Starting phenix.real_space_refine on Tue Mar 3 23:45:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qvd_4649/03_2026/6qvd_4649.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qvd_4649/03_2026/6qvd_4649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qvd_4649/03_2026/6qvd_4649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qvd_4649/03_2026/6qvd_4649.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qvd_4649/03_2026/6qvd_4649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qvd_4649/03_2026/6qvd_4649.map" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6094 2.51 5 N 1472 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9212 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4606 Classifications: {'peptide': 596} Link IDs: {'CIS': 2, 'PTRANS': 26, 'TRANS': 567} Chain breaks: 2 Restraints were copied for chains: A Time building chain proxies: 3.06, per 1000 atoms: 0.33 Number of scatterers: 9212 At special positions: 0 Unit cell: (101.65, 95.23, 108.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1576 8.00 N 1472 7.00 C 6094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 301.4 milliseconds 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 66.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 115 through 154 removed outlier: 4.768A pdb=" N GLN B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 181 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.359A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.785A pdb=" N PHE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.614A pdb=" N PHE B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.582A pdb=" N GLY B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 298 through 323 removed outlier: 4.103A pdb=" N ARG B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 377 removed outlier: 3.572A pdb=" N PHE B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 365 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 removed outlier: 3.791A pdb=" N SER B 383 " --> pdb=" O HIS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 403 removed outlier: 4.557A pdb=" N GLY B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.571A pdb=" N ALA B 447 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 450 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 477 removed outlier: 3.503A pdb=" N ILE B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 472 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 473 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 521 through 538 removed outlier: 4.572A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.948A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 574 Processing helix chain 'B' and resid 576 through 585 Processing helix chain 'B' and resid 621 through 632 Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 833 through 845 Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'A' and resid 116 through 154 removed outlier: 4.768A pdb=" N GLN A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 181 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 199 removed outlier: 4.360A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.784A pdb=" N PHE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.613A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.581A pdb=" N GLY A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 298 through 323 removed outlier: 4.102A pdb=" N ARG A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 377 removed outlier: 3.572A pdb=" N PHE A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N CYS A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 3.792A pdb=" N SER A 383 " --> pdb=" O HIS A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 403 removed outlier: 4.557A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.570A pdb=" N ALA A 447 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 450 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.504A pdb=" N ILE A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 472 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 521 through 538 removed outlier: 4.572A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.949A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'A' and resid 621 through 632 Processing helix chain 'A' and resid 654 through 666 Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 862 through 871 Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA2, first strand: chain 'B' and resid 636 through 640 removed outlier: 5.569A pdb=" N LEU B 637 " --> pdb=" O SER B 651 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 651 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 639 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 651 " --> pdb=" O ASP B 822 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP B 822 " --> pdb=" O SER B 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853 removed outlier: 6.553A pdb=" N ALA B 849 " --> pdb=" O VAL B 860 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 860 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 851 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'A' and resid 636 through 640 removed outlier: 5.569A pdb=" N LEU A 637 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 651 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 639 " --> pdb=" O LEU A 649 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 651 " --> pdb=" O ASP A 822 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP A 822 " --> pdb=" O SER A 651 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853 removed outlier: 6.553A pdb=" N ALA A 849 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 860 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1623 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: 1.27 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1631 1.32 - 1.45: 2434 1.45 - 1.57: 5257 1.57 - 1.69: 4 1.69 - 1.81: 116 Bond restraints: 9442 Sorted by residual: bond pdb=" CB LYS B 518 " pdb=" CG LYS B 518 " ideal model delta sigma weight residual 1.520 1.628 -0.108 3.00e-02 1.11e+03 1.29e+01 bond pdb=" CB LYS A 518 " pdb=" CG LYS A 518 " ideal model delta sigma weight residual 1.520 1.628 -0.108 3.00e-02 1.11e+03 1.29e+01 bond pdb=" CG1 ILE B 516 " pdb=" CD1 ILE B 516 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.12e+00 bond pdb=" CG1 ILE A 516 " pdb=" CD1 ILE A 516 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 7.00e+00 bond pdb=" CA TYR B 589 " pdb=" C TYR B 589 " ideal model delta sigma weight residual 1.523 1.556 -0.033 1.34e-02 5.57e+03 5.96e+00 ... (remaining 9437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 12311 3.90 - 7.81: 409 7.81 - 11.71: 87 11.71 - 15.61: 7 15.61 - 19.52: 16 Bond angle restraints: 12830 Sorted by residual: angle pdb=" C PRO B 588 " pdb=" N TYR B 589 " pdb=" CA TYR B 589 " ideal model delta sigma weight residual 121.54 140.12 -18.58 1.91e+00 2.74e-01 9.47e+01 angle pdb=" C PRO A 588 " pdb=" N TYR A 589 " pdb=" CA TYR A 589 " ideal model delta sigma weight residual 121.54 140.12 -18.58 1.91e+00 2.74e-01 9.46e+01 angle pdb=" N ILE B 510 " pdb=" CA ILE B 510 " pdb=" C ILE B 510 " ideal model delta sigma weight residual 108.82 120.55 -11.73 1.22e+00 6.72e-01 9.25e+01 angle pdb=" N ILE A 510 " pdb=" CA ILE A 510 " pdb=" C ILE A 510 " ideal model delta sigma weight residual 108.82 120.53 -11.71 1.22e+00 6.72e-01 9.21e+01 angle pdb=" N TYR B 589 " pdb=" CA TYR B 589 " pdb=" C TYR B 589 " ideal model delta sigma weight residual 110.80 125.10 -14.30 2.13e+00 2.20e-01 4.51e+01 ... (remaining 12825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 4976 15.62 - 31.24: 396 31.24 - 46.87: 110 46.87 - 62.49: 20 62.49 - 78.11: 6 Dihedral angle restraints: 5508 sinusoidal: 2086 harmonic: 3422 Sorted by residual: dihedral pdb=" CA GLY A 594 " pdb=" C GLY A 594 " pdb=" N TRP A 595 " pdb=" CA TRP A 595 " ideal model delta harmonic sigma weight residual 180.00 125.75 54.25 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA GLY B 594 " pdb=" C GLY B 594 " pdb=" N TRP B 595 " pdb=" CA TRP B 595 " ideal model delta harmonic sigma weight residual 180.00 125.77 54.23 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA LYS B 324 " pdb=" C LYS B 324 " pdb=" N ASP B 325 " pdb=" CA ASP B 325 " ideal model delta harmonic sigma weight residual -180.00 -140.86 -39.14 0 5.00e+00 4.00e-02 6.13e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1194 0.104 - 0.208: 256 0.208 - 0.312: 54 0.312 - 0.416: 10 0.416 - 0.520: 4 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CG LEU B 427 " pdb=" CB LEU B 427 " pdb=" CD1 LEU B 427 " pdb=" CD2 LEU B 427 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CG