Starting phenix.real_space_refine on Thu Jul 2 10:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpb_16148/07_2026/8bpb_16148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpb_16148/07_2026/8bpb_16148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bpb_16148/07_2026/8bpb_16148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpb_16148/07_2026/8bpb_16148.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpb_16148/07_2026/8bpb_16148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpb_16148/07_2026/8bpb_16148_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 3 6.06 5 S 55 5.16 5 C 5329 2.51 5 N 1447 2.21 5 O 1548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8384 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4403 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 113} Chain breaks: 1 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 5 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1, 'ACT': 1} Classifications: {'undetermined': 2} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7743 SG CYS C 289 37.781 59.224 44.747 1.00 57.24 S ATOM 7769 SG CYS C 292 35.184 57.659 42.331 1.00 45.08 S ATOM 7952 SG CYS C 315 38.825 56.578 42.087 1.00 59.56 S ATOM 7627 SG CYS C 274 37.775 47.115 47.263 1.00 38.25 S ATOM 7651 SG CYS C 277 37.170 43.505 48.360 1.00 48.40 S ATOM 7835 SG CYS C 300 40.704 44.735 47.787 1.00 41.17 S Time building chain proxies: 1.75, per 1000 atoms: 0.21 Number of scatterers: 8384 At special positions: 0 Unit cell: (122.094, 92.34, 109.782, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Ca 2 19.99 S 55 16.00 O 1548 8.00 N 1447 7.00 C 5329 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=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 350.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 179 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 292 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 315 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 289 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 300 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 277 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 274 " Number of angles added : 6 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 59.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.862A pdb=" N PHE A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 336 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 446 through 484 removed outlier: 3.795A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 4.222A pdb=" N GLU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 519 through 530 Processing helix chain 'A' and resid 530 through 561 Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 563 through 573 removed outlier: 5.035A pdb=" N LEU A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.095A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 removed outlier: 3.557A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.626A pdb=" N LEU A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 661 through 667 Processing helix chain 'A' and resid 746 through 786 removed outlier: 3.652A pdb=" N LEU A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 Processing helix chain 'A' and resid 808 through 829 removed outlier: 5.040A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 817 - end of helix Processing helix chain 'A' and resid 832 through 845 Processing helix chain 'A' and resid 846 through 852 removed outlier: 4.708A pdb=" N TYR A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 850 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 871 Processing helix chain 'A' and resid 871 through 887 removed outlier: 3.530A pdb=" N LEU A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 915 removed outlier: 5.412A pdb=" N ALA A 902 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.725A pdb=" N TYR B 23 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 46 removed outlier: 3.923A pdb=" N ARG B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 87 removed outlier: 4.114A pdb=" N MET B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 87 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.702A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.582A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 234 through 254 removed outlier: 3.618A pdb=" N LYS B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 278 through 292 removed outlier: 4.069A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.648A pdb=" N GLY B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.714A pdb=" N VAL C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 340 removed outlier: 3.616A pdb=" N ARG C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.718A pdb=" N ILE A 397 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624 removed outlier: 4.314A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 6.618A pdb=" N CYS B 13 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 133 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 258 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU B 299 