Starting phenix.real_space_refine on Thu Jul 2 11:35:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6k_36921/07_2026/8k6k_36921.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6k_36921/07_2026/8k6k_36921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k6k_36921/07_2026/8k6k_36921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6k_36921/07_2026/8k6k_36921.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k6k_36921/07_2026/8k6k_36921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6k_36921/07_2026/8k6k_36921.map" } resolution = 2.4 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= 0.017 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 Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5416 2.51 5 N 1487 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s 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: 8593 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4156 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 502} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 388} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1} Unresolved non-hydrogen planarities: 25 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1759 SG CYS A 226 52.458 65.121 35.741 1.00 68.72 S ATOM 1730 SG CYS A 222 53.553 69.898 31.737 1.00 73.94 S ATOM 1690 SG CYS A 216 51.999 64.698 29.070 1.00 67.33 S Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8593 At special positions: 0 Unit cell: (104.06, 109.22, 76.54, 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) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1636 8.00 N 1487 7.00 C 5416 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 323.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 43.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.597A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.787A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.127A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 351 through 354 removed outlier: 4.525A pdb=" N ASP A 354 " --> pdb=" O ASN A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.550A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.146A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.837A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 522 through 542 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 101 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 51 through 57 removed outlier: 4.225A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.536A pdb=" N GLY C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 142 removed outlier: 3.861A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.654A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 Processing helix chain 'C' and resid 279 through 292 removed outlier: 3.643A pdb=" N SER C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.901A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 445 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.752A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.752A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER A 7 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA A 282 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.747A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.339A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP A 404 " --> pdb=" O ASN A 369 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY A 328 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET A 469 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.164A pdb=" N ASN A 320 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 482 " --> pdb=" O ASN A 320 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA8, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA9, first strand: chain 'C' and resid 387 through 388 338 hydrogen bonds defined for protein. 921 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: 1.54 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8734 1.76 - 2.29: 90 2.29 - 2.83: 0 2.83 - 3.37: 0 3.37 - 3.91: 3 Bond restraints: 8827 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.906 -1.606 2.00e-02 2.50e+03 6.45e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.814 -1.556 2.00e-02 2.50e+03 6.05e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.783 -1.550 2.00e-02 2.50e+03 6.00e+03 bond pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " ideal model delta sigma weight residual 1.334 1.479 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C2C HEC C 501 " pdb=" C3C HEC C 501 " ideal model delta sigma weight residual 1.334 1.477 -0.143 2.00e-02 2.50e+03 5.12e+01 ... (remaining 8822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.48: 12051 9.48 - 18.96: 6 18.96 - 28.44: 0 28.44 - 37.92: 8 37.92 - 47.40: 2 Bond angle restraints: 12067 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.35 47.40 3.00e+00 1.11e-01 2.50e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 68.12 44.47 