Starting phenix.real_space_refine on Fri Aug 22 22:28:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpb_16148/08_2025/8bpb_16148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpb_16148/08_2025/8bpb_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_16148/08_2025/8bpb_16148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpb_16148/08_2025/8bpb_16148.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpb_16148/08_2025/8bpb_16148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpb_16148/08_2025/8bpb_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-2.0-5787/lib/python3.9/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, 7 Unusual residues: {' CA': 2, ' ZN': 1, 'ACT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 1.92, per 1000 atoms: 0.23 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: 0.76 Conformation dependent library (CDL) restraints added in 403.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 1.13 Time building geometry restraints manager: 0.99 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: 0.610 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.890 Find NCS groups from input model: 0.030 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 aren 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 covalent geometry : bond 0.00359 ( 8556) covalent geometry : angle 0.61438 (11545) hydrogen bonds : bond 0.13024 ( 425) hydrogen bonds : angle 5.75338 ( 1233) metal coordination : bond 0.01217 ( 9) metal coordination : angle 1.78296 ( 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 : 0.250 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: 0.6041 time to fit residues: 73.6984 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 : 0.301 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3986 r_free = 0.3986 target = 0.170208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132705 restraints weight = 10116.184| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.66 r_work: 0.3330 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 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 = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8565 Z= 0.117 Angle : 0.511 6.804 11551 Z= 0.272 Chirality : 0.039 0.149 1233 Planarity : 0.004 0.041 1498 Dihedral : 6.220 55.469 1165 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.06 % Allowed : 22.83 % 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 aren not related in a simple way. whole: 1.23 (0.27), residues: 1016 helix: 1.74 (0.22), residues: 564 sheet: 0.95 (0.63), residues: 76 loop : -0.60 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 279 TYR 0.012 0.001 TYR B 304 PHE 0.009 0.001 PHE A 662 TRP 0.005 0.001 TRP A 749 HIS 0.006 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8556) covalent geometry : angle 0.51022 (11545) hydrogen bonds : bond 0.04720 ( 425) hydrogen bonds : angle 4.27913 ( 1233) metal coordination : bond 0.01080 ( 9) metal coordination : angle 1.38767 ( 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 136 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.325 Fit side-chains REVERT: A 327 PHE cc_start: 0.7314 (t80) cc_final: 0.7025 (t80) REVERT: A 449 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 668 PHE cc_start: 0.4380 (OUTLIER) cc_final: 0.3929 (m-10) REVERT: A 842 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: A 865 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7475 (mt) REVERT: A 867 HIS cc_start: 0.7115 (t70) cc_final: 0.6636 (t70) REVERT: A 880 LEU cc_start: 0.6419 (mt) cc_final: 0.6145 (tp) REVERT: A 927 GLN cc_start: 0.6238 (tt0) cc_final: 0.5606 (mp10) REVERT: A 937 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8070 (pt0) REVERT: C 302 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7178 (mm-30) outliers start: 37 outliers final: 20 residues processed: 126 average time/residue: 0.5558 time to fit residues: 74.2351 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 : 0.191 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN A 582 ASN A 931 GLN B 34 HIS C 318 HIS C 321 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.166863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128763 restraints weight = 9947.706| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.65 r_work: 0.3285 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.956 8565 Z= 0.265 Angle : 0.573 9.425 11551 Z= 0.301 Chirality : 0.042 0.134 1233 Planarity : 0.004 0.039 1498 Dihedral : 6.059 55.747 1154 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.94 % Allowed : 22.61 % 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 aren not related in a simple way. whole: 1.03 (0.26), residues: 1016 helix: 1.62 (0.22), residues: 564 sheet: 0.87 (0.63), residues: 76 loop : -0.78 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 396 TYR 0.015 0.002 TYR B 304 PHE 0.016 0.002 PHE A 744 TRP 0.008 0.002 TRP A 749 HIS 0.011 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 8556) covalent geometry : angle 0.57162 (11545) hydrogen bonds : bond 0.05584 ( 425) hydrogen bonds : angle 4.32378 ( 1233) metal coordination : bond 0.31898 ( 9) metal coordination : angle 1.87292 ( 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 136 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 