Starting phenix.real_space_refine on Thu Jul 2 11:03:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpc_16149/07_2026/8bpc_16149_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpc_16149/07_2026/8bpc_16149.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/8bpc_16149/07_2026/8bpc_16149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpc_16149/07_2026/8bpc_16149.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpc_16149/07_2026/8bpc_16149_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpc_16149/07_2026/8bpc_16149_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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 3 6.06 5 S 55 5.16 5 C 5342 2.51 5 N 1449 2.21 5 O 1582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8433 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4405 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 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: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1, 'SHH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7745 SG CYS C 289 37.812 59.778 45.110 1.00 57.24 S ATOM 7771 SG CYS C 292 35.245 58.180 42.684 1.00 45.08 S ATOM 7954 SG CYS C 315 38.906 57.170 42.432 1.00 59.56 S ATOM 7629 SG CYS C 274 38.038 47.655 47.545 1.00 38.25 S ATOM 7653 SG CYS C 277 37.502 44.027 48.618 1.00 48.40 S ATOM 7837 SG CYS C 300 41.011 45.328 48.053 1.00 41.17 S Time building chain proxies: 1.49, per 1000 atoms: 0.18 Number of scatterers: 8433 At special positions: 0 Unit cell: (121.92, 93.472, 110.744, 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 1582 8.00 N 1449 7.00 C 5342 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: 0.65 Conformation dependent library (CDL) restraints added in 284.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 179 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 292 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 315 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 289 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 300 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 277 " pdb="ZN ZN C 402 " - 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: 44 helices and 4 sheets defined 59.5% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.861A 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 441 through 445 removed outlier: 3.548A pdb=" N LYS A 445 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 484 removed outlier: 3.647A 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: 3.556A 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: 3.651A 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: 3.594A 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: 5.831A pdb=" N ARG A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.726A 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: 5.620A 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: 3.703A 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: 4.070A 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: 6.435A 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: 7.938A 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: 7.795A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 6.856A 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: 6.450A 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: 7.794A 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 288 428 hydrogen bonds defined for protein. 1239 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: 1.26 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2156 1.33 - 1.46: 1852 1.46 - 1.58: 4484 1.58 - 1.70: 0 1.70 - 1.83: 82 Bond restraints: 8574 Sorted by residual: bond pdb=" CA SER A 430 " pdb=" CB SER A 430 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.34e-02 5.57e+03 1.08e+01 bond pdb=" N THR A 446 " pdb=" CA THR A 446 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.14e-02 7.69e+03 8.99e+00 bond pdb=" N TRP A 434 " pdb=" CA TRP A 434 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.16e-02 7.43e+03 8.80e+00 bond pdb=" N VAL A 429 " pdb=" CA VAL A 429 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.19e-02 7.06e+03 7.82e+00 bond pdb=" N LYS B 11 " pdb=" CA