3.00e+00 1.11e-01 2.20e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 69.24 34.02 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 69.99 33.26 3.00e+00 1.11e-01 1.23e+02 angle pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 74.86 41.84 33.02 3.00e+00 1.11e-01 1.21e+02 ... (remaining 12062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 4458 17.07 - 34.14: 532 34.14 - 51.21: 153 51.21 - 68.29: 60 68.29 - 85.36: 18 Dihedral angle restraints: 5221 sinusoidal: 2072 harmonic: 3149 Sorted by residual: dihedral pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -0.18 60.18 2 1.00e+01 1.00e-02 3.61e+01 dihedral pdb=" C2B HEC C 502 " pdb=" C3B HEC C 502 " pdb=" CAB HEC C 502 " pdb=" CBB HEC C 502 " ideal model delta sinusoidal sigma weight residual 60.00 0.04 59.96 2 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" C2B HEC C 503 " pdb=" C3B HEC C 503 " pdb=" CAB HEC C 503 " pdb=" CBB HEC C 503 " ideal model delta sinusoidal sigma weight residual -120.00 -179.34 59.34 2 1.00e+01 1.00e-02 3.55e+01 ... (remaining 5218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.432: 1275 3.432 - 6.865: 0 6.865 - 10.297: 0 10.297 - 13.729: 0 13.729 - 17.162: 1 Chirality restraints: 1276 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.39 17.16 2.00e-01 2.50e+01 7.36e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CB THR C 328 " pdb=" CA THR C 328 " pdb=" OG1 THR C 328 " pdb=" CG2 THR C 328 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1273 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " -0.060 2.00e-02 2.50e+03 1.83e-01 1.00e+03 pdb=" C1M U10 C 504 " -0.257 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " -0.001 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " 0.103 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " -0.076 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.062 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.075 2.00e-02 2.50e+03 pdb=" C7 U10 C 504 " 0.170 2.00e-02 2.50e+03 pdb=" O2 U10 C 504 " -0.030 2.00e-02 2.50e+03 pdb=" O3 U10 C 504 " 0.303 2.00e-02 2.50e+03 pdb=" O4 U10 C 504 " -0.411 2.00e-02 2.50e+03 pdb=" O5 U10 C 504 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 U10 C 504 " 0.078 2.00e-02 2.50e+03 6.55e-02 5.36e+01 pdb=" C18 U10 C 504 " -0.101 2.00e-02 2.50e+03 pdb=" C19 U10 C 504 " -0.032 2.00e-02 2.50e+03 pdb=" C20 U10 C 504 " -0.008 2.00e-02 2.50e+03 pdb=" C21 U10 C 504 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 U10 C 504 " 0.044 2.00e-02 2.50e+03 3.66e-02 1.67e+01 pdb=" C23 U10 C 504 " -0.059 2.00e-02 2.50e+03 pdb=" C24 U10 C 504 " -0.011 2.00e-02 2.50e+03 pdb=" C25 U10 C 504 " -0.007 2.00e-02 2.50e+03 pdb=" C26 U10 C 504 " 0.033 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 251 2.70 - 3.25: 8478 3.25 - 3.80: 15245 3.80 - 4.35: 20377 4.35 - 4.90: 32745 Nonbonded interactions: 77096 Sorted by model distance: nonbonded pdb=" O LEU C 154 " pdb=" OG SER C 159 " model vdw 2.147 3.040 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O SER A 517 " model vdw 2.208 3.040 nonbonded pdb=" S3 F3S A 602 " pdb="FE3 F3S A 602 " model vdw 2.254 2.688 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.255 2.688 ... (remaining 77091 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.090 Find NCS groups from input model: 0.040 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 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 : 0.031 1.606 8842 Z= 1.630 Angle : 1.343 47.404 12076 Z= 0.495 Chirality : 0.483 17.162 1276 Planarity : 0.007 0.183 1566 Dihedral : 17.798 85.357 3211 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.15 % Allowed : 18.33 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.87 (0.26), residues: 1082 helix: 1.69 (0.28), residues: 380 sheet: 0.66 (0.56), residues: 84 loop : -0.09 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 52 TYR 0.011 0.001 TYR A 443 PHE 0.016 0.001 PHE A 80 TRP 0.007 0.001 TRP A 338 HIS 0.005 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.03029 / 1.51 ( 8827) covalent geometry : angle 1.33260 / 0.50 (12067) hydrogen bonds : bond 0.15747 / 11.61 ( 331) hydrogen bonds : angle 6.92057 / 4.84 ( 921) metal coordination : bond 0.00163 / 0.08 ( 3) metal coordination : angle 6.25523 / 3.13 ( 9) Misc. bond : bond 0.17079 / 9.