91 time to evaluate : 0.276 Fit side-chains REVERT: A 327 PHE cc_start: 0.7301 (t80) cc_final: 0.7006 (t80) REVERT: A 450 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7216 (mm-30) REVERT: A 668 PHE cc_start: 0.4443 (OUTLIER) cc_final: 0.3891 (m-10) REVERT: A 835 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: A 842 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: A 865 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7597 (mt) REVERT: A 867 HIS cc_start: 0.7313 (t70) cc_final: 0.6902 (t70) REVERT: A 886 LYS cc_start: 0.5798 (OUTLIER) cc_final: 0.5591 (ttpp) REVERT: A 913 ARG cc_start: 0.3592 (OUTLIER) cc_final: 0.3338 (tmm160) REVERT: A 937 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8142 (pt0) REVERT: C 302 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7148 (mm-30) outliers start: 45 outliers final: 25 residues processed: 124 average time/residue: 0.5839 time to fit residues: 76.5944 Evaluate side-chains 121 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 334 PHE 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 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 835 GLN 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 886 LYS 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 63 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU 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: 3.9990 chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.169237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130832 restraints weight = 10143.864| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.73 r_work: 0.3308 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 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 = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 8565 Z= 0.125 Angle : 0.511 7.683 11551 Z= 0.268 Chirality : 0.039 0.137 1233 Planarity : 0.004 0.038 1498 Dihedral : 5.866 56.608 1153 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.61 % Allowed : 23.27 % 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 aren not related in a simple way. whole: 1.21 (0.26), residues: 1016 helix: 1.79 (0.22), residues: 564 sheet: 0.93 (0.63), residues: 76 loop : -0.75 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.013 0.001 TYR B 304 PHE 0.011 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 covalent geometry : bond 0.00273 ( 8556) covalent geometry : angle 0.50736 (11545) hydrogen bonds : bond 0.04663 ( 425) hydrogen bonds : angle 4.10567 ( 1233) metal coordination : bond 0.03179 ( 9) metal coordination : angle 2.70889 ( 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 138 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.284 Fit side-chains REVERT: A 449 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7294 (mm-30) REVERT: A 450 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: A 668 PHE cc_start: 0.4519 (OUTLIER) cc_final: 0.4001 (m-10) REVERT: A 842 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: A 865 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7603 (mt) REVERT: A 927 GLN cc_start: 0.6227 (tt0) cc_final: 0.5478 (mp10) REVERT: A 937 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: B 67 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8225 (mttm) REVERT: C 302 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7151 (mm-30) outliers start: 42 outliers final: 17 residues processed: 128 average time/residue: 0.5820 time to fit residues: 78.7869 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 : 0.254 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 12 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129827 restraints weight = 10001.946| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.77 r_work: 0.3291 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 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 = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 8565 Z= 0.155 Angle : 0.545 9.207 11551 Z= 0.282 Chirality : 0.040 0.137 1233 Planarity : 0.004 0.038 1498 Dihedral : 5.807 56.850 1150 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.83 % Allowed : 22.72 % 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 aren not related in a simple way. whole: 1.19 (0.26), residues: 1016 helix: 1.80 (0.22), residues: 559 sheet: 0.88 (0.63), residues: 76 loop : -0.76 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.014 0.001 TYR B 304 PHE 0.013 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 covalent geometry : bond 0.00352 ( 8556) covalent geometry : angle 0.53380 (11545) hydrogen bonds : bond 0.04953 ( 425) hydrogen bonds : angle 4.12441 ( 1233) metal coordination : bond 0.05384 ( 9) metal coordination : angle 4.79127 ( 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: 44 poor density : 97 time to evaluate : 0.337 Fit side-chains REVERT: A 319 LYS cc_start: 0.7027 (mmmt) cc_final: 0.6802 (mmmm) REVERT: A 327 PHE cc_start: 0.7197 (t80) cc_final: 0.6875 (t80) REVERT: A 449 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7283 (mm-30) REVERT: A 450 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: A 668 PHE cc_start: 0.4414 (OUTLIER) cc_final: 0.3909 (m-10) REVERT: A 842 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: A 865 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7642 (mt) REVERT: A 937 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: B 91 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8525 (mt0) REVERT: C 302 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7171 (mm-30) outliers start: 44 outliers final: 22 residues processed: 133 average time/residue: 0.6009 time to fit residues: 84.8327 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 : 0.335 ------------------------------------------------------------------------------- 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 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 937 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 231 ASP 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 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: 8.