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 260 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 172 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 171 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 197 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR B 173 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE B 199 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B 175 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LYS B 201 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL B 225 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE B 227 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER B 198 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N MET B 229 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N HIS B 200 " --> pdb=" O MET B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 286 through 288 425 hydrogen bonds defined for protein. 1233 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: 1.22 Time building geometry restraints manager: 0.71 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: 2745 1.34 - 1.46: 1962 1.46 - 1.58: 3767 1.58 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 8556 Sorted by residual: bond pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.40e+00 bond pdb=" N LYS C 32 " pdb=" CA LYS C 32 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.43e+00 bond pdb=" N CYS A 788 " pdb=" CA CYS A 788 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.33e+00 bond pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" N LEU A 787 " pdb=" CA LEU A 787 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.22e-02 6.72e+03 6.18e+00 ... (remaining 8551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 11358 2.13 - 4.25: 164 4.25 - 6.38: 19 6.38 - 8.51: 3 8.51 - 10.63: 1 Bond angle restraints: 11545 Sorted by residual: angle pdb=" O PRO C 30 " pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 121.31 117.41 3.90 4.60e-01 4.73e+00 7.20e+01 angle pdb=" CA PRO C 30 " pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 117.73 121.74 -4.01 9.00e-01 1.23e+00 1.99e+01 angle pdb=" C GLU A 789 " pdb=" CA GLU A 789 " pdb=" CB GLU A 789 " ideal model delta sigma weight residual 116.63 111.50 5.13 1.16e+00 7.43e-01 1.96e+01 angle pdb=" N CYS A 788 " pdb=" CA CYS A 788 " pdb=" C CYS A 788 " ideal model delta sigma weight residual 113.28 108.13 5.15 1.22e+00 6.72e-01 1.78e+01 angle pdb=" CA GLU A 562 " pdb=" CB GLU A 562 " pdb=" CG GLU A 562 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 ... (remaining 11540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4418 17.81 - 35.63: 528 35.63 - 53.44: 184 53.44 - 71.26: 33 71.26 - 89.07: 12 Dihedral angle restraints: 5175 sinusoidal: 2151 harmonic: 3024 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLU A 562 " pdb=" C GLU A 562 " pdb=" N GLN A 563 " pdb=" CA GLN A 563 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR B 304 " pdb=" C TYR B 304 " pdb=" N THR B 305 " pdb=" CA THR B 305 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 787 0.034 - 0.067: 327 0.067 - 0.101: 81 0.101 - 0.135: 36 0.135 - 0.168: 2 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CA LEU A 786 " pdb=" N LEU A 786 " pdb=" C LEU A 786 " pdb=" CB LEU A 786 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA GLU A 562 " pdb=" N GLU A 562 " pdb=" C GLU A 562 " pdb=" CB GLU A 562 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA VAL B 171 " pdb=" N VAL B 171 " pdb=" C VAL B 171 " pdb=" CB VAL B 171 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1230 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 269 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO C 270 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 270 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 270 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 39 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C THR B 39 " -0.029 2.00e-02 2.50e+03 pdb=" O THR B 39 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS B 40 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 864 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C GLN A 864 " -0.026 2.00e-02 2.50e+03 pdb=" O GLN A 864 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 865 " 0.009 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 25 2.38 - 3.01: 4713 3.01 - 3.64: 12392 3.64 - 4.27: 19083 4.27 - 4.90: 31978 Nonbonded interactions: 68191 Sorted by model distance: nonbonded pdb=" O ASN B 22 " pdb=" O HOH B 601 " model vdw 1.755 3.040 nonbonded pdb="ZN ZN B 501 " pdb=" O ACT B 504 " model vdw 1.878 2.230 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 501 " model vdw 1.918 2.230 nonbonded pdb=" OD1 ASP B 177 " pdb="ZN ZN B 501 " model vdw 1.947 2.230 nonbonded pdb=" O HOH A1204 " pdb=" O HOH A1205 " model vdw 1.993 3.040 ... (remaining 68186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.004 0.064 8565 Z= 0.183 Angle : 0.616 10.634 11551 Z= 0.360 Chirality : 0.041 0.168 1233 Planarity : 0.004 0.047 1498 Dihedral : 17.771 89.069 3225 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.96 % Allowed : 24.59 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.26), residues: 1016 helix: 1.17 (0.23), residues: 550 sheet: 0.78 (0.62), residues: 76 loop : -0.67 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 279 TYR 0.014 0.001 TYR B 304 PHE 0.012 0.001 PHE A 744 TRP 0.006 0.001 TRP A 909 HIS 0.007 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 ( 8556) covalent geometry : angle 0.61438 / 0.36 (11545) hydrogen bonds : bond 0.13024 / 8.12 ( 425) hydrogen bonds : angle 5.75338 / 4.17 ( 1233) metal coordination : bond 0.01217 / 0.76 ( 9) metal coordination : angle 1.78296 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.324 Fit side-chains REVERT: A 449 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7423 (mm-30) REVERT: A 668 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3499 (m-10) outliers start: 27 outliers final: 21 residues processed: 115 average time/residue: 0.5169 time to fit residues: 63.1296 Evaluate side-chains 113 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.0060 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 ASN A 756 HIS B 226 ASN C 321 HIS C 328 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132913 restraints weight = 10175.963| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.80 r_work: 0.3333 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8565 Z= 0.117 Angle : 0.511 6.773 11551 Z= 0.272 Chirality : 0.039 0.150 1233 Planarity : 0.004 0.041 1498 Dihedral : 6.218 55.434 1165 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.84 % Allowed : 23.05 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.23 (0.27), residues: 1016 helix: 1.73 (0.22), residues: 564 sheet: 0.96 (0.63), residues: 76 loop : -0.61 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 279 TYR 0.013 0.001 TYR B 23 PHE 0.009 0.001 PHE B 108 TRP 0.005 0.001 TRP A 749 HIS 0.006 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 ( 8556) covalent geometry : angle 0.50969 / 0.27 (11545) hydrogen bonds : bond 0.04792 / 3.18 ( 425) hydrogen bonds : angle 4.28145 / 3.13 ( 1233) metal coordination : bond 0.01034 / 0.70 ( 9) metal coordination : angle 1.37031 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7290 (t80) cc_final: 0.6996 (t80) REVERT: A 449 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 668 PHE cc_start: 0.4375 (OUTLIER) cc_final: 0.3927 (m-10) REVERT: A 842 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: A 865 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7474 (mt) REVERT: A 867 HIS cc_start: 0.7120 (t70) cc_final: 0.6639 (t70) REVERT: A 880 LEU cc_start: 0.6395 (mt) cc_final: 0.6125 (tp) REVERT: A 927 GLN cc_start: 0.6214 (tt0) cc_final: 0.5589 (mp10) REVERT: A 937 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: C 302 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7187 (mm-30) outliers start: 35 outliers final: 20 residues processed: 125 average time/residue: 0.5088 time to fit residues: 67.3249 Evaluate side-chains 116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 347 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 99 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131028 restraints weight = 9991.118| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.65 r_work: 0.3316 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8565 Z= 0.132 Angle : 0.511 8.216 11551 Z= 0.269 Chirality : 0.039 0.134 1233 Planarity : 0.004 0.037 1498 Dihedral : 5.703 55.637 1154 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.83 % Allowed : 22.39 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.35 (0.27), residues: 1016 helix: 1.88 (0.22), residues: 560 sheet: 1.03 (0.62), residues: 76 loop : -0.63 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.013 0.001 TYR B 304 PHE 0.011 0.001 PHE A 744 TRP 0.007 0.001 TRP A 749 HIS 0.008 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8556) covalent geometry : angle 0.51010 / 0.27 (11545) hydrogen bonds : bond 0.04786 / 3.20 ( 425) hydrogen bonds : angle 4.13320 / 3.01 ( 1233) metal coordination : bond 0.01379 / 0.93 ( 9) metal coordination : angle 1.72978 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 0.236 Fit side-chains REVERT: A 327 PHE cc_start: 0.7264 (t80) cc_final: 0.6973 (t80) REVERT: A 668 PHE cc_start: 0.4309 (OUTLIER) cc_final: 0.3797 (m-10) REVERT: A 842 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: A 865 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7563 (mt) REVERT: A 913 ARG cc_start: 0.3430 (OUTLIER) cc_final: 0.3176 (tmm160) REVERT: A 927 GLN cc_start: 0.6211 (tt0) cc_final: 0.5544 (mp10) REVERT: A 937 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: C 302 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7168 (mm-30) outliers start: 44 outliers final: 18 residues processed: 129 average time/residue: 0.5294 time to fit residues: 72.3868 Evaluate side-chains 113 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 ASN A 931 GLN B 34 HIS C 321 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.169300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128336 