Chirality : 0.040 0.218 1334 Planarity : 0.004 0.041 1508 Dihedral : 7.947 146.117 1230 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.52 % Allowed : 18.33 % Favored : 79.14 % Cbeta Deviations : 0.00 % 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: -0.68 (0.26), residues: 1061 helix: 0.71 (0.21), residues: 674 sheet: -3.20 (0.76), residues: 38 loop : -2.46 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 67 TYR 0.012 0.001 TYR B 239 PHE 0.020 0.001 PHE A 15 TRP 0.008 0.001 TRP B 686 HIS 0.005 0.001 HIS B 907 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8786) covalent geometry : angle 0.54084 / 0.27 (11889) hydrogen bonds : bond 0.03292 / 2.03 ( 427) hydrogen bonds : angle 3.66912 / 2.49 ( 1254) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.351 Fit side-chains REVERT: B 109 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7084 (m) REVERT: B 115 TYR cc_start: 0.8306 (m-80) cc_final: 0.7888 (m-10) REVERT: B 211 GLU cc_start: 0.7944 (mp0) cc_final: 0.7104 (tp30) REVERT: B 219 LYS cc_start: 0.8656 (tmtt) cc_final: 0.8375 (tptm) REVERT: B 297 TYR cc_start: 0.7920 (m-80) cc_final: 0.7433 (m-80) REVERT: B 652 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8129 (mp) outliers start: 23 outliers final: 15 residues processed: 124 average time/residue: 0.0946 time to fit residues: 16.5350 Evaluate side-chains 123 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 899 THR 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 98 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN ** B 573 ASN ** 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 = 0.3575 r_free = 0.3575 target = 0.145549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118371 restraints weight = 9745.366| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.38 r_work: 0.3046 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8787 Z= 0.110 Angle : 0.524 10.569 11889 Z= 0.263 Chirality : 0.039 0.200 1334 Planarity : 0.004 0.039 1508 Dihedral : 7.861 144.435 1230 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.31 % Allowed : 18.88 % Favored : 78.81 % Cbeta Deviations : 0.00 % 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: -0.53 (0.26), residues: 1061 helix: 0.84 (0.21), residues: 673 sheet: -3.34 (0.74), residues: 39 loop : -2.40 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 67 TYR 0.012 0.001 TYR B 239 PHE 0.019 0.001 PHE A 15 TRP 0.008 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 8786) covalent geometry : angle 0.52427 / 0.26 (11889) hydrogen bonds : bond 0.03188 / 1.96 ( 427) hydrogen bonds : angle 3.63567 / 2.46 ( 1254) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: B 109 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7075 (m) REVERT: B 115 TYR cc_start: 0.8288 (m-80) cc_final: 0.7839 (m-10) REVERT: B 211 GLU cc_start: 0.7930 (mp0) cc_final: 0.7197 (tp30) REVERT: B 219 LYS cc_start: 0.8641 (tmtt) cc_final: 0.8364 (tptm) REVERT: B 297 TYR cc_start: 0.7922 (m-80) cc_final: 0.7445 (m-80) REVERT: B 652 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8085 (mp) REVERT: B 785 GLU cc_start: 0.8206 (tt0) cc_final: 0.7994 (tt0) REVERT: B 827 LYS cc_start: 0.7672 (ptmt) cc_final: 0.7409 (ptmm) outliers start: 21 outliers final: 17 residues processed: 124 average time/residue: 0.0921 time to fit residues: 16.0915 Evaluate side-chains 126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 65 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 970 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 80 optimal weight: 0.0170 chunk 103 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 891 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.147151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.121616 restraints weight = 9691.229| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.11 r_work: 0.3105 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8787 Z= 0.112 Angle : 0.539 10.996 11889 Z= 0.268 Chirality : 0.040 0.197 1334 Planarity : 0.004 0.039 1508 Dihedral : 7.809 145.238 1230 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.20 % Allowed : 19.21 % Favored : 78.59 % Cbeta Deviations : 0.00 % 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: -0.46 (0.27), residues: 1061 helix: 0.89 (0.21), residues: 675 sheet: -3.09 (0.85), residues: 34 loop : -2.41 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 67 TYR 0.011 0.001 TYR B 239 PHE 0.018 0.001 PHE A 15 TRP 0.008 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 8786) covalent geometry : angle 0.53933 / 0.27 (11889) hydrogen bonds : bond 0.03178 / 1.97 ( 427) hydrogen bonds : angle 3.64493 / 2.47 ( 1254) Misc. bond : bond 0.00024 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.274 Fit side-chains REVERT: B 109 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.6995 (m) REVERT: B 115 TYR cc_start: 0.8238 (m-80) cc_final: 0.7822 (m-10) REVERT: B 211 GLU cc_start: 0.7867 (mp0) cc_final: 0.7283 (tp30) REVERT: B 219 LYS cc_start: 0.8636 (tmtt) cc_final: 0.8377 (tptm) REVERT: B 297 TYR cc_start: 0.7913 (m-80) cc_final: 0.7413 (m-80) REVERT: B 579 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7676 (tt0) REVERT: B 652 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8060 (mp) REVERT: B 827 LYS cc_start: 0.7629 (ptmt) cc_final: 0.7395 (ptmm) outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 0.0987 time to fit residues: 16.9550 Evaluate side-chains 126 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 65 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 75 optimal weight: 0.0870 chunk 18 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 798 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.163816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138506 restraints weight = 9579.846| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.23 r_work: 0.3107 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8787 Z= 0.107 Angle : 0.534 10.211 11889 Z= 0.269 Chirality : 0.039 0.192 1334 Planarity : 0.004 0.039 1508 Dihedral : 7.727 144.955 1230 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.87 % Allowed : 19.98 % Favored : 78.16 % Cbeta Deviations : 0.00 % 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: -0.35 (0.27), residues: 1061 helix: 0.94 (0.21), residues: 681 sheet: -2.99 (0.83), residues: 33 loop : -2.34 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 67 TYR 0.011 0.001 TYR B 140 PHE 0.018 0.001 PHE A 15 TRP 0.008 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 8786) covalent geometry : angle 0.53386 / 0.27 (11889) hydrogen bonds : bond 0.03114 / 1.93 ( 427) hydrogen bonds : angle 3.63519 / 2.47 ( 1254) Misc. bond : bond 0.00014 / 0.01 ( 1) =============================================================================== Job complete usr+sys time: 2205.16 seconds wall clock time: 38 minutes 27.98 seconds (2307.98 seconds total)