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 66 optimal weight: 0.0070 chunk 15 optimal weight: 0.9980 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128604 restraints weight = 10043.667| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.68 r_work: 0.3275 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 8565 Z= 0.178 Angle : 0.574 9.174 11551 Z= 0.298 Chirality : 0.041 0.136 1233 Planarity : 0.004 0.040 1498 Dihedral : 6.003 57.123 1150 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.16 % Allowed : 22.72 % 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 aren not related in a simple way. whole: 1.03 (0.26), residues: 1016 helix: 1.69 (0.22), residues: 555 sheet: 0.81 (0.64), residues: 76 loop : -0.83 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.014 0.002 TYR B 304 PHE 0.027 0.002 PHE A 334 TRP 0.006 0.001 TRP A 749 HIS 0.009 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8556) covalent geometry : angle 0.57115 (11545) hydrogen bonds : bond 0.05319 ( 425) hydrogen bonds : angle 4.19687 ( 1233) metal coordination : bond 0.04186 ( 9) metal coordination : angle 2.36696 ( 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 136 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 89 time to evaluate : 0.284 Fit side-chains REVERT: A 319 LYS cc_start: 0.7037 (mmmt) cc_final: 0.6813 (mmmm) REVERT: A 327 PHE cc_start: 0.7243 (t80) cc_final: 0.6882 (t80) REVERT: A 354 LYS cc_start: 0.4384 (OUTLIER) cc_final: 0.3412 (ttmm) REVERT: A 449 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 450 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: A 476 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8275 (mp) REVERT: A 584 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.7124 (t) REVERT: A 668 PHE cc_start: 0.4676 (OUTLIER) cc_final: 0.4077 (m-10) REVERT: A 842 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7615 (pt0) REVERT: A 865 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7664 (mt) REVERT: A 937 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: B 38 MET cc_start: 0.8940 (mtp) cc_final: 0.8730 (mtm) REVERT: B 67 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8255 (mttm) REVERT: B 91 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: C 302 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: C 308 MET cc_start: 0.8139 (mmt) cc_final: 0.7820 (tpp) outliers start: 47 outliers final: 24 residues processed: 127 average time/residue: 0.5733 time to fit residues: 77.1978 Evaluate side-chains 123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 584 THR 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 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 LEU 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 91 GLN 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 231 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 319 VAL 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 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: 4.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 GLN C 321 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130733 restraints weight = 10195.039| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.86 r_work: 0.3282 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 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 = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8565 Z= 0.140 Angle : 0.530 8.646 11551 Z= 0.276 Chirality : 0.040 0.137 1233 Planarity : 0.004 0.040 1498 Dihedral : 5.947 58.000 1149 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.60 % Allowed : 21.73 % 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 aren not related in a simple way. whole: 1.13 (0.26), residues: 1016 helix: 1.78 (0.22), residues: 555 sheet: 0.81 (0.64), residues: 76 loop : -0.81 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.014 0.001 TYR B 304 PHE 0.012 0.001 PHE A 744 TRP 0.007 0.001 TRP A 909 HIS 0.007 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8556) covalent geometry : angle 0.52801 (11545) hydrogen bonds : bond 0.04856 ( 425) hydrogen bonds : angle 4.10356 ( 1233) metal coordination : bond 0.02381 ( 9) metal coordination : angle 1.87533 ( 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 146 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 95 time to evaluate : 0.296 Fit side-chains REVERT: A 319 LYS cc_start: 0.7037 (mmmt) cc_final: 0.6825 (mmmm) REVERT: A 327 PHE cc_start: 0.7271 (t80) cc_final: 0.6880 (t80) REVERT: A 354 LYS cc_start: 