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 MET cc_start: 0.8786 (tpt) cc_final: 0.7957 (tpt) outliers start: 19 outliers final: 16 residues processed: 115 average time/residue: 0.5875 time to fit residues: 71.9919 Evaluate side-chains 112 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 303 ASN A 306 ASN A 505 ASN A 539 ASN C 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.077180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.060829 restraints weight = 13130.884| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.89 r_work: 0.2583 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.185 8842 Z= 0.245 Angle : 1.603 81.775 12076 Z= 0.517 Chirality : 0.095 2.966 1276 Planarity : 0.005 0.063 1566 Dihedral : 11.013 87.473 1308 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.83 % Allowed : 16.97 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1082 helix: 1.81 (0.28), residues: 383 sheet: 0.25 (0.56), residues: 84 loop : -0.10 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.011 0.001 TYR A 79 PHE 0.018 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 ( 8827) covalent geometry : angle 1.40199 / 0.51 (12067) hydrogen bonds : bond 0.03990 / 2.72 ( 331) hydrogen bonds : angle 5.56185 / 3.89 ( 921) metal coordination : bond 0.00731 / 0.37 ( 3) metal coordination : angle 28.51103 / 14.24 ( 9) Misc. bond : bond 0.06565 / 4.30 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8559 (tptm) REVERT: B 136 GLU cc_start: 0.7991 (pm20) cc_final: 0.7581 (pm20) REVERT: C 118 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8629 (tpt) REVERT: C 395 MET cc_start: 0.8886 (ttp) cc_final: 0.8515 (ttt) outliers start: 25 outliers final: 11 residues processed: 123 average time/residue: 0.6007 time to fit residues: 78.5725 Evaluate side-chains 118 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 ASN A 306 ASN A 505 ASN B 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.078005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.062280 restraints weight = 13594.593| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 1.90 r_work: 0.2615 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 8842 Z= 0.209 Angle : 1.445 70.213 12076 Z= 0.448 Chirality : 0.057 1.248 1276 Planarity : 0.005 0.054 1566 Dihedral : 10.591 89.830 1297 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.83 % Allowed : 16.40 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.91 (0.26), residues: 1082 helix: 1.86 (0.28), residues: 382 sheet: 0.08 (0.57), residues: 84 loop : -0.08 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 94 TYR 0.012 0.001 TYR A 443 PHE 0.016 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 ( 8827) covalent geometry : angle 1.18588 / 0.44 (12067) hydrogen bonds : bond 0.03607 / 2.44 ( 331) hydrogen bonds : angle 5.33074 / 3.73 ( 921) metal coordination : bond 0.00394 / 0.21 ( 3) metal coordination : angle 30.29197 / 14.74 ( 9) Misc. bond : bond 0.05631 / 3.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8536 (tptm) REVERT: B 136 GLU cc_start: 0.8018 (pm20) cc_final: 0.7550 (pm20) REVERT: C 118 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8663 (tpt) outliers start: 25 outliers final: 10 residues processed: 125 average time/residue: 0.5987 time to fit residues: 79.4889 Evaluate side-chains 117 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 ASN A 539 ASN B 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.078105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.060798 restraints weight = 13500.201| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.03 r_work: 0.2569 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 8842 Z= 0.181 Angle : 1.454 84.422 12076 Z= 0.418 Chirality : 0.060 1.407 1276 Planarity : 0.005 0.053 1566 Dihedral : 10.432 88.768 1296 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.38 % Allowed : 16.74 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.90 (0.26), residues: 1082 helix: 1.83 (0.28), residues: 384 sheet: 0.01 (0.57), residues: 84 loop : -0.07 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 94 TYR 0.012 0.001 TYR A 443 PHE 0.016 0.001 PHE A 270 TRP 0.007 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 8827) covalent geometry : angle 1.07429 / 0.41 (12067) hydrogen bonds : bond 0.03516 / 2.37 ( 331) hydrogen bonds : angle 5.21776 / 3.65 ( 921) metal coordination : bond 0.00727 / 0.37 ( 3) metal coordination : angle 35.92625 / 19.63 ( 9) Misc. bond : bond 0.05788 / 3.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7975 (pm20) cc_final: 0.7387 (pm20) REVERT: C 118 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8728 (tpt) outliers start: 21 outliers final: 10 residues processed: 118 average time/residue: 0.5263 time to fit residues: 66.2366 Evaluate side-chains 116 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.076918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.060208 restraints weight = 13479.040| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 1.96 r_work: 0.2558 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 8842 Z= 0.196 Angle : 1.463 84.056 12076 Z= 0.421 Chirality : 0.061 1.430 1276 Planarity : 0.005 0.053 1566 Dihedral : 10.379 88.388 1294 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.26 % Allowed : 16.97 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.87 (0.26), residues: 1082 helix: 1.86 (0.28), residues: 383 sheet: -0.07 (0.57), residues: 84 loop : -0.10 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 386 TYR 0.012 0.001 TYR A 443 PHE 0.019 0.001 PHE A 80 TRP 0.008 0.001 TRP B 128 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 8827) covalent geometry : angle 1.08117 / 0.41 (12067) hydrogen bonds : bond 0.03551 / 2.39 ( 331) hydrogen bonds : angle 5.19785 / 3.64 ( 921) metal coordination : bond 0.00434 / 0.22 ( 3) metal coordination : angle 36.09655 / 19.61 ( 9) Misc. bond : bond 0.06862 / 3.