LYS B 11 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.44e+00 ... (remaining 8569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 11317 2.13 - 4.26: 214 4.26 - 6.39: 31 6.39 - 8.52: 3 8.52 - 10.65: 2 Bond angle restraints: 11567 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 121.31 117.73 3.58 4.60e-01 4.73e+00 6.06e+01 angle pdb=" C THR A 427 " pdb=" N TRP A 428 " pdb=" CA TRP A 428 " ideal model delta sigma weight residual 122.64 112.99 9.65 1.70e+00 3.46e-01 3.22e+01 angle pdb=" N PRO C 31 " pdb=" CA PRO C 31 " pdb=" CB PRO C 31 " ideal model delta sigma weight residual 102.35 105.94 -3.59 7.10e-01 1.98e+00 2.56e+01 angle pdb=" C VAL A 429 " pdb=" N SER A 430 " pdb=" CA SER A 430 " ideal model delta sigma weight residual 122.77 116.84 5.93 1.33e+00 5.65e-01 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 116.63 111.48 5.15 1.16e+00 7.43e-01 1.97e+01 ... (remaining 11562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4429 17.83 - 35.66: 528 35.66 - 53.49: 185 53.49 - 71.31: 30 71.31 - 89.14: 11 Dihedral angle restraints: 5183 sinusoidal: 2159 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 -157.68 -22.32 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 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1116 0.071 - 0.142: 110 0.142 - 0.213: 5 0.213 - 0.284: 1 0.284 - 0.355: 2 Chirality restraints: 1234 Sorted by residual: chirality pdb=" CB VAL B 12 " pdb=" CA VAL B 12 " pdb=" CG1 VAL B 12 " pdb=" CG2 VAL B 12 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB VAL A 441 " pdb=" CA VAL A 441 " pdb=" CG1 VAL A 441 " pdb=" CG2 VAL A 441 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL A 429 " pdb=" CA VAL A 429 " pdb=" CG1 VAL A 429 " pdb=" CG2 VAL A 429 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1231 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 SHH B 501 " 0.008 2.00e-02 2.50e+03 1.91e-02 6.40e+00 pdb=" C11 SHH B 501 " -0.012 2.00e-02 2.50e+03 pdb=" C12 SHH B 501 " -0.007 2.00e-02 2.50e+03 pdb=" C13 SHH B 501 " 0.001 2.00e-02 2.50e+03 pdb=" C14 SHH B 501 " -0.004 2.00e-02 2.50e+03 pdb=" C9 SHH B 501 " 0.040 2.00e-02 2.50e+03 pdb=" N2 SHH B 501 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 269 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+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=" C7 SHH B 501 " -0.015 2.00e-02 2.50e+03 1.57e-02 3.09e+00 pdb=" C8 SHH B 501 " 0.008 2.00e-02 2.50e+03 pdb=" C9 SHH B 501 " -0.019 2.00e-02 2.50e+03 pdb=" N2 SHH B 501 " 0.024 2.00e-02 2.50e+03 pdb=" O3 SHH B 501 " 0.001 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 12 2.23 - 2.89: 3249 2.89 - 3.56: 11985 3.56 - 4.23: 19656 4.23 - 4.90: 34082 Nonbonded interactions: 68984 Sorted by model distance: nonbonded pdb=" O HOH B 608 " pdb=" O HOH B 632 " model vdw 1.557 3.040 nonbonded pdb=" OH TYR B 16 " pdb=" O HOH B 601 " model vdw 1.648 3.040 nonbonded pdb=" OE2 GLU A 461 " pdb=" O HOH A1201 " model vdw 1.815 3.040 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 502 " model vdw 1.919 2.230 nonbonded pdb=" OD1 ASP B 177 " pdb="ZN ZN B 502 " model vdw 1.946 2.230 ... (remaining 68979 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: 0.680 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 0.065 8583 Z= 0.240 Angle : 0.687 10.650 11573 Z= 0.411 Chirality : 0.045 0.355 1234 Planarity : 0.004 0.047 1500 Dihedral : 17.594 89.143 3233 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.18 % Allowed : 24.34 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.27), residues: 1016 helix: 1.13 (0.23), residues: 551 sheet: 0.60 (0.62), residues: 76 loop : -0.73 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 495 TYR 0.014 0.001 TYR B 304 PHE 0.012 0.001 PHE A 744 TRP 0.008 0.001 TRP A 434 HIS 0.007 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.24 ( 8574) covalent geometry : angle 0.68557 / 0.41 (11567) hydrogen bonds : bond 0.13582 / 9.22 ( 428) hydrogen bonds : angle 5.87599 / 4.12 ( 1239) metal coordination : bond 0.01223 / 0.76 ( 9) metal coordination : angle 1.78147 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5660 (mp) REVERT: A 395 LYS cc_start: 0.3960 (mttt) cc_final: 0.3610 (ttpt) REVERT: A 402 ARG cc_start: 0.7158 (mpt180) cc_final: 0.6954 (mtp85) REVERT: A 486 MET cc_start: 0.6555 (ptt) cc_final: 0.6302 (ptp) REVERT: C 21 MET cc_start: 0.8165 (tpp) cc_final: 0.7847 (tpt) outliers start: 29 outliers final: 5 residues processed: 210 average time/residue: 0.5062 time to fit residues: 112.2130 Evaluate side-chains 107 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 319 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 ASN A 603 HIS A 756 HIS A 773 GLN A 919 ASN B 22 ASN B 58 HIS B 96 ASN B 226 ASN C 288 GLN C 328 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.168716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122426 restraints weight = 10831.965| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.96 r_work: 0.3348 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 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 = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8583 Z= 0.169 Angle : 0.588 11.017 11573 Z= 0.306 Chirality : 0.042 0.197 1234 Planarity : 0.004 0.041 1500 Dihedral : 4.950 48.405 1148 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.26 % Allowed : 21.60 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1016 helix: 1.44 (0.22), residues: 570 sheet: 0.72 (0.62), residues: 76 loop : -0.75 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 127 TYR 0.018 0.002 TYR B 304 PHE 0.015 0.001 PHE A 662 TRP 0.012 0.001 TRP A 428 HIS 0.008 0.002 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8574) covalent geometry : angle 0.58618 / 0.31 (11567) hydrogen bonds : bond 0.04967 / 3.21 ( 428) hydrogen bonds : angle 4.33872 / 3.10 ( 1239) metal coordination : bond 0.00654 / 0.41 ( 9) metal coordination : angle 2.02375 / 1.16 ( 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 160 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.307 Fit side-chains REVERT: A 342 SER cc_start: 0.3625 (OUTLIER) cc_final: 0.3113 (m) REVERT: A 395 LYS cc_start: 0.3862 (mttt) cc_final: 0.3059 (ttmt) REVERT: A 402 ARG cc_start: 0.7707 (mpt180) cc_final: 0.7245 (mtt-85) REVERT: A 486 MET cc_start: 0.7440 (ptt) cc_final: 0.6717 (ptp) REVERT: A 493 LYS cc_start: 0.7910 (mmmm) cc_final: 0.7377 (ptpp) REVERT: A 813 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: A 913 ARG cc_start: 0.4283 (OUTLIER) cc_final: 0.3899 (ptm160) REVERT: B 44 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8186 (mp) REVERT: B 63 GLU cc_start: 0.8456 (mp0) cc_final: 0.8205 (mp0) REVERT: B 75 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7957 (tttt) REVERT: B 358 GLU cc_start: 0.8367 (pm20) cc_final: 0.7888 (tt0) outliers start: 48 outliers final: 14 residues processed: 145 average time/residue: 0.5494 time to fit residues: 84.2170 Evaluate side-chains 101 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 369 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 0.0020 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.0170 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.9630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS B 40 HIS C 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.165654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119708 restraints weight = 10801.367| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.92 r_work: 0.3308 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8583 Z= 0.143 Angle : 0.522 7.258 11573 Z= 0.276 Chirality : 0.040 0.138 1234 Planarity : 0.004 0.041 1500 Dihedral : 4.466 31.915 1144 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.50 % Allowed : 22.59 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 1016 helix: 1.75 (0.22), residues: 562 sheet: 0.82 (0.63), residues: 76 loop : -0.74 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 928 TYR 0.017 0.001 TYR B 304 PHE 0.016 0.001 PHE A 662 TRP 0.004 0.001 TRP A 428 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 8574) covalent geometry : angle 0.52042 / 0.28 (11567) hydrogen bonds : bond 0.04468 / 2.88 ( 428) hydrogen bonds : angle 4.16874 / 3.00 ( 1239) metal coordination : bond 0.02442 / 1.75 ( 9) metal coordination : angle 2.10737 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 0.201 Fit side-chains REVERT: A 342 SER cc_start: 0.3088 (OUTLIER) cc_final: 0.2527 (m) REVERT: A 395 LYS cc_start: 0.3934 (mttt) cc_final: 0.3174 (ttmt) REVERT: A 402 ARG cc_start: 0.7734 (mpt180) cc_final: 0.7360 (mtt-85) REVERT: A 456 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: A 486 MET cc_start: 0.7441 (ptt) cc_final: 0.6847 (ptp) REVERT: A 493 LYS cc_start: 0.7845 (mmmm) cc_final: 0.7426 (ptpt) REVERT: A 886 LYS cc_start: 0.6956 (mttt) cc_final: 0.6666 (mmtt) REVERT: A 913 ARG cc_start: 0.4448 (OUTLIER) cc_final: 0.4089 (ptm160) REVERT: B 63 GLU cc_start: 0.8398 (mp0) cc_final: 0.8138 (mp0) REVERT: B 75 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8106 (tttt) REVERT: B 358 GLU cc_start: 0.8501 (pm20) cc_final: 0.8005 (tt0) REVERT: C 287 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8441 (mt) REVERT: C 288 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7593 (tp-100) outliers start: 41 outliers final: 13 residues processed: 130 average time/residue: 0.5289 time to fit residues: 72.7659 Evaluate side-chains 100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 86 SER 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 306 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 288 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS C 288 GLN C 321 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.164650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118408 restraints weight = 11046.049| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.97 r_work: 0.3290 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 8583 Z= 0.136 Angle : 0.517 6.408 11573 Z= 0.270 Chirality : 0.039 0.159 1234 Planarity : 0.004 0.042 1500 Dihedral : 4.449 33.025 1144 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.73 % Allowed : 23.46 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.27), residues: 1016 helix: 1.85 (0.22), residues: 562 sheet: 0.82 (0.64), residues: 76 loop : -0.79 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 863 TYR 0.023 0.001 TYR A 740 PHE 0.015 0.001 PHE A 662 TRP 0.003 0.001 TRP A 434 HIS 0.006 0.001 HIS C 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 8574) covalent geometry : angle 0.51387 / 0.27 (11567) hydrogen bonds : bond 0.04246 / 2.73 ( 428) hydrogen bonds : angle 4.07589 / 2.93 ( 1239) metal coordination : bond 0.03219 / 2.31 ( 9) metal coordination : angle 2.41930 / 1.27 ( 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 116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.336 Fit side-chains REVERT: A 342 SER cc_start: 0.3119 (OUTLIER) cc_final: 0.2574 (m) REVERT: A 402 ARG cc_start: 0.7726 (mpt180) cc_final: 0.7330 (mtt-85) REVERT: A 456 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: A 486 MET cc_start: 0.7575 (ptt) cc_final: 0.7021 (ptp) REVERT: A 493 LYS cc_start: 0.7842 (mmmm) cc_final: 0.7405 (ptpt) REVERT: A 875 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7318 (mt) REVERT: A 886 LYS cc_start: 0.6958 (mttt) cc_final: 0.6674 (mmtt) REVERT: A 913 ARG cc_start: 0.4614 (OUTLIER) cc_final: 0.4205 (ptm160) REVERT: A 922 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8767 (tttm) REVERT: A 924 MET cc_start: 0.8379 (ttm) cc_final: 0.8093 (ttt) REVERT: B 63 GLU cc_start: 0.8366 (mp0) cc_final: 0.8067 (mp0) REVERT: B 75 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8139 (tttt) REVERT: B 358 GLU cc_start: 0.8503 (pm20) cc_final: 0.7992 (tt0) REVERT: C 23 GLN cc_start: 0.7468 (mt0) cc_final: 0.7177 (mt0) REVERT: C 272 LYS cc_start: 0.8000 (ptpp) cc_final: 0.7385 (mtpp) REVERT: C 287 ILE cc_start: 0.8896 (mt) cc_final: 0.8669 (mt) REVERT: C 288 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7447 (tp-100) outliers start: 34 outliers final: 16 residues processed: 110 average time/residue: 0.4749 time to fit residues: 55.7120 Evaluate side-chains 100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 86 SER 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 306 ILE Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 81 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 ASN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS C 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.165548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119349 