Starting phenix.real_space_refine on Sun Jun 15 12:32:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9au7_43872/06_2025/9au7_43872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9au7_43872/06_2025/9au7_43872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9au7_43872/06_2025/9au7_43872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9au7_43872/06_2025/9au7_43872.map" model { file = "/net/cci-nas-00/data/ceres_data/9au7_43872/06_2025/9au7_43872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9au7_43872/06_2025/9au7_43872.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 5544 2.51 5 N 1436 2.21 5 O 1565 1.98 5 H 8703 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17304 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 9679 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 24, 'TRANS': 572} Chain breaks: 5 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2934 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 175} Chain: "C" Number of atoms: 4514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4514 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain breaks: 2 Chain: "D" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 177 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Time building chain proxies: 8.10, per 1000 atoms: 0.47 Number of scatterers: 17304 At special positions: 0 Unit cell: (69.01, 107.12, 167.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 1565 8.00 N 1436 7.00 C 5544 6.00 H 8703 1.00 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: 4.60 Conformation dependent library (CDL) restraints added in 1.4 seconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 51.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 116 through 128 removed outlier: 4.004A pdb=" N LYS A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 201 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 226 through 253 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.257A pdb=" N LEU A 307 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 310 through 323 Proline residue: A 317 - end of helix removed outlier: 3.609A pdb=" N ILE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.841A pdb=" N PHE A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.625A pdb=" N LYS A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.771A pdb=" N THR A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 460 through 475 removed outlier: 4.130A pdb=" N LEU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 481 through 494 Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.627A pdb=" N ASN A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 535 through 541 removed outlier: 5.637A pdb=" N PHE A 539 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 557 Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 569 through 576 removed outlier: 3.754A pdb=" N PHE A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 Processing helix chain 'A' and resid 603 through 619 Processing helix chain 'A' and resid 626 through 642 Processing helix chain 'A' and resid 650 through 664 Processing helix chain 'A' and resid 667 through 688 removed outlier: 3.620A pdb=" N LEU A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 718 through 734 Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 769 through 784 Processing helix chain 'B' and resid 23 through 30 removed outlier: 4.023A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.739A pdb=" N TYR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.513A pdb=" N LEU C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.957A pdb=" N LEU C 172 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.234A pdb=" N ILE B 38 " --> pdb=" O HIS B 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 81 removed outlier: 6.714A pdb=" N LEU B 115 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 9 Processing sheet with id=AA4, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 79 removed outlier: 8.049A pdb=" N ILE C 71 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N VAL