LEU A 427 " pdb=" CB LEU A 427 " pdb=" CD1 LEU A 427 " pdb=" CD2 LEU A 427 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CB ILE B 329 " pdb=" CA ILE B 329 " pdb=" CG1 ILE B 329 " pdb=" CG2 ILE B 329 " both_signs ideal model delta sigma weight residual False 2.64 3.07 -0.42 2.00e-01 2.50e+01 4.50e+00 ... (remaining 1515 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 508 " 0.047 2.00e-02 2.50e+03 9.25e-02 8.56e+01 pdb=" C ASP A 508 " -0.160 2.00e-02 2.50e+03 pdb=" O ASP A 508 " 0.059 2.00e-02 2.50e+03 pdb=" N GLY A 509 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 508 " -0.047 2.00e-02 2.50e+03 9.20e-02 8.47e+01 pdb=" C ASP B 508 " 0.159 2.00e-02 2.50e+03 pdb=" O ASP B 508 " -0.058 2.00e-02 2.50e+03 pdb=" N GLY B 509 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 588 " 0.028 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C PRO B 588 " -0.101 2.00e-02 2.50e+03 pdb=" O PRO B 588 " 0.038 2.00e-02 2.50e+03 pdb=" N TYR B 589 " 0.035 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 895 2.73 - 3.28: 9696 3.28 - 3.82: 16348 3.82 - 4.36: 17975 4.36 - 4.90: 28730 Nonbonded interactions: 73644 Sorted by model distance: nonbonded pdb=" O ILE B 472 " pdb=" OG1 THR B 476 " model vdw 2.193 3.040 nonbonded pdb=" O ILE A 472 " pdb=" OG1 THR A 476 " model vdw 2.194 3.040 nonbonded pdb=" O CYS A 179 " pdb=" OG SER A 183 " model vdw 2.219 3.040 nonbonded pdb=" O CYS B 179 " pdb=" OG SER B 183 " model vdw 2.220 3.040 nonbonded pdb=" O SER B 289 " pdb=" OG1 THR B 293 " model vdw 2.235 3.040 ... (remaining 73639 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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 group one per residue 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.010 0.108 9442 Z= 0.446 Angle : 1.807 19.518 12830 Z= 0.948 Chirality : 0.096 0.520 1518 Planarity : 0.012 0.093 1568 Dihedral : 12.959 78.110 3308 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.58 % Favored : 90.08 % Rotamer: Outliers : 3.61 % Allowed : 10.62 % Favored : 85.77 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 3.85 % Twisted General : 0.88 % 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: -4.01 (0.20), residues: 1180 helix: -2.27 (0.15), residues: 764 sheet: -0.92 (0.99), residues: 20 loop : -3.28 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 390 TYR 0.046 0.005 TYR B 146 PHE 0.070 0.007 PHE B 464 TRP 0.086 0.007 TRP A 469 HIS 0.008 0.003 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00971 ( 9442) covalent geometry : angle 1.80672 (12830) hydrogen bonds : bond 0.15426 ( 555) hydrogen bonds : angle 6.92652 ( 1623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.331 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: B 135 MET cc_start: 0.9271 (ptp) cc_final: 0.8954 (ptt) REVERT: B 307 PHE cc_start: 0.9356 (t80) cc_final: 0.8904 (t80) REVERT: B 315 VAL cc_start: 0.9594 (t) cc_final: 0.9357 (m) REVERT: B 339 MET cc_start: 0.8880 (ptp) cc_final: 0.8608 (pmm) REVERT: B 341 PHE cc_start: 0.8529 (t80) cc_final: 0.7624 (t80) REVERT: B 404 PHE cc_start: 0.9225 (m-10) cc_final: 0.8835 (m-80) REVERT: B 464 PHE cc_start: 0.8934 (p90) cc_final: 0.8559 (p90) REVERT: B 468 PHE cc_start: 0.9021 (m-10) cc_final: 0.8715 (m-10) REVERT: B 470 MET cc_start: 0.9282 (ttm) cc_final: 0.8975 (ttm) REVERT: B 479 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.6551 (mp) REVERT: B 494 PHE cc_start: 0.9483 (t80) cc_final: 0.9240 (t80) REVERT: B 559 MET cc_start: 0.9772 (ppp) cc_final: 0.9202 (ppp) REVERT: B 643 LYS cc_start: 0.9606 (pttp) cc_final: 0.9013 (mmmt) REVERT: A 135 MET cc_start: 0.9200 (ptp) cc_final: 0.8908 (ptt) REVERT: A 307 PHE cc_start: 0.9322 (t80) cc_final: 0.8773 (t80) REVERT: A 315 VAL cc_start: 0.9607 (t) cc_final: 0.9378 (m) REVERT: A 339 MET cc_start: 0.9040 (ptp) cc_final: 0.8417 (pmm) REVERT: A 341 PHE cc_start: 0.8824 (t80) cc_final: 0.8351 (t80) REVERT: A 404 PHE cc_start: 0.9420 (m-10) cc_final: 0.9078 (m-80) REVERT: A 427 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8947 (tp) REVERT: A 435 LYS cc_start: 0.9716 (mmtt) cc_final: 0.9429 (tptp) REVERT: A 464 PHE cc_start: 0.8895 (p90) cc_final: 0.8557 (p90) REVERT: A 468 PHE cc_start: 0.8983 (m-10) cc_final: 0.8775 (m-80) REVERT: A 470 MET cc_start: 0.9224 (ttm) cc_final: 0.8800 (ttm) REVERT: A 494 PHE cc_start: 0.9325 (t80) cc_final: 0.8951 (t80) REVERT: A 557 LEU cc_start: 0.9664 (mm) cc_final: 0.9399 (tt) REVERT: A 559 MET cc_start: 0.9823 (ppp) cc_final: 0.9370 (ppp) outliers start: 36 outliers final: 9 residues processed: 233 average time/residue: 0.0843 time to fit residues: 27.9120 Evaluate side-chains 157 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.0970 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS A 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.065246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.051534 restraints weight = 59921.