restraints weight = 10942.609| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.97 r_work: 0.3307 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8583 Z= 0.108 Angle : 0.479 6.064 11573 Z= 0.251 Chirality : 0.038 0.157 1234 Planarity : 0.003 0.033 1500 Dihedral : 4.237 30.851 1144 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.40 % Allowed : 23.57 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.27), residues: 1016 helix: 2.00 (0.22), residues: 562 sheet: 0.80 (0.65), residues: 76 loop : -0.75 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 863 TYR 0.015 0.001 TYR B 304 PHE 0.012 0.001 PHE A 662 TRP 0.003 0.001 TRP A 434 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 8574) covalent geometry : angle 0.47660 / 0.25 (11567) hydrogen bonds : bond 0.03893 / 2.52 ( 428) hydrogen bonds : angle 3.97663 / 2.86 ( 1239) metal coordination : bond 0.01578 / 1.12 ( 9) metal coordination : angle 1.97615 / 1.01 ( 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 117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.248 Fit side-chains REVERT: A 342 SER cc_start: 0.3079 (OUTLIER) cc_final: 0.2507 (m) REVERT: A 402 ARG cc_start: 0.7716 (mpt180) cc_final: 0.7358 (mtt-85) REVERT: A 456 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: A 486 MET cc_start: 0.7546 (ptt) cc_final: 0.7012 (ptp) REVERT: A 493 LYS cc_start: 0.7857 (mmmm) cc_final: 0.7409 (ptpt) REVERT: A 879 GLU cc_start: 0.6414 (pt0) cc_final: 0.6214 (tt0) REVERT: A 886 LYS cc_start: 0.6955 (mttt) cc_final: 0.6673 (mmtt) REVERT: A 913 ARG cc_start: 0.4626 (OUTLIER) cc_final: 0.4275 (ptm160) REVERT: B 63 GLU cc_start: 0.8403 (mp0) cc_final: 0.8114 (mp0) REVERT: B 75 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8131 (tttt) REVERT: B 358 GLU cc_start: 0.8491 (pm20) cc_final: 0.7990 (tt0) REVERT: C 23 GLN cc_start: 0.7472 (mt0) cc_final: 0.7194 (mt0) REVERT: C 272 LYS cc_start: 0.8068 (ptpp) cc_final: 0.7471 (mtpp) REVERT: C 288 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7455 (tp-100) outliers start: 31 outliers final: 14 residues processed: 112 average time/residue: 0.5028 time to fit residues: 59.9274 Evaluate side-chains 98 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 86 SER 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 306 ILE Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN B 58 HIS C 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.164817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118741 restraints weight = 10905.568| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.92 r_work: 0.3298 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8583 Z= 0.120 Angle : 0.484 6.413 11573 Z= 0.253 Chirality : 0.039 0.156 1234 Planarity : 0.003 0.032 1500 Dihedral : 4.239 29.862 1144 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.96 % Allowed : 24.23 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.27), residues: 1016 helix: 1.94 (0.22), residues: 562 sheet: 0.67 (0.60), residues: 86 loop : -0.67 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 863 TYR 0.021 0.001 TYR A 740 PHE 0.013 0.001 PHE A 662 TRP 0.005 0.001 TRP C 313 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8574) covalent geometry : angle 0.48169 / 0.25 (11567) hydrogen bonds : bond 0.03924 / 2.54 ( 428) hydrogen bonds : angle 3.98353 / 2.85 ( 1239) metal coordination : bond 0.01275 / 0.90 ( 9) metal coordination : angle 2.01802 / 1.03 ( 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 109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.214 Fit side-chains REVERT: A 342 SER cc_start: 0.3108 (OUTLIER) cc_final: 0.2520 (m) REVERT: A 402 ARG cc_start: 0.7664 (mpt180) cc_final: 0.7315 (mtt-85) REVERT: A 456 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: A 486 MET cc_start: 0.7528 (ptt) cc_final: 0.6988 (ptp) REVERT: A 493 LYS cc_start: 0.7822 (mmmm) cc_final: 0.7409 (ptpt) REVERT: A 886 LYS cc_start: 0.7097 (mttt) cc_final: 0.6789 (mmtt) REVERT: A 913 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.4328 (ptm160) REVERT: B 63 GLU cc_start: 0.8390 (mp0) cc_final: 0.8114 (mp0) REVERT: B 75 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8111 (tttt) REVERT: B 358 GLU cc_start: 0.8533 (pm20) cc_final: 0.8091 (tt0) REVERT: C 23 GLN cc_start: 0.7422 (mt0) cc_final: 0.7152 (mt0) REVERT: C 272 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7538 (mtpp) REVERT: C 288 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7516 (tp-100) outliers start: 27 outliers final: 15 residues processed: 105 average time/residue: 0.4877 time to fit residues: 54.6404 Evaluate side-chains 98 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 87 optimal weight: 0.0270 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS C 288 GLN C 321 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.165098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119110 restraints weight = 10998.715| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.94 r_work: 0.3300 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8583 Z= 0.112 Angle : 0.483 6.271 11573 Z= 0.253 Chirality : 0.038 0.154 1234 Planarity : 0.003 0.032 1500 Dihedral : 4.161 29.432 1143 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.74 % Allowed : 25.00 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.27), residues: 1016 helix: 1.99 (0.22), residues: 563 sheet: 0.69 (0.60), residues: 86 loop : -0.61 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 863 TYR 0.016 0.001 TYR B 304 PHE 0.013 0.001 PHE A 662 TRP 0.012 0.001 TRP C 313 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8574) covalent geometry : angle 0.48129 / 0.25 (11567) hydrogen bonds : bond 0.03824 / 2.49 ( 428) hydrogen bonds : angle 3.94112 / 2.82 ( 1239) metal coordination : bond 0.01225 / 0.87 ( 9) metal coordination : angle 1.87272 / 0.95 ( 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 106 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.215 Fit side-chains REVERT: A 342 SER cc_start: 0.2969 (OUTLIER) cc_final: 0.2380 (m) REVERT: A 402 ARG cc_start: 0.7679 (mpt180) cc_final: 0.7319 (mtt-85) REVERT: A 456 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: A 486 MET cc_start: 0.7499 (ptt) cc_final: 0.6934 (ptp) REVERT: A 493 LYS cc_start: 0.7794 (mmmm) cc_final: 0.7414 (ptpt) REVERT: A 879 GLU cc_start: 0.7106 (tt0) cc_final: 0.6452 (tp30) REVERT: A 886 LYS cc_start: 0.7129 (mttt) cc_final: 0.6818 (mmtt) REVERT: A 913 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.4327 (ptm160) REVERT: B 63 GLU cc_start: 0.8384 (mp0) cc_final: 0.8100 (mp0) REVERT: B 75 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8143 (tttt) REVERT: B 358 GLU cc_start: 0.8491 (pm20) cc_final: 0.8082 (tt0) REVERT: C 23 GLN cc_start: 0.7483 (mt0) cc_final: 0.7219 (mt0) REVERT: C 272 LYS cc_start: 0.8103 (ptpp) cc_final: 0.7558 (mtpp) REVERT: C 288 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7209 (tm130) outliers start: 25 outliers final: 15 residues processed: 102 average time/residue: 0.5394 time to fit residues: 58.4223 Evaluate side-chains 96 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 0.0000 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS B 93 GLN C 288 GLN C 321 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.165585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119837 restraints weight = 10964.631| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.93 r_work: 0.3312 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.098 | | 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) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8583 Z= 0.100 Angle : 0.472 6.326 11573 Z= 0.247 Chirality : 0.038 0.153 1234 Planarity : 0.003 0.033 1500 Dihedral : 4.085 29.336 1143 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.74 % Allowed : 24.56 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.27), residues: 1016 helix: 2.04 (0.22), residues: 563 sheet: 0.72 (0.61), residues: 86 loop : -0.58 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 900 TYR 0.020 0.001 TYR A 740 PHE 0.012 0.001 PHE A 662 TRP 0.009 0.001 TRP C 313 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 8574) covalent geometry : angle 0.47050 / 0.25 (11567) hydrogen bonds : bond 0.03648 / 2.38 ( 428) hydrogen bonds : angle 3.90156 / 2.80 ( 1239) metal coordination : bond 