C 47 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN C 73 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY C 45 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N THR C 75 " --> pdb=" O MET C 43 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET C 43 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU C 77 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 41 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY C 38 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 155 through 159 removed outlier: 3.624A pdb=" N LEU C 182 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 180 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU C 177 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 200 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 227 through 239 removed outlier: 6.929A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 279 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 209 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 277 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU C 211 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN C 275 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 213 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU C 273 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG C 215 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU C 271 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU C 217 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS C 269 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 227 through 239 removed outlier: 6.929A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 279 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 209 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 277 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU C 211 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN C 275 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 213 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU C 273 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG C 215 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU C 271 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU C 217 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS C 269 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C 272 " --> pdb=" O LEU C 292 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1329 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: 5.77 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8672 1.03 - 1.23: 87 1.23 - 1.43: 3537 1.43 - 1.62: 5107 1.62 - 1.82: 81 Bond restraints: 17484 Sorted by residual: bond pdb=" C ASN B 135 " pdb=" O ASN B 135 " ideal model delta sigma weight residual 1.242 1.202 0.040 1.16e-02 7.43e+03 1.19e+01 bond pdb=" N ILE C 250 " pdb=" CA ILE C 250 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.40e+00 bond pdb=" N SER C 208 " pdb=" H SER C 208 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" N LYS B 27 " pdb=" H LYS B 27 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" N GLU C 210 " pdb=" CA GLU C 210 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.43e+00 ... (remaining 17479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 31145 1.76 - 3.51: 485 3.51 - 5.27: 60 5.27 - 7.02: 2 7.02 - 8.78: 3 Bond angle restraints: 31695 Sorted by residual: angle pdb=" N PHE C 258 " pdb=" CA PHE C 258 " pdb=" C PHE C 258 " ideal model delta sigma weight residual 112.54 103.84 8.70 1.22e+00 6.72e-01 5.09e+01 angle pdb=" N ASP D 467 " pdb=" CA ASP D 467 " pdb=" C ASP D 467 " ideal model delta sigma weight residual 111.07 106.29 4.78 1.07e+00 8.73e-01 2.00e+01 angle pdb=" CA ASP C 283 " pdb=" C ASP C 283 " pdb=" O ASP C 283 " ideal model delta sigma weight residual 121.54 117.11 4.43 1.16e+00 7.43e-01 1.46e+01 angle pdb=" N HIS A 369 " pdb=" CA HIS A 369 " pdb=" C HIS A 369 " ideal model delta sigma weight residual 113.17 108.57 4.60 1.26e+00 6.30e-01 1.33e+01 angle pdb=" CA ASN B 43 " pdb=" C ASN B 43 " pdb=" O ASN B 43 " ideal model delta sigma weight residual 121.54 