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.052893 restraints weight = 44471.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.053905 restraints weight = 35521.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.054701 restraints weight = 29479.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.055338 restraints weight = 25272.802| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9442 Z= 0.178 Angle : 0.902 12.178 12830 Z= 0.465 Chirality : 0.051 0.274 1518 Planarity : 0.006 0.069 1568 Dihedral : 6.985 33.068 1256 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -2.12 (0.23), residues: 1180 helix: -0.73 (0.17), residues: 768 sheet: -0.36 (0.96), residues: 20 loop : -2.71 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 496 TYR 0.014 0.001 TYR B 137 PHE 0.039 0.003 PHE A 464 TRP 0.034 0.002 TRP A 595 HIS 0.005 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9442) covalent geometry : angle 0.90153 (12830) hydrogen bonds : bond 0.05548 ( 555) hydrogen bonds : angle 4.94678 ( 1623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.253 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: B 135 MET cc_start: 0.9185 (ptp) cc_final: 0.8885 (ptt) REVERT: B 339 MET cc_start: 0.8491 (ptp) cc_final: 0.7666 (pmm) REVERT: B 341 PHE cc_start: 0.8138 (t80) cc_final: 0.7654 (t80) REVERT: B 400 VAL cc_start: 0.9145 (m) cc_final: 0.8939 (p) REVERT: B 404 PHE cc_start: 0.9152 (m-10) cc_final: 0.8802 (m-80) REVERT: B 410 MET cc_start: 0.8935 (tpt) cc_final: 0.8270 (tpt) REVERT: B 427 LEU cc_start: 0.9603 (tt) cc_final: 0.9335 (tt) REVERT: B 470 MET cc_start: 0.9554 (ttm) cc_final: 0.9261 (mmm) REVERT: B 494 PHE cc_start: 0.9622 (t80) cc_final: 0.9276 (t80) REVERT: B 547 PHE cc_start: 0.9446 (p90) cc_final: 0.9190 (m-80) REVERT: B 568 MET cc_start: 0.9441 (ppp) cc_final: 0.9224 (ppp) REVERT: B 643 LYS cc_start: 0.9539 (pttp) cc_final: 0.9029 (mmmt) REVERT: A 122 VAL cc_start: 0.9156 (m) cc_final: 0.8953 (m) REVERT: A 135 MET cc_start: 0.9000 (ptp) cc_final: 0.8626 (ptt) REVERT: A 227 ILE cc_start: 0.9196 (tp) cc_final: 0.8891 (tp) REVERT: A 250 MET cc_start: 0.8748 (tpp) cc_final: 0.7889 (tpp) REVERT: A 307 PHE cc_start: 0.9299 (t80) cc_final: 0.8957 (t80) REVERT: A 339 MET cc_start: 0.9031 (ptp) cc_final: 0.7657 (pmm) REVERT: A 341 PHE cc_start: 0.8567 (t80) cc_final: 0.8176 (t80) REVERT: A 400 VAL cc_start: 0.9298 (m) cc_final: 0.8949 (m) REVERT: A 436 HIS cc_start: 0.9014 (m-70) cc_final: 0.8740 (m-70) REVERT: A 464 PHE cc_start: 0.8993 (p90) cc_final: 0.8651 (p90) REVERT: A 468 PHE cc_start: 0.9059 (m-10) cc_final: 0.8788 (m-80) REVERT: A 470 MET cc_start: 0.9525 (ttm) cc_final: 0.9276 (mmp) REVERT: A 494 PHE cc_start: 0.9387 (t80) cc_final: 0.8930 (t80) REVERT: A 556 ILE cc_start: 0.9767 (tt) cc_final: 0.9445 (tp) REVERT: A 559 MET cc_start: 0.9807 (ppp) cc_final: 0.9318 (ppp) REVERT: A 564 ILE cc_start: 0.9621 (mm) cc_final: 0.9411 (pt) REVERT: A 643 LYS cc_start: 0.9558 (pttp) cc_final: 0.8964 (mmpt) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0760 time to fit residues: 22.8944 Evaluate side-chains 163 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 HIS B 379 HIS B 847 HIS A 369 HIS A 436 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.060543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.047641 restraints weight = 63675.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.048880 restraints weight = 47294.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.049820 restraints weight = 37587.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.050361 restraints weight = 31638.