0.4366 (OUTLIER) cc_final: 0.3335 (ttmm) REVERT: A 449 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 450 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: A 668 PHE cc_start: 0.4694 (OUTLIER) cc_final: 0.4138 (m-10) REVERT: A 842 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: A 865 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7638 (mt) REVERT: A 937 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: B 67 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8250 (mttm) REVERT: B 91 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8513 (mt0) REVERT: C 302 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: C 308 MET cc_start: 0.8181 (mmt) cc_final: 0.7871 (tpp) REVERT: C 312 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.5387 (mmm160) outliers start: 51 outliers final: 28 residues processed: 138 average time/residue: 0.5818 time to fit residues: 84.9232 Evaluate side-chains 129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 354 LYS Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 457 ASP 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 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 885 LYS 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 91 GLN 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 231 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 319 VAL 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 312 ARG Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 341 PHE 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: 0.9990 chunk 76 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 GLN C 321 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.168649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131071 restraints weight = 10010.480| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.73 r_work: 0.3303 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8565 Z= 0.131 Angle : 0.536 8.686 11551 Z= 0.279 Chirality : 0.040 0.132 1233 Planarity : 0.004 0.038 1498 Dihedral : 5.940 59.077 1149 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.94 % Allowed : 23.16 % 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 aren not related in a simple way. whole: 1.16 (0.26), residues: 1016 helix: 1.82 (0.22), residues: 556 sheet: 0.83 (0.64), residues: 76 loop : -0.82 (0.29), residues: 384 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 0.031 0.001 PHE A 334 TRP 0.007 0.001 TRP A 749 HIS 0.006 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8556) covalent geometry : angle 0.53494 (11545) hydrogen bonds : bond 0.04689 ( 425) hydrogen bonds : angle 4.05834 ( 1233) metal coordination : bond 0.01677 ( 9) metal coordination : angle 1.58500 ( 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 140 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.260 Fit side-chains REVERT: A 319 LYS cc_start: 0.7030 (mmmt) cc_final: 0.6818 (mmmm) REVERT: A 354 LYS cc_start: 0.4320 (OUTLIER) cc_final: 0.3278 (ttmm) REVERT: A 449 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 450 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7251 (mm-30) REVERT: A 668 PHE cc_start: 0.4500 (OUTLIER) cc_final: 0.3976 (m-10) REVERT: A 842 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: A 865 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7607 (mt) REVERT: A 937 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8069 (pt0) REVERT: B 67 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8236 (mttm) REVERT: B 91 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8497 (mt0) REVERT: C 302 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: C 312 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.5395 (mmm160) outliers start: 45 outliers final: 26 residues processed: 131 average time/residue: 0.5776 time to fit residues: 80.1331 Evaluate side-chains 129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 885 LYS 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 91 GLN 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 231 ASP 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 312 ARG Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 341 PHE 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: 0.8980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.0470 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131132 restraints weight = 10125.054| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.78 r_work: 0.3303 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 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 = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8565 Z= 0.128 Angle : 0.525 8.087 11551 Z= 0.275 Chirality : 0.040 0.131 1233 Planarity : 0.004 0.039 1498 Dihedral : 5.927 57.980 1149 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.39 % Allowed : 23.71 % 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 aren not related in a simple way. whole: 1.27 (0.26), residues: 1016 helix: 1.91 (0.22), residues: 551 sheet: 0.88 (0.63), residues: 76 loop : -0.74 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 279 TYR 0.014 0.001 TYR B 304 PHE 0.011 0.001 PHE A 744 TRP 0.006 0.001 TRP A 909 HIS 0.006 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8556) covalent geometry : angle 0.52378 (11545) hydrogen bonds : bond 