117.32 4.22 1.16e+00 7.43e-01 1.32e+01 ... (remaining 31690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7392 17.92 - 35.85: 603 35.85 - 53.77: 164 53.77 - 71.69: 43 71.69 - 89.61: 11 Dihedral angle restraints: 8213 sinusoidal: 4460 harmonic: 3753 Sorted by residual: dihedral pdb=" CD ARG C 256 " pdb=" NE ARG C 256 " pdb=" CZ ARG C 256 " pdb=" NH1 ARG C 256 " ideal model delta sinusoidal sigma weight residual 0.00 56.89 -56.89 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA ILE B 95 " pdb=" C ILE B 95 " pdb=" N PRO B 96 " pdb=" CA PRO B 96 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO B 136 " pdb=" C PRO B 136 " pdb=" N GLY B 137 " pdb=" CA GLY B 137 " ideal model delta harmonic sigma weight residual -180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 8210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1084 0.044 - 0.089: 202 0.089 - 0.133: 77 0.133 - 0.178: 10 0.178 - 0.222: 2 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA ILE C 250 " pdb=" N ILE C 250 " pdb=" C ILE C 250 " pdb=" CB ILE C 250 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU A 733 " pdb=" N LEU A 733 " pdb=" C LEU A 733 " pdb=" CB LEU A 733 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA LEU C 211 " pdb=" N LEU C 211 " pdb=" C LEU C 211 " pdb=" CB LEU C 211 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 1372 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 135 " 0.055 2.00e-02 2.50e+03 4.41e-01 2.91e+03 pdb=" CG ASN B 135 " -0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN B 135 " -0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN B 135 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 135 " 0.764 2.00e-02 2.50e+03 pdb="HD22 ASN B 135 " -0.759 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 43 " -0.201 2.00e-02 2.50e+03 2.32e-01 8.04e+02 pdb=" CG ASN B 43 " 0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN B 43 " 0.201 2.00e-02 2.50e+03 pdb=" ND2 ASN B 43 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 43 " 0.346 2.00e-02 2.50e+03 pdb="HD22 ASN B 43 " -0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 459 " 0.166 2.00e-02 2.50e+03 1.86e-01 5.17e+02 pdb=" CG ASN D 459 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN D 459 " -0.164 2.00e-02 2.50e+03 pdb=" ND2 ASN D 459 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 459 " 0.278 2.00e-02 2.50e+03 pdb="HD22 ASN D 459 " -0.273 2.00e-02 2.50e+03 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1360 2.21 - 2.81: 37182 2.81 - 3.40: 47271 3.40 - 4.00: 61047 4.00 - 4.60: 94478 Nonbonded interactions: 241338 Sorted by model distance: nonbonded pdb="HH11 ARG C 11 " pdb=" O VAL C 15 " model vdw 1.612 2.450 nonbonded pdb=" H ASN A 622 " pdb=" OG1 THR A 625 " model vdw 1.612 2.450 nonbonded pdb=" O THR A 711 " pdb=" HG SER A 714 " model vdw 1.626 2.450 nonbonded pdb=" H ARG C 126 " pdb=" OD1 ASP C 132 " model vdw 1.641 2.450 nonbonded pdb=" OE1 GLN A 545 " pdb=" H GLN A 545 " model vdw 1.656 2.450 ... (remaining 241333 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: 2.100 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: 0.300 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.940 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 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 0.040 8781 Z= 0.210 Angle : 0.656 8.781 11887 Z= 0.388 Chirality : 0.043 0.222 1375 Planarity : 0.012 0.414 1505 Dihedral : 14.952 89.613 3242 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.21 % Allowed : 9.40 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1057 helix: 0.74 (0.24), residues: 485 sheet: -0.12 (0.38), residues: 186 loop : -0.43 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.009 0.001 HIS A 618 PHE 0.036 0.002 PHE B 110 TYR 0.021 0.002 TYR A 725 ARG 0.007 0.001 ARG C 296 Details of bonding type rmsd hydrogen bonds : bond 0.12077 ( 459) hydrogen bonds : angle 6.30245 ( 1329) covalent geometry : bond 0.00388 ( 8781) covalent geometry : angle 0.65616 (11887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.7598 (t80) cc_final: 0.7154 (t80) REVERT: A 431 VAL cc_start: 0.5136 (t) cc_final: 0.4917 (t) REVERT: A 533 MET cc_start: 0.6272 (mmm) cc_final: 0.5896 (mmm) REVERT: C 1 MET cc_start: 0.4699 (mmm) cc_final: 0.4498 (mmm) REVERT: C 10 LYS cc_start: 0.7597 (ttpp) cc_final: 0.7059 (ttmm) REVERT: C 78 MET cc_start: 0.5682 (tpt) cc_final: 0.5469 (tpt) REVERT: C 264 GLU cc_start: 0.6777 (mp0) cc_final: 0.6566 (mp0) outliers start: 2 outliers final: 1 residues processed: 187 average time/residue: 0.5148 time to fit residues: 130.6602 Evaluate side-chains 161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.5980 chunk 80 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN C 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.176887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.162120 restraints weight = 42166.216| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.89 r_work: 0.4142 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8781 Z= 0.220 Angle : 0.730 10.330 11887 Z= 0.384 Chirality : 0.045 0.200 1375 Planarity : 0.007 0.100 1505 Dihedral : 5.602 89.321 1146 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 1.96 % Allowed : 10.54 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1057 helix: 0.43 (0.22), residues: 495 sheet: -0.01 (0.38), residues: 183 loop : -0.48 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 490 HIS 0.008 0.002 HIS B 119 PHE 0.036 0.003 PHE A 361 TYR 0.017 0.002 TYR A 338 ARG 0.006 0.001 ARG A 336 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 459) hydrogen bonds : angle 5.34057 ( 1329) covalent geometry : bond 0.00500 ( 8781) covalent geometry : angle 0.72960 (11887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LEU cc_start: 0.4877 (mt) cc_final: 0.4621 (mp) REVERT: A 404 TYR cc_start: 0.7916 (t80) cc_final: 0.7589 (t80) REVERT: A 405 HIS cc_start: 0.6259 (OUTLIER) cc_final: 0.5972 (t70) REVERT: A 512 TYR cc_start: 0.6093 (t80) cc_final: 0.5791 (t80) REVERT: A 533 MET cc_start: 0.6023 (mmm) cc_final: 0.5744 (mmm) REVERT: C 10 LYS cc_start: 0.7870 (ttpp) cc_final: 0.7306 (ttmm) REVERT: C 234 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: C 285 LEU cc_start: 0.5454 (mt) cc_final: 0.5153 (mt) REVERT: D 463 GLU cc_start: 0.6497 (tm-30) cc_final: 0.6209 (tm-30) outliers start: 19 outliers final: 9 residues processed: 190 average time/residue: 0.4897 time to fit residues: 126.5351 Evaluate side-chains 179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 234 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN C 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.174368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.159084 restraints weight = 41812.286| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 3.00 r_work: 0.4097 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 8781 Z= 0.206 Angle : 0.600 8.877 11887 Z= 0.325 Chirality : 0.042 0.165 1375 Planarity : 0.005 0.069 1505 Dihedral : 5.379 89.235 1144 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.07 % Allowed : 13.74 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1057 helix: 0.78 (0.23), residues: 495 sheet: 0.05 (0.38), residues: 187 loop : -0.24 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 280 HIS 0.005 0.001 HIS A 462 PHE 0.050 0.002 PHE B 110 TYR 0.021 0.002 TYR B 73 ARG 0.004 0.001 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 459) hydrogen bonds : angle 5.18967 ( 1329) covalent geometry : bond 0.00473 ( 8781) covalent geometry : angle 0.59950 (11887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7215 (mtpt) cc_final: 0.6999 (mtpt) REVERT: A 404 TYR cc_start: 0.8120 (t80) cc_final: 0.7829 (t80) REVERT: A 405 HIS cc_start: 0.6569 (OUTLIER) cc_final: 0.6324 (t70) REVERT: A 512 TYR cc_start: 0.6509 (t80) cc_final: 0.6279 (t80) REVERT: A 528 ASP cc_start: 0.6283 (OUTLIER) cc_final: 0.5644 (t0) REVERT: A 615 LYS cc_start: 0.7986 (tmmt) cc_final: 0.7519 (tmmt) REVERT: A 721 ARG cc_start: 0.6907 (ttm170) cc_final: 0.6533 (mtm180) REVERT: C 10 LYS cc_start: 0.7881 (ttpp) cc_final: 0.7342 (ttmm) REVERT: C 196 GLU cc_start: 0.5030 (mp0) cc_final: 0.4682 (mp0) REVERT: C 234 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7023 (m-40) REVERT: C 258 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.3734 (m-80) REVERT: C 285 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5519 (mt) outliers start: 20 outliers final: 9 residues processed: 197 average time/residue: 0.5651 time to fit residues: 153.2248 Evaluate side-chains 196 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.175256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.159978 restraints weight = 41921.220| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.99 r_work: 0.4108 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8781 Z= 0.161 Angle : 0.570 5.634 11887 Z= 0.303 Chirality : 0.040 0.147 1375 Planarity : 0.005 0.068 1505 Dihedral : 5.267 89.123 1144 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.07 % Allowed : 13.95 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1057 helix: 0.90 (0.23), residues: 499 sheet: 0.11 (0.38), residues: 187 loop : -0.25 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 397 HIS 0.005 0.001 HIS A 462 PHE 0.034 0.002 PHE B 110 TYR 0.016 0.001 TYR B 73 ARG 0.004 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 459) hydrogen bonds : angle 5.01336 ( 1329) covalent geometry : bond 0.00357 ( 8781) covalent geometry : angle 0.56996 (11887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 THR cc_start: 0.6687 (OUTLIER) cc_final: 0.6482 (t) REVERT: A 404 TYR cc_start: 0.8107 (t80) cc_final: 0.7877 (t80) REVERT: A 528 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5682 (t0) REVERT: A 615 LYS cc_start: 0.8027 (tmmt) cc_final: 0.7529 (tmmt) REVERT: A 721 ARG cc_start: 0.6994 (ttm170) cc_final: 0.6620 (ttm170) REVERT: B 107 GLN cc_start: 0.6657 (tm-30) cc_final: 0.6040 (tm-30) REVERT: B 108 ARG cc_start: 0.7557 (tpp80) cc_final: 0.7213 (mmm-85) REVERT: C 10 LYS cc_start: 0.7890 (ttpp) cc_final: 0.7316 (ttmm) REVERT: C 95 PHE cc_start: 0.5953 (m-80) cc_final: 0.5576 (m-10) REVERT: C 196 GLU cc_start: 0.5101 (mp0) cc_final: 0.4732 (mp0) REVERT: C 258 PHE cc_start: 0.6135 (OUTLIER) cc_final: 0.3752 (m-80) REVERT: C 285 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5692 (mt) outliers start: 20 outliers final: 11 residues processed: 207 average time/residue: 0.5556 time to fit residues: 156.7591 Evaluate side-chains 206 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.0040 chunk 23 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN B 17 HIS ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.175258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.159962 restraints weight = 41501.188| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.92 r_work: 0.4101 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8781 Z= 0.176 Angle : 0.571 5.550 11887 Z= 0.303 Chirality : 0.041 0.175 1375 Planarity : 0.005 0.066 1505 Dihedral : 5.255 88.707 1144 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.38 % Allowed : 15.08 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1057 helix: 1.04 (0.23), residues: 499 sheet: 0.15 (0.38), residues: 187 loop : -0.28 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 397 HIS 0.005 0.001 HIS A 462 PHE 0.031 0.002 PHE B 110 TYR 0.014 0.001 TYR B 73 ARG 0.005 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 459) hydrogen bonds : angle 4.94168 ( 1329) covalent geometry : bond 0.00370 ( 8781) covalent geometry : angle 0.57085 (11887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8124 (t80) cc_final: 0.7849 (t80) REVERT: A 528 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5675 (t0) REVERT: A 568 LYS cc_start: 0.7729 (mttt) cc_final: 0.7522 (mttt) REVERT: A 658 VAL cc_start: 0.8018 (m) cc_final: 0.7732 (p) REVERT: A 721 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6616 (ttm170) REVERT: B 97 TRP cc_start: 0.7441 (m-10) cc_final: 0.6764 (m-10) REVERT: B 100 MET cc_start: 0.6618 (mtm) cc_final: 0.6288 (mtm) REVERT: C 10 LYS cc_start: 0.7894 (ttpp) cc_final: 0.7319 (ttmm) REVERT: C 95 PHE cc_start: 0.6046 (m-80) cc_final: 0.5657 (m-10) REVERT: C 196 GLU cc_start: 0.5232 (mp0) cc_final: 0.4803 (mp0) REVERT: C 259 THR cc_start: 0.7019 (p) cc_final: 0.6799 (p) outliers start: 23 outliers final: 15 residues processed: 210 average time/residue: 0.5903 time to fit residues: 169.8894 Evaluate side-chains 212 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 28 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN B 121 HIS C 146 GLN C 234 ASN C 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.173798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.158541 restraints weight = 41724.087| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.91 r_work: 0.4066 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8781 Z= 0.198 Angle : 0.595 6.155 11887 Z= 0.318 Chirality : 0.041 0.147 1375 Planarity : 0.005 0.066 1505 Dihedral : 5.345 88.375 1144 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.27 % Allowed : 17.05 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1057 helix: 0.86 (0.23), residues: 499 sheet: 0.07 (0.38), residues: 187 loop : -0.45 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 397 HIS 0.005 0.001 HIS A 462 PHE 0.027 0.002 PHE B 110 TYR 0.016 0.002 TYR B 73 ARG 0.007 0.001 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 459) hydrogen bonds : angle 5.08047 ( 1329) covalent geometry : bond 0.00446 ( 8781) covalent geometry : angle 0.59515 (11887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8078 (t80) cc_final: 0.7765 (t80) REVERT: A 512 TYR cc_start: 0.7015 (t80) cc_final: 0.6706 (t80) REVERT: A 528 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5686 (t0) REVERT: A 721 ARG cc_start: 0.7195 (ttm170) cc_final: 0.6780 (ttm170) REVERT: B 48 GLU cc_start: 0.7276 (mp0) cc_final: 0.6695 (mp0) REVERT: B 97 TRP cc_start: 0.7644 (m-10) cc_final: 0.6962 (m-10) REVERT: B 107 GLN cc_start: 0.6877 (tm-30) cc_final: 0.6193 (tm-30) REVERT: C 10 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7338 (ttmm) REVERT: C 95 PHE cc_start: 0.6100 (m-80) cc_final: 0.5747 (m-10) REVERT: C 196 GLU cc_start: 0.5369 (mp0) cc_final: 0.4861 (mp0) REVERT: C 231 GLU cc_start: 0.7545 (pt0) cc_final: 0.7146 (pt0) REVERT: C 258 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.3105 (t80) REVERT: C 259 THR cc_start: 0.7062 (p) cc_final: 0.6777 (p) outliers start: 22 outliers final: 17 residues processed: 213 average time/residue: 0.5140 time to fit residues: 148.9340 Evaluate side-chains 215 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN A 653 GLN C 191 GLN C 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.173089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.157887 restraints weight = 41398.752| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.88 r_work: 0.4060 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8781 Z= 0.194 Angle : 0.593 6.639 11887 Z= 0.318 Chirality : 0.041 0.147 1375 Planarity : 0.005 0.065 1505 Dihedral : 5.409 89.986 1144 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.17 % Allowed : 17.87 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1057 helix: 0.82 (0.23), residues: 499 sheet: 0.01 (0.38), residues: 187 loop : -0.60 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 397 HIS 0.005 0.001 HIS A 462 PHE 0.025 0.002 PHE B 110 TYR 0.011 0.002 TYR B 143 ARG 0.004 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 459) hydrogen bonds : angle 5.06719 ( 1329) covalent geometry : bond 0.00435 ( 8781) covalent geometry : angle 0.59302 (11887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8100 (t80) cc_final: 0.7767 (t80) REVERT: A 512 TYR cc_start: 0.6983 (t80) cc_final: 0.6646 (t80) REVERT: A 528 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5660 (t0) REVERT: A 721 ARG cc_start: 0.7244 (ttm170) cc_final: 0.6822 (ttm170) REVERT: B 48 GLU cc_start: 0.7185 (mp0) cc_final: 0.6614 (mp0) REVERT: B 107 GLN cc_start: 0.6952 (tm-30) cc_final: 0.6206 (tm-30) REVERT: B 108 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7306 (mmm-85) REVERT: C 10 LYS cc_start: 0.7931 (ttpp) cc_final: 0.7333 (ttmm) REVERT: C 95 PHE cc_start: 0.6115 (m-80) cc_final: 0.5758 (m-10) REVERT: C 196 GLU cc_start: 0.5401 (mp0) cc_final: 0.4938 (mp0) REVERT: C 231 GLU cc_start: 0.7605 (pt0) cc_final: 0.7101 (pt0) REVERT: C 259 THR cc_start: 0.7029 (p) cc_final: 0.6742 (p) outliers start: 21 outliers final: 14 residues processed: 210 average time/residue: 0.5248 time to fit residues: 148.1012 Evaluate side-chains 209 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 643 MET Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 53 optimal weight: 0.0000 chunk 55 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.174109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.158930 restraints weight = 41333.845| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.90 r_work: 0.4071 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.6935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8781 Z= 0.146 Angle : 0.579 7.671 11887 Z= 0.301 Chirality : 0.040 0.142 1375 Planarity : 0.005 0.064 1505 Dihedral : 5.225 87.636 1144 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.34 % Allowed : 19.32 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1057 helix: 1.08 (0.23), residues: 498 sheet: -0.08 (0.37), residues: 194 loop : -0.51 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 397 HIS 0.004 0.001 HIS A 462 PHE 0.030 0.002 PHE A 361 TYR 0.010 0.001 TYR B 52 ARG 0.004 0.000 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 459) hydrogen bonds : angle 4.87955 ( 1329) covalent geometry : bond 0.00336 ( 8781) covalent geometry : angle 0.57906 (11887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8123 (t80) cc_final: 0.7740 (t80) REVERT: A 435 PHE cc_start: 0.6534 (m-80) cc_final: 0.6251 (m-80) REVERT: A 512 TYR cc_start: 0.6956 (t80) cc_final: 0.6619 (t80) REVERT: A 528 ASP cc_start: 0.6160 (OUTLIER) cc_final: 0.5697 (t0) REVERT: A 721 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6802 (ttm170) REVERT: B 15 ILE cc_start: 0.6939 (mp) cc_final: 0.6736 (mm) REVERT: B 27 LYS cc_start: 0.5867 (mmmm) cc_final: 0.5655 (mttp) REVERT: B 48 GLU cc_start: 0.7155 (mp0) cc_final: 0.6592 (mp0) REVERT: B 107 GLN cc_start: 0.6966 (tm-30) cc_final: 0.6216 (tm-30) REVERT: B 108 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7357 (mmm-85) REVERT: C 10 LYS cc_start: 0.7929 (ttpp) cc_final: 0.7323 (ttmm) REVERT: C 196 GLU cc_start: 0.5395 (mp0) cc_final: 0.4895 (mp0) REVERT: C 231 GLU cc_start: 0.7478 (pt0) cc_final: 0.6991 (pt0) outliers start: 13 outliers final: 11 residues processed: 202 average time/residue: 0.5246 time to fit residues: 142.9384 Evaluate side-chains 200 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN C 234 ASN C 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.171890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.156353 restraints weight = 41687.006| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.90 r_work: 0.4050 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.7395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8781 Z= 0.180 Angle : 0.599 8.345 11887 Z= 0.316 Chirality : 0.041 0.159 1375 Planarity : 0.005 0.064 1505 Dihedral : 5.310 88.844 1144 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.34 % Allowed : 19.42 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1057 helix: 1.02 (0.23), residues: 501 sheet: -0.14 (0.37), residues: 193 loop : -0.55 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 397 HIS 0.005 0.001 HIS A 462 PHE 0.024 0.002 PHE B 110 TYR 0.011 0.002 TYR A 725 ARG 0.005 0.001 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 459) hydrogen bonds : angle 4.96643 ( 1329) covalent geometry : bond 0.00409 ( 8781) covalent geometry : angle 0.59858 (11887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8127 (t80) cc_final: 0.7726 (t80) REVERT: A 495 LYS cc_start: 0.7908 (mttt) cc_final: 0.7588 (mtmm) REVERT: A 512 TYR cc_start: 0.7104 (t80) cc_final: 0.6625 (t80) REVERT: A 528 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5795 (t0) REVERT: A 615 LYS cc_start: 0.8259 (tmmt) cc_final: 0.7827 (tmmt) REVERT: A 721 ARG cc_start: 0.7326 (ttm170) cc_final: 0.6892 (ttm170) REVERT: B 27 LYS cc_start: 0.6091 (mmmm) cc_final: 0.5884 (mtmm) REVERT: B 48 GLU cc_start: 0.7353 (mp0) cc_final: 0.6819 (mp0) REVERT: B 79 VAL cc_start: 0.6244 (m) cc_final: 0.4723 (p) REVERT: B 107 GLN cc_start: 0.7028 (tm-30) cc_final: 0.6237 (tm-30) REVERT: B 108 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7639 (mmm-85) REVERT: C 10 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7319 (ttmm) REVERT: C 160 THR cc_start: 0.7162 (OUTLIER) cc_final: 0.6859 (p) REVERT: C 196 GLU cc_start: 0.5349 (mp0) cc_final: 0.5068 (mp0) REVERT: C 231 GLU cc_start: 0.7494 (pt0) cc_final: 0.7027 (pt0) outliers start: 13 outliers final: 9 residues processed: 206 average time/residue: 0.5098 time to fit residues: 141.5020 Evaluate side-chains 201 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.172767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.157204 restraints weight = 41762.284| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.94 r_work: 0.4063 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8781 Z= 0.145 Angle : 0.581 9.346 11887 Z= 0.303 Chirality : 0.041 0.139 1375 Planarity : 0.005 0.063 1505 Dihedral : 5.185 85.850 1144 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.03 % Allowed : 20.66 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1057 helix: 1.17 (0.23), residues: 500 sheet: -0.09 (0.36), residues: 203 loop : -0.49 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 397 HIS 0.004 0.001 HIS A 462 PHE 0.025 0.002 PHE B 110 TYR 0.009 0.001 TYR A 725 ARG 0.007 0.000 ARG A 702 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 459) hydrogen bonds : angle 4.88561 ( 1329) covalent geometry : bond 0.00333 ( 8781) covalent geometry : angle 0.58130 (11887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ASP cc_start: 0.7175 (t0) cc_final: 0.6900 (m-30) REVERT: A 404 TYR cc_start: 0.8074 (t80) cc_final: 0.7655 (t80) REVERT: A 512 TYR cc_start: 0.7089 (t80) cc_final: 0.6609 (t80) REVERT: A 528 ASP cc_start: 0.6171 (OUTLIER) cc_final: 0.5720 (t0) REVERT: A 615 LYS cc_start: 0.8204 (tmmt) cc_final: 0.7758 (tmmt) REVERT: B 27 LYS cc_start: 0.6040 (mmmm) cc_final: 0.5750 (mtmm) REVERT: B 48 GLU cc_start: 0.7307 (mp0) cc_final: 0.6769 (mp0) REVERT: B 79 VAL cc_start: 0.6295 (m) cc_final: 0.4719 (p) REVERT: C 10 LYS cc_start: 0.7934 (ttpp) cc_final: 0.7328 (ttmm) REVERT: C 126 ARG cc_start: 0.5941 (mmt90) cc_final: 0.5697 (mtt90) REVERT: C 160 THR cc_start: 0.7208 (p) cc_final: 0.6890 (p) REVERT: C 196 GLU cc_start: 0.5307 (mp0) cc_final: 0.5026 (mp0) REVERT: C 231 GLU cc_start: 0.7519 (pt0) cc_final: 0.6933 (pt0) outliers start: 10 outliers final: 9 residues processed: 198 average time/residue: 0.5180 time to fit residues: 138.7757 Evaluate side-chains 201 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.170549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.154903 restraints weight = 41444.536| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.90 r_work: 0.4034 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.7841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8781 Z= 0.209 Angle : 0.616 9.595 11887 Z= 0.328 Chirality : 0.042 0.145 1375 Planarity : 0.005 0.063 1505 Dihedral : 5.386 87.484 1144 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.24 % Allowed : 20.56 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1057 helix: 1.03 (0.23), residues: 501 sheet: -0.08 (0.36), residues: 203 loop : -0.71 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 397 HIS 0.005 0.001 HIS A 369 PHE 0.023 0.002 PHE B 110 TYR 0.013 0.002 TYR B 143 ARG 0.011 0.001 ARG A 702 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 459) hydrogen bonds : angle 5.08186 ( 1329) covalent geometry : bond 0.00470 ( 8781) covalent geometry : angle 0.61578 (11887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8556.47 seconds wall clock time: 149 minutes 15.82 seconds (8955.82 seconds total)