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7989 (pm20) cc_final: 0.7453 (pm20) REVERT: C 118 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8748 (tpt) outliers start: 20 outliers final: 10 residues processed: 118 average time/residue: 0.5155 time to fit residues: 64.5600 Evaluate side-chains 115 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN B 123 GLN C 89 HIS C 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.078920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.061869 restraints weight = 13441.106| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.03 r_work: 0.2589 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 8842 Z= 0.159 Angle : 1.442 84.046 12076 Z= 0.411 Chirality : 0.060 1.433 1276 Planarity : 0.004 0.051 1566 Dihedral : 10.103 87.595 1294 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.81 % Allowed : 17.31 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1082 helix: 1.89 (0.28), residues: 390 sheet: -0.05 (0.59), residues: 84 loop : -0.13 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.013 0.001 TYR A 443 PHE 0.015 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8827) covalent geometry : angle 1.06311 / 0.40 (12067) hydrogen bonds : bond 0.03189 / 2.13 ( 331) hydrogen bonds : angle 5.06298 / 3.55 ( 921) metal coordination : bond 0.00384 / 0.19 ( 3) metal coordination : angle 35.70725 / 19.41 ( 9) Misc. bond : bond 0.05539 / 2.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7980 (pm20) cc_final: 0.7376 (pm20) REVERT: C 118 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8735 (tpt) outliers start: 16 outliers final: 10 residues processed: 121 average time/residue: 0.5303 time to fit residues: 68.3140 Evaluate side-chains 115 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 73 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 123 GLN C 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.080134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.063026 restraints weight = 13778.014| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.07 r_work: 0.2616 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 8842 Z= 0.147 Angle : 1.384 83.648 12076 Z= 0.405 Chirality : 0.059 1.427 1276 Planarity : 0.004 0.049 1566 Dihedral : 9.965 88.333 1293 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.04 % Allowed : 17.19 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.26), residues: 1082 helix: 1.93 (0.28), residues: 394 sheet: -0.05 (0.59), residues: 84 loop : -0.12 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 205 TYR 0.014 0.001 TYR A 96 PHE 0.015 0.001 PHE B 183 TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8827) covalent geometry : angle 1.05769 / 0.40 (12067) hydrogen bonds : bond 0.02985 / 1.98 ( 331) hydrogen bonds : angle 4.93934 / 3.46 ( 921) metal coordination : bond 0.00382 / 0.19 ( 3) metal coordination : angle 32.74102 / 17.54 ( 9) Misc. bond : bond 0.04265 / 1.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7921 (pm20) cc_final: 0.7361 (pm20) REVERT: B 164 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.6453 (m-70) REVERT: C 118 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8744 (tpt) REVERT: C 143 LYS cc_start: 0.8969 (ptmm) cc_final: 0.8587 (mmtm) outliers start: 18 outliers final: 8 residues processed: 118 average time/residue: 0.5903 time to fit residues: 74.2502 Evaluate side-chains 115 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 351 ASN A 539 ASN C 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.063517 restraints weight = 13541.478| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.06 r_work: 0.2625 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 8842 Z= 0.144 Angle : 1.346 83.765 12076 Z= 0.404 Chirality : 0.059 1.435 1276 Planarity : 0.004 0.049 1566 Dihedral : 9.889 88.515 1291 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.47 % Allowed : 18.10 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.90 (0.26), residues: 1082 helix: 1.90 (0.27), residues: 396 sheet: 0.04 (0.60), residues: 84 loop : -0.17 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.013 0.001 TYR A 443 PHE 0.014 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8827) covalent geometry : angle 1.05768 / 0.40 (12067) hydrogen bonds : bond 0.02960 / 1.97 ( 331) hydrogen bonds : angle 4.89228 / 3.43 ( 921) metal coordination : bond 0.00324 / 0.16 ( 3) metal coordination : angle 30.49070 / 15.80 ( 9) Misc. bond : bond 0.04147 / 1.