restraints weight = 10213.211| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.82 r_work: 0.3316 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8565 Z= 0.131 Angle : 0.512 8.115 11551 Z= 0.269 Chirality : 0.039 0.134 1233 Planarity : 0.004 0.036 1498 Dihedral : 5.529 57.087 1150 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.17 % Allowed : 23.49 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.34 (0.26), residues: 1016 helix: 1.91 (0.22), residues: 559 sheet: 0.95 (0.62), residues: 76 loop : -0.67 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 396 TYR 0.012 0.001 TYR B 304 PHE 0.011 0.001 PHE A 744 TRP 0.006 0.001 TRP A 749 HIS 0.007 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8556) covalent geometry : angle 0.51097 / 0.27 (11545) hydrogen bonds : bond 0.04637 / 3.13 ( 425) hydrogen bonds : angle 4.07051 / 2.97 ( 1233) metal coordination : bond 0.01252 / 0.84 ( 9) metal coordination : angle 1.49793 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 450 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: A 668 PHE cc_start: 0.4433 (OUTLIER) cc_final: 0.3917 (m-10) REVERT: A 842 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: A 865 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7672 (mt) REVERT: A 880 LEU cc_start: 0.6495 (mt) cc_final: 0.6215 (tp) REVERT: A 927 GLN cc_start: 0.6230 (tt0) cc_final: 0.5517 (mp10) REVERT: A 937 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8079 (pt0) REVERT: C 302 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7170 (mm-30) outliers start: 38 outliers final: 16 residues processed: 126 average time/residue: 0.4786 time to fit residues: 63.8526 Evaluate side-chains 111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 347 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.169870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131662 restraints weight = 10070.865| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.69 r_work: 0.3320 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8565 Z= 0.116 Angle : 0.496 7.947 11551 Z= 0.260 Chirality : 0.039 0.135 1233 Planarity : 0.003 0.037 1498 Dihedral : 5.460 57.696 1149 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.39 % Allowed : 22.94 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.41 (0.27), residues: 1016 helix: 1.99 (0.22), residues: 558 sheet: 0.86 (0.62), residues: 76 loop : -0.64 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.012 0.001 TYR B 304 PHE 0.024 0.001 PHE A 334 TRP 0.006 0.001 TRP A 909 HIS 0.006 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 8556) covalent geometry : angle 0.49532 / 0.26 (11545) hydrogen bonds : bond 0.04385 / 2.96 ( 425) hydrogen bonds : angle 3.98061 / 2.90 ( 1233) metal coordination : bond 0.00818 / 0.52 ( 9) metal coordination : angle 1.35579 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.6960 (mmmt) cc_final: 0.6727 (mmmm) REVERT: A 327 PHE cc_start: 0.7253 (t80) cc_final: 0.6908 (t80) REVERT: A 450 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: A 668 PHE cc_start: 0.4290 (OUTLIER) cc_final: 0.3731 (m-10) REVERT: A 842 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: A 865 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 880 LEU cc_start: 0.6458 (mt) cc_final: 0.6191 (tp) REVERT: A 927 GLN cc_start: 0.6213 (tt0) cc_final: 0.5504 (mp10) REVERT: B 91 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: C 302 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7152 (mm-30) outliers start: 40 outliers final: 19 residues processed: 133 average time/residue: 0.4769 time to fit residues: 67.2785 Evaluate side-chains 116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 15 optimal weight: 0.1980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.166180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125434 restraints weight = 10009.923| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.83 r_work: 0.3279 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8565 Z= 0.214 Angle : 0.609 9.945 11551 Z= 0.318 Chirality : 0.043 0.135 1233 Planarity : 0.004 0.038 1498 Dihedral : 5.978 56.475 1149 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.82 % Allowed : 21.95 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 0.93 (0.26), residues: 1016 helix: 1.58 (0.22), residues: 561 sheet: 0.80 (0.63), residues: 76 loop : -0.88 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 396 TYR 0.015 0.002 TYR B 304 PHE 0.018 0.002 PHE A 744 TRP 0.008 0.002 TRP A 749 HIS 0.011 0.002 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 ( 8556) covalent geometry : angle 0.60727 / 0.32 (11545) hydrogen bonds : bond 0.05724 / 3.86 ( 425) hydrogen bonds : angle 4.26044 / 3.11 ( 1233) metal coordination : bond 0.01885 / 1.22 ( 9) metal coordination : angle 1.99321 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 87 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7043 (mmmt) cc_final: 0.6815 (mmmm) REVERT: A 449 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 450 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: A 584 THR cc_start: 0.7418 (OUTLIER) cc_final: 0.7161 (t) REVERT: A 668 PHE cc_start: 0.4653 (OUTLIER) cc_final: 0.4113 (m-10) REVERT: A 842 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: A 937 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: B 38 MET cc_start: 0.8983 (mtp) cc_final: 0.8743 (mtm) REVERT: B 67 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8289 (mttm) REVERT: C 302 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: C 308 MET cc_start: 0.8092 (mmt) cc_final: 0.7799 (tpp) outliers start: 53 outliers final: 25 residues processed: 131 average time/residue: 0.4960 time to fit residues: 69.0475 Evaluate side-chains 121 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130874 restraints weight = 10175.231| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.79 r_work: 0.3296 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8565 Z= 0.131 Angle : 0.524 9.366 11551 Z= 0.274 Chirality : 0.040 0.131 1233 Planarity : 0.004 0.038 1498 Dihedral : 5.828 57.562 1149 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.28 % Allowed : 23.60 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.14 (0.26), residues: 1016 helix: 1.79 (0.22), residues: 557 sheet: 0.83 (0.63), residues: 76 loop : -0.80 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.012 0.001 TYR B 304 PHE 0.029 0.001 PHE A 334 TRP 0.007 0.001 TRP A 909 HIS 0.006 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8556) covalent geometry : angle 0.52311 / 0.27 (11545) hydrogen bonds : bond 0.04736 / 3.21 ( 425) hydrogen bonds : angle 4.07081 / 2.97 ( 1233) metal coordination : bond 0.00859 / 0.54 ( 9) metal coordination : angle 1.49791 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7043 (mmmt) cc_final: 0.6829 (mmmm) REVERT: A 327 PHE cc_start: 0.7188 (t80) cc_final: 0.6864 (t80) REVERT: A 354 LYS cc_start: 0.5200 (OUTLIER) cc_final: 0.3538 (ttmm) REVERT: A 449 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 450 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7284 (mm-30) REVERT: A 668 PHE cc_start: 0.4584 (OUTLIER) cc_final: 0.4068 (m-10) REVERT: A 740 TYR cc_start: 0.5833 (p90) cc_final: 0.5440 (p90) REVERT: A 842 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7617 (pt0) REVERT: A 937 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: B 67 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8227 (mttm) REVERT: C 302 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: C 308 MET cc_start: 0.8117 (mmt) cc_final: 0.7852 (tpp) outliers start: 39 outliers final: 22 residues processed: 124 average time/residue: 0.4925 time to fit residues: 64.7491 Evaluate side-chains 120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.168476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130849 restraints weight = 10023.498| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.76 r_work: 0.3297 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8565 Z= 0.139 Angle : 0.538 8.988 11551 Z= 0.281 Chirality : 0.040 0.129 1233 Planarity : 0.004 0.038 1498 Dihedral : 5.873 57.056 1149 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.61 % Allowed : 23.16 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.15 (0.26), residues: 1016 helix: 1.80 (0.22), residues: 557 sheet: 0.83 (0.63), residues: 76 loop : -0.80 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 279 TYR 0.013 0.001 TYR B 304 PHE 0.011 0.001 PHE A 744 TRP 0.007 0.001 TRP A 749 HIS 0.007 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8556) covalent geometry : angle 0.53680 / 0.28 (11545) hydrogen bonds : bond 0.04792 / 3.25 ( 425) hydrogen bonds : angle 4.05412 / 2.95 ( 1233) metal coordination : bond 0.01004 / 0.64 ( 9) metal coordination : angle 1.50300 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7027 (mmmt) cc_final: 0.6813 (mmmm) REVERT: A 327 PHE cc_start: 0.7162 (t80) cc_final: 0.6814 (t80) REVERT: A 354 LYS cc_start: 0.5035 (OUTLIER) cc_final: 0.3389 (ttmm) REVERT: A 449 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7295 (mm-30) REVERT: A 450 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: A 668 PHE cc_start: 0.4643 (OUTLIER) cc_final: 0.4140 (m-10) REVERT: A 842 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: A 937 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: B 67 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8223 (mttm) REVERT: C 302 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: C 308 MET cc_start: 0.8150 (mmt) cc_final: 0.7900 (tpp) outliers start: 42 outliers final: 24 residues processed: 124 average time/residue: 0.5287 time to fit residues: 69.2558 Evaluate side-chains 123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 100 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130996 restraints weight = 10138.471| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.76 r_work: 0.3303 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8565 Z= 0.134 Angle : 0.532 9.614 11551 Z= 0.278 Chirality : 0.040 0.138 1233 Planarity : 0.004 0.039 1498 Dihedral : 5.898 58.778 1149 