0.04593 ( 425) hydrogen bonds : angle 4.03406 ( 1233) metal coordination : bond 0.01488 ( 9) metal coordination : angle 1.57446 ( 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 137 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.380 Fit side-chains REVERT: A 319 LYS cc_start: 0.7008 (mmmt) cc_final: 0.6796 (mmmm) REVERT: A 327 PHE cc_start: 0.7102 (t80) cc_final: 0.6792 (t80) REVERT: A 354 LYS cc_start: 0.4316 (OUTLIER) cc_final: 0.3282 (ttmm) REVERT: A 449 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 450 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: A 668 PHE cc_start: 0.4459 (OUTLIER) cc_final: 0.3949 (m-10) REVERT: A 842 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: A 865 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 882 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6259 (tp) REVERT: A 937 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8028 (pt0) REVERT: B 67 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8213 (mttm) REVERT: B 91 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: C 302 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7217 (mm-30) outliers start: 40 outliers final: 23 residues processed: 129 average time/residue: 0.6743 time to fit residues: 91.9683 Evaluate side-chains 126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 885 LYS 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 91 GLN 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 319 VAL 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 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: 0.0970 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131522 restraints weight = 10050.119| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.83 r_work: 0.3285 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8565 Z= 0.132 Angle : 0.530 8.140 11551 Z= 0.279 Chirality : 0.040 0.142 1233 Planarity : 0.004 0.041 1498 Dihedral : 5.933 59.023 1149 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.06 % Allowed : 23.93 % Favored : 72.01 % 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 aren not related in a simple way. whole: 1.27 (0.26), residues: 1016 helix: 1.91 (0.22), residues: 552 sheet: 0.87 (0.63), residues: 76 loop : -0.74 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 279 TYR 0.013 0.001 TYR B 304 PHE 0.033 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 covalent geometry : bond 0.00298 ( 8556) covalent geometry : angle 0.52888 (11545) hydrogen bonds : bond 0.04630 ( 425) hydrogen bonds : angle 4.02819 ( 1233) metal coordination : bond 0.01560 ( 9) metal coordination : angle 1.55690 ( 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 132 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.424 Fit side-chains REVERT: A 319 LYS cc_start: 0.7000 (mmmt) cc_final: 0.6788 (mmmm) REVERT: A 327 PHE cc_start: 0.7155 (t80) cc_final: 0.6856 (t80) REVERT: A 354 LYS cc_start: 0.4305 (OUTLIER) cc_final: 0.3261 (ttmm) REVERT: A 449 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 450 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7262 (mm-30) REVERT: A 668 PHE cc_start: 0.4430 (OUTLIER) cc_final: 0.3945 (m-10) REVERT: A 842 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: A 937 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: B 67 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8227 (mttm) REVERT: B 91 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: C 302 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7194 (mm-30) outliers start: 37 outliers final: 24 residues processed: 124 average time/residue: 0.6863 time to fit residues: 89.9701 Evaluate side-chains 126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 873 VAL Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 885 LYS 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 91 GLN 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 306 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 352 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 99 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132957 restraints weight = 10092.338| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.77 r_work: 0.3323 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 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 = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8565 Z= 0.109 Angle : 0.505 7.680 11551 Z= 0.266 Chirality : 0.039 0.133 1233 Planarity : 0.004 0.042 1498 Dihedral : 5.636 59.832 1147 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.07 % Allowed : 24.81 % 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 aren not related in a simple way. whole: 1.37 (0.27), residues: 1016 helix: 1.96 (0.22), residues: 560 sheet: 0.98 (0.64), residues: 76 loop : -0.70 (0.30), residues: 380 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 0.009 0.001 PHE A 744 TRP 0.008 0.001 TRP A 909 HIS 0.004 0.001 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8556) covalent geometry : angle 0.50472 (11545) hydrogen bonds : bond 0.04184 ( 425) hydrogen bonds : angle 3.93949 ( 1233) metal coordination : bond 0.01100 ( 9) metal coordination : angle 1.30819 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3397.42 seconds wall clock time: 58 minutes 35.52 seconds (3515.52 seconds total)