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7962 (pm20) cc_final: 0.7407 (pm20) REVERT: B 164 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.6381 (m-70) REVERT: B 183 PHE cc_start: 0.6699 (OUTLIER) cc_final: 0.5220 (p90) REVERT: C 118 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8767 (tpt) REVERT: C 143 LYS cc_start: 0.8974 (ptmm) cc_final: 0.8606 (mmtm) outliers start: 13 outliers final: 7 residues processed: 119 average time/residue: 0.6492 time to fit residues: 82.0375 Evaluate side-chains 116 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0570 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.064706 restraints weight = 13385.877| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.06 r_work: 0.2646 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 8842 Z= 0.139 Angle : 1.326 83.863 12076 Z= 0.401 Chirality : 0.059 1.427 1276 Planarity : 0.004 0.051 1566 Dihedral : 9.826 88.520 1291 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.36 % Allowed : 18.78 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.98 (0.26), residues: 1082 helix: 2.00 (0.28), residues: 390 sheet: 0.12 (0.59), residues: 84 loop : -0.12 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.013 0.001 TYR A 443 PHE 0.014 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.005 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8827) covalent geometry : angle 1.05634 / 0.40 (12067) hydrogen bonds : bond 0.02824 / 1.88 ( 331) hydrogen bonds : angle 4.83193 / 3.40 ( 921) metal coordination : bond 0.00319 / 0.16 ( 3) metal coordination : angle 29.36452 / 14.94 ( 9) Misc. bond : bond 0.03647 / 1.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7989 (pm20) cc_final: 0.7427 (pm20) REVERT: B 164 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.6379 (m-70) REVERT: B 183 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.4817 (p90) REVERT: C 118 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8735 (tpt) REVERT: C 143 LYS cc_start: 0.8974 (ptmm) cc_final: 0.8617 (mmtp) outliers start: 12 outliers final: 7 residues processed: 116 average time/residue: 0.5937 time to fit residues: 73.5479 Evaluate side-chains 117 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 ASN C 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.079619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.062482 restraints weight = 13526.457| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.05 r_work: 0.2604 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 8842 Z= 0.164 Angle : 1.337 83.919 12076 Z= 0.410 Chirality : 0.060 1.430 1276 Planarity : 0.004 0.048 1566 Dihedral : 10.002 88.742 1291 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.24 % Allowed : 19.12 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 1.00 (0.26), residues: 1082 helix: 2.01 (0.28), residues: 385 sheet: 0.15 (0.59), residues: 84 loop : -0.10 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.011 0.001 TYR A 443 PHE 0.015 0.001 PHE A 270 TRP 0.008 0.001 TRP B 128 HIS 0.005 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 8827) covalent geometry : angle 1.07007 / 0.40 (12067) hydrogen bonds : bond 0.03112 / 2.08 ( 331) hydrogen bonds : angle 4.90459 / 3.45 ( 921) metal coordination : bond 0.00361 / 0.18 ( 3) metal coordination : angle 29.36169 / 14.69 ( 9) Misc. bond : bond 0.04432 / 2.13 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7987 (pm20) cc_final: 0.7431 (pm20) REVERT: B 183 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.4921 (p90) REVERT: C 143 LYS cc_start: 0.8976 (ptmm) cc_final: 0.8624 (mmtp) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.6143 time to fit residues: 74.6457 Evaluate side-chains 113 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 0.0670 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 ASN C 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.065007 restraints weight = 13329.177| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.06 r_work: 0.2652 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 8842 Z= 0.139 Angle : 1.337 83.886 12076 Z= 0.403 Chirality : 0.059 1.419 1276 Planarity : 0.004 0.048 1566 Dihedral : 9.802 87.912 1291 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.02 % Allowed : 19.23 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 0.99 (0.26), residues: 1082 helix: 2.01 (0.27), residues: 391 sheet: 0.19 (0.60), residues: 84 loop : -0.13 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.012 0.001 TYR A 443 PHE 0.013 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.005 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8827) covalent geometry : angle 1.07621 / 0.40 (12067) hydrogen bonds : bond 0.02813 / 1.87 ( 331) hydrogen bonds : angle 4.80952 / 3.39 ( 921) metal coordination : bond 0.00340 / 0.17 ( 3) metal coordination : angle 29.05513 / 14.50 ( 9) Misc. bond : bond 0.06013 / 2.73 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3203.57 seconds wall clock time: 55 minutes 32.40 seconds (3332.40 seconds total)