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.84 % Allowed : 23.93 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.26), residues: 1016 helix: 1.82 (0.22), residues: 561 sheet: 0.85 (0.63), residues: 76 loop : -0.79 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 279 TYR 0.013 0.001 TYR B 304 PHE 0.032 0.001 PHE A 334 TRP 0.008 0.001 TRP A 909 HIS 0.006 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8556) covalent geometry : angle 0.53141 / 0.28 (11545) hydrogen bonds : bond 0.04690 / 3.18 ( 425) hydrogen bonds : angle 4.03130 / 2.94 ( 1233) metal coordination : bond 0.00915 / 0.58 ( 9) metal coordination : angle 1.43218 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.6994 (mmmt) cc_final: 0.6784 (mmmm) REVERT: A 327 PHE cc_start: 0.7092 (t80) cc_final: 0.6761 (t80) REVERT: A 354 LYS cc_start: 0.4967 (OUTLIER) cc_final: 0.3337 (ttmm) REVERT: A 449 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 450 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: A 668 PHE cc_start: 0.4556 (OUTLIER) cc_final: 0.4060 (m-10) REVERT: A 842 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: A 937 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7832 (pt0) REVERT: B 38 MET cc_start: 0.8830 (mtp) cc_final: 0.8592 (mtm) REVERT: B 67 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8209 (mttm) REVERT: C 302 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7228 (mm-30) outliers start: 35 outliers final: 25 residues processed: 122 average time/residue: 0.4999 time to fit residues: 64.6380 Evaluate side-chains 125 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 628 GLN Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 4.9990 chunk 89 optimal weight: 0.0470 chunk 21 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 96 optimal weight: 0.0050 chunk 74 optimal weight: 1.9990 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132841 restraints weight = 10056.699| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.77 r_work: 0.3322 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8565 Z= 0.111 Angle : 0.513 9.371 11551 Z= 0.269 Chirality : 0.039 0.130 1233 Planarity : 0.003 0.039 1498 Dihedral : 5.846 59.793 1149 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.73 % Allowed : 24.37 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.36 (0.27), residues: 1016 helix: 1.95 (0.22), residues: 561 sheet: 0.90 (0.64), residues: 76 loop : -0.71 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 279 TYR 0.012 0.001 TYR B 304 PHE 0.008 0.001 PHE B 335 TRP 0.008 0.001 TRP A 909 HIS 0.004 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 8556) covalent geometry : angle 0.51189 / 0.27 (11545) hydrogen bonds : bond 0.04200 / 2.85 ( 425) hydrogen bonds : angle 3.93992 / 2.87 ( 1233) metal coordination : bond 0.00665 / 0.42 ( 9) metal coordination : angle 1.30944 / 0.77 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7032 (mmmt) cc_final: 0.6812 (mmmm) REVERT: A 327 PHE cc_start: 0.7080 (t80) cc_final: 0.6718 (t80) REVERT: A 354 LYS cc_start: 0.4950 (OUTLIER) cc_final: 0.3326 (ttmm) REVERT: A 449 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7258 (mm-30) REVERT: A 450 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7255 (mm-30) REVERT: A 668 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.4289 (m-80) REVERT: A 842 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: A 927 GLN cc_start: 0.6219 (tt0) cc_final: 0.5530 (mp10) REVERT: A 937 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: B 67 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8201 (mttm) REVERT: B 324 GLU cc_start: 0.7668 (tt0) cc_final: 0.7463 (tt0) REVERT: C 302 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7225 (mm-30) outliers start: 34 outliers final: 20 residues processed: 128 average time/residue: 0.5379 time to fit residues: 73.1496 Evaluate side-chains 123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 354 LYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133346 restraints weight = 10089.732| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.75 r_work: 0.3337 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8565 Z= 0.106 Angle : 0.496 8.057 11551 Z= 0.262 Chirality : 0.039 0.132 1233 Planarity : 0.003 0.038 1498 Dihedral : 5.636 59.689 1147 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.18 % Allowed : 24.92 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 1.41 (0.27), residues: 1016 helix: 1.98 (0.22), residues: 566 sheet: 0.99 (0.64), residues: 76 loop : -0.71 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 279 TYR 0.012 0.001 TYR B 304 PHE 0.034 0.001 PHE A 334 TRP 0.007 0.001 TRP A 749 HIS 0.004 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 8556) covalent geometry : angle 0.49582 / 0.26 (11545) hydrogen bonds : bond 0.04078 / 2.76 ( 425) hydrogen bonds : angle 3.90425 / 2.85 ( 1233) metal coordination : bond 0.00592 / 0.37 ( 9) metal coordination : angle 1.17019 / 0.70 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.01 seconds wall clock time: 50 minutes 12.70 seconds (3012.70 seconds total)