0.00937 / 0.66 ( 9) metal coordination : angle 1.52843 / 0.76 ( 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 109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.231 Fit side-chains REVERT: A 342 SER cc_start: 0.2895 (OUTLIER) cc_final: 0.2342 (m) REVERT: A 402 ARG cc_start: 0.7619 (mpt180) cc_final: 0.7292 (mtt-85) REVERT: A 456 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: A 486 MET cc_start: 0.7430 (ptt) cc_final: 0.6851 (ptp) REVERT: A 493 LYS cc_start: 0.7801 (mmmm) cc_final: 0.7416 (ptpt) REVERT: A 879 GLU cc_start: 0.7038 (tt0) cc_final: 0.6390 (tp30) REVERT: A 886 LYS cc_start: 0.7066 (mttt) cc_final: 0.6780 (mmtt) REVERT: A 913 ARG cc_start: 0.4739 (OUTLIER) cc_final: 0.4384 (ptm160) REVERT: A 924 MET cc_start: 0.8355 (ttm) cc_final: 0.8053 (ttt) REVERT: B 63 GLU cc_start: 0.8438 (mp0) cc_final: 0.8171 (mp0) REVERT: B 75 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8129 (tttt) REVERT: B 127 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7208 (mtm180) REVERT: B 358 GLU cc_start: 0.8476 (pm20) cc_final: 0.8082 (tt0) REVERT: C 23 GLN cc_start: 0.7466 (mt0) cc_final: 0.7211 (mt0) REVERT: C 272 LYS cc_start: 0.7984 (ptpp) cc_final: 0.7473 (mtpp) REVERT: C 288 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7233 (tm130) REVERT: C 320 GLU cc_start: 0.5808 (OUTLIER) cc_final: 0.5392 (mm-30) outliers start: 25 outliers final: 16 residues processed: 104 average time/residue: 0.5480 time to fit residues: 60.5184 Evaluate side-chains 102 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 75 LYS 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 306 ILE Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 93 optimal weight: 0.0170 chunk 41 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 33 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS B 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.165589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119977 restraints weight = 10899.229| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.91 r_work: 0.3308 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8583 Z= 0.103 Angle : 0.476 6.380 11573 Z= 0.249 Chirality : 0.038 0.150 1234 Planarity : 0.003 0.038 1500 Dihedral : 4.059 29.021 1143 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.85 % Allowed : 24.56 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.27), residues: 1016 helix: 2.08 (0.22), residues: 563 sheet: 0.71 (0.61), residues: 86 loop : -0.56 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 37 TYR 0.015 0.001 TYR B 304 PHE 0.012 0.001 PHE A 662 TRP 0.006 0.001 TRP C 313 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 8574) covalent geometry : angle 0.47517 / 0.25 (11567) hydrogen bonds : bond 0.03621 / 2.37 ( 428) hydrogen bonds : angle 3.87508 / 2.78 ( 1239) metal coordination : bond 0.00767 / 0.53 ( 9) metal coordination : angle 1.55904 / 0.78 ( 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 111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.191 Fit side-chains REVERT: A 342 SER cc_start: 0.2764 (OUTLIER) cc_final: 0.2223 (m) REVERT: A 402 ARG cc_start: 0.7685 (mpt180) cc_final: 0.7356 (mtt-85) REVERT: A 456 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: A 486 MET cc_start: 0.7415 (ptt) cc_final: 0.6826 (ptp) REVERT: A 493 LYS cc_start: 0.7792 (mmmm) cc_final: 0.7404 (ptpt) REVERT: A 562 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: A 879 GLU cc_start: 0.7134 (tt0) cc_final: 0.6433 (tp30) REVERT: A 886 LYS cc_start: 0.7085 (mttt) cc_final: 0.6819 (mmtt) REVERT: A 913 ARG cc_start: 0.4851 (OUTLIER) cc_final: 0.4513 (ptm160) REVERT: A 924 MET cc_start: 0.8373 (ttm) cc_final: 0.8068 (ttt) REVERT: B 75 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8142 (tttt) REVERT: B 127 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7201 (mtm180) REVERT: B 358 GLU cc_start: 0.8476 (pm20) cc_final: 0.8080 (tt0) REVERT: C 23 GLN cc_start: 0.7465 (mt0) cc_final: 0.7203 (mt0) REVERT: C 272 LYS cc_start: 0.7980 (ptpp) cc_final: 0.7494 (mtpp) REVERT: C 288 GLN cc_start: 0.7787 (tp40) cc_final: 0.7156 (tm130) REVERT: C 320 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.5348 (mm-30) outliers start: 26 outliers final: 15 residues processed: 106 average time/residue: 0.5251 time to fit residues: 59.1533 Evaluate side-chains 100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 813 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 75 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS A 656 HIS B 58 HIS B 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.164747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.118838 restraints weight = 10913.977| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.92 r_work: 0.3298 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8583 Z= 0.110 Angle : 0.479 6.608 11573 Z= 0.250 Chirality : 0.038 0.152 1234 Planarity : 0.003 0.040 1500 Dihedral : 4.084 27.815 1143 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.30 % Allowed : 24.89 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.27), residues: 1016 helix: 2.06 (0.22), residues: 565 sheet: 0.56 (0.60), residues: 87 loop : -0.53 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 900 TYR 0.020 0.001 TYR A 740 PHE 0.012 0.001 PHE A 662 TRP 0.005 0.001 TRP A 749 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8574) covalent geometry : angle 0.47648 / 0.25 (11567) hydrogen bonds : bond 0.03714 / 2.42 ( 428) hydrogen bonds : angle 3.89377 / 2.79 ( 1239) metal coordination : bond 0.00631 / 0.44 ( 9) metal coordination : angle 2.23177 / 1.17 ( 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 102 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.318 Fit side-chains REVERT: A 342 SER cc_start: 0.2660 (OUTLIER) cc_final: 0.2112 (m) REVERT: A 402 ARG cc_start: 0.7832 (mpt180) cc_final: 0.7476 (mtt-85) REVERT: A 456 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: A 486 MET cc_start: 0.7416 (ptt) cc_final: 0.6788 (ptp) REVERT: A 493 LYS cc_start: 0.7832 (mmmm) cc_final: 0.7468 (ptpt) REVERT: A 562 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: A 879 GLU cc_start: 0.7246 (tt0) cc_final: 0.6599 (tp30) REVERT: A 886 LYS cc_start: 0.7104 (mttt) cc_final: 0.6835 (mmtt) REVERT: A 913 ARG cc_start: 0.4972 (OUTLIER) cc_final: 0.4658 (ptm160) REVERT: A 924 MET cc_start: 0.8389 (ttm) cc_final: 0.8083 (ttt) REVERT: B 75 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8146 (tttt) REVERT: B 127 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7240 (mtm-85) REVERT: B 358 GLU cc_start: 0.8489 (pm20) cc_final: 0.8092 (tt0) REVERT: C 23 GLN cc_start: 0.7461 (mt0) cc_final: 0.7209 (mt0) REVERT: C 272 LYS cc_start: 0.8005 (ptpp) cc_final: 0.7592 (mtpp) REVERT: C 288 GLN cc_start: 0.7927 (tp40) cc_final: 0.7188 (tm130) REVERT: C 320 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.5543 (mm-30) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 0.5290 time to fit residues: 55.8063 Evaluate side-chains 99 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 0.7980 chunk 7 optimal weight: 0.0000 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 HIS A 656 HIS A 773 GLN B 58 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.165187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119703 restraints weight = 10887.422| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.90 r_work: 0.3316 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8583 Z= 0.102 Angle : 0.464 6.533 11573 Z= 0.243 Chirality : 0.038 0.148 1234 Planarity : 0.003 0.039 1500 Dihedral : 3.999 27.141 1143 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.63 % Allowed : 24.34 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.27), residues: 1016 helix: 2.11 (0.22), residues: 565 sheet: 0.63 (0.60), residues: 86 loop : -0.52 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 37 TYR 0.015 0.001 TYR B 304 PHE 0.010 0.001 PHE A 662 TRP 0.005 0.001 TRP C 313 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 8574) covalent geometry : angle 0.46388 / 0.24 (11567) hydrogen bonds : bond 0.03544 / 2.32 ( 428) hydrogen bonds : angle 3.83480 / 2.75 ( 1239) metal coordination : bond 0.00439 / 0.29 ( 9) metal coordination : angle 1.03871 / 0.56 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3137.25 seconds wall clock time: 54 minutes 3.69 seconds (3243.69 seconds total)