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.051028 restraints weight = 27730.687| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9442 Z= 0.204 Angle : 0.866 10.239 12830 Z= 0.450 Chirality : 0.049 0.239 1518 Planarity : 0.006 0.049 1568 Dihedral : 6.596 32.364 1256 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.23), residues: 1180 helix: -0.08 (0.18), residues: 770 sheet: 0.34 (0.97), residues: 20 loop : -2.76 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 496 TYR 0.018 0.002 TYR A 137 PHE 0.032 0.003 PHE A 365 TRP 0.037 0.003 TRP A 595 HIS 0.007 0.002 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9442) covalent geometry : angle 0.86643 (12830) hydrogen bonds : bond 0.05134 ( 555) hydrogen bonds : angle 4.62265 ( 1623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.234 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: B 135 MET cc_start: 0.9170 (ptp) cc_final: 0.8889 (ptt) REVERT: B 227 ILE cc_start: 0.9222 (tp) cc_final: 0.8924 (tp) REVERT: B 250 MET cc_start: 0.8438 (mmm) cc_final: 0.7820 (mmm) REVERT: B 339 MET cc_start: 0.8779 (ptp) cc_final: 0.8215 (ptp) REVERT: B 341 PHE cc_start: 0.8105 (t80) cc_final: 0.7639 (t80) REVERT: B 404 PHE cc_start: 0.9190 (m-10) cc_final: 0.8800 (m-80) REVERT: B 410 MET cc_start: 0.9001 (tpt) cc_final: 0.8476 (tpt) REVERT: B 464 PHE cc_start: 0.9155 (p90) cc_final: 0.8714 (p90) REVERT: B 470 MET cc_start: 0.9351 (ttm) cc_final: 0.9114 (mtp) REVERT: B 494 PHE cc_start: 0.9569 (t80) cc_final: 0.9194 (t80) REVERT: B 568 MET cc_start: 0.9472 (ppp) cc_final: 0.9262 (ppp) REVERT: B 643 LYS cc_start: 0.9559 (pttp) cc_final: 0.8944 (mmmt) REVERT: B 836 LYS cc_start: 0.9606 (mttt) cc_final: 0.9358 (tppt) REVERT: A 122 VAL cc_start: 0.9168 (m) cc_final: 0.8946 (m) REVERT: A 135 MET cc_start: 0.9107 (ptp) cc_final: 0.8846 (ptt) REVERT: A 227 ILE cc_start: 0.9280 (tp) cc_final: 0.8956 (tp) REVERT: A 341 PHE cc_start: 0.8450 (t80) cc_final: 0.8013 (t80) REVERT: A 400 VAL cc_start: 0.9314 (m) cc_final: 0.9106 (p) REVERT: A 468 PHE cc_start: 0.9041 (m-10) cc_final: 0.8776 (m-80) REVERT: A 556 ILE cc_start: 0.9770 (tt) cc_final: 0.9517 (pt) REVERT: A 559 MET cc_start: 0.9757 (ppp) cc_final: 0.9464 (ppp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.0828 time to fit residues: 22.7947 Evaluate side-chains 144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 HIS A 379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.061782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.048525 restraints weight = 63675.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.049729 restraints weight = 47804.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.050690 restraints weight = 38212.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051466 restraints weight = 32353.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.052059 restraints weight = 27939.342| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9442 Z= 0.172 Angle : 0.813 9.062 12830 Z= 0.419 Chirality : 0.048 0.241 1518 Planarity : 0.006 0.054 1568 Dihedral : 6.263 30.877 1256 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.14 % Favored : 91.69 % Rotamer: Outliers : 0.10 % Allowed : 6.11 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.24), residues: 1180 helix: 0.16 (0.18), residues: 772 sheet: 0.19 (1.09), residues: 20 loop : -2.82 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 496 TYR 0.015 0.001 TYR B 137 PHE 0.031 0.003 PHE A 547 TRP 0.023 0.002 TRP A 595 HIS 0.007 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9442) covalent geometry : angle 0.81255 (12830) hydrogen bonds : bond 0.04954 ( 555) hydrogen bonds : angle 4.52636 ( 1623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.340 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: B 135 MET cc_start: 0.9099 (ptp) cc_final: 0.8860 (ptt) REVERT: B 307 PHE cc_start: 0.9311 (t80) cc_final: 0.9075 (t80) REVERT: B 341 PHE cc_start: 0.8153 (t80) cc_final: 0.7694 (t80) REVERT: B 404 PHE cc_start: 0.9183 (m-10) cc_final: 0.8714 (m-80) REVERT: B 410 MET cc_start: 0.9007 (tpt) cc_final: 0.8301 (tpt) REVERT: B 464 PHE cc_start: 0.9159 (p90) cc_final: 0.8729 (p90) REVERT: B 494 PHE cc_start: 0.9571 (t80) cc_final: 0.9200 (t80) REVERT: B 568 MET cc_start: 0.9453 (ppp) cc_final: 0.9236 (ppp) REVERT: B 643 LYS cc_start: 0.9545 (pttp) cc_final: 0.8927 (mmmt) REVERT: B 836 LYS cc_start: 0.9583 (mttt) cc_final: 0.9332 (tppt) REVERT: A 135 MET cc_start: 0.9045 (ptp) cc_final: 0.8801 (ptt) REVERT: A 250 MET cc_start: 0.8649 (mmm) cc_final: 0.8354 (mmm) REVERT: A 339 MET cc_start: 0.8942 (ptp) cc_final: 0.7936 (pmm) REVERT: A 341 PHE cc_start: 0.8419 (t80) cc_final: 0.7901 (t80) REVERT: A 379 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7636 (t-90) REVERT: A 400 VAL cc_start: 0.9246 (m) cc_final: 0.9009 (p) REVERT: A 490 LEU cc_start: 0.9742 (mm) cc_final: 0.9521 (mm) REVERT: A 559 MET cc_start: 0.9721 (ppp) cc_final: 0.9346 (ppp) REVERT: A 836 LYS cc_start: 0.9458 (mttt) cc_final: 0.9148 (tppt) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.0830 time to fit residues: 21.5491 Evaluate side-chains 139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.062884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.049925 restraints weight = 61502.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.051243 restraints weight = 45625.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052276 restraints weight = 36229.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.052943 restraints weight = 30144.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.053602 restraints weight = 26388.931| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9442 Z= 0.155 Angle : 0.794 9.857 12830 Z= 0.405 Chirality : 0.048 0.233 1518 Planarity : 0.005 0.045 1568 Dihedral : 6.053 29.233 1256 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.97 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.95 (0.25), residues: 1180 helix: 0.39 (0.18), residues: 772 sheet: 0.57 (1.12), residues: 20 loop : -2.81 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.019 0.001 TYR A 146 PHE 0.027 0.002 PHE B 365 TRP 0.049 0.002 TRP A 469 HIS 0.006 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9442) covalent geometry : angle 0.79403 (12830) hydrogen bonds : bond 0.04601 ( 555) hydrogen bonds : angle 4.27615 ( 1623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.290 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: B 227 ILE cc_start: 0.9147 (tp) cc_final: 0.8867 (tp) REVERT: B 341 PHE cc_start: 0.8112 (t80) cc_final: 0.7644 (t80) REVERT: B 404 PHE cc_start: 0.9138 (m-10) cc_final: 0.8713 (m-80) REVERT: B 410 MET cc_start: 0.8881 (tpt) cc_final: 0.8162 (tpt) REVERT: B 464 PHE cc_start: 0.9138 (p90) cc_final: 0.8748 (p90) REVERT: B 494 PHE cc_start: 0.9559 (t80) cc_final: 0.9169 (t80) REVERT: A 122 VAL cc_start: 0.9048 (m) cc_final: 0.8826 (m) REVERT: A 250 MET cc_start: 0.8644 (mmm) cc_final: 0.8336 (mmm) REVERT: A 307 PHE cc_start: 0.9425 (t80) cc_final: 0.9087 (t80) REVERT: A 339 MET cc_start: 0.8927 (ptp) cc_final: 0.8678 (pmm) REVERT: A 341 PHE cc_start: 0.8332 (t80) cc_final: 0.7782 (t80) REVERT: A 400 VAL cc_start: 0.9219 (m) cc_final: 0.8991 (p) REVERT: A 410 MET cc_start: 0.9140 (tpt) cc_final: 0.8894 (tpt) REVERT: A 556 ILE cc_start: 0.9714 (pt) cc_final: 0.9289 (mt) REVERT: A 559 MET cc_start: 0.9692 (ppp) cc_final: 0.9319 (ppp) REVERT: A 836 LYS cc_start: 0.9448 (mttt) cc_final: 0.9111 (tppt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0747 time to fit residues: 20.2016 Evaluate side-chains 138 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 0.0060 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.063033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.049973 restraints weight = 62274.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051306 restraints weight = 46375.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.052408 restraints weight = 36761.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.053205 restraints weight = 30442.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.053823 restraints weight = 26018.858| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9442 Z= 0.164 Angle : 0.813 9.129 12830 Z= 0.416 Chirality : 0.047 0.229 1518 Planarity : 0.005 0.041 1568 Dihedral : 5.954 28.125 1256 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.56 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.79 (0.25), residues: 1180 helix: 0.52 (0.19), residues: 772 sheet: 0.82 (1.12), residues: 20 loop : -2.80 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.021 0.002 TYR B 146 PHE 0.037 0.002 PHE A 468 TRP 0.017 0.001 TRP A 469 HIS 0.006 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9442) covalent geometry : angle 0.81290 (12830) hydrogen bonds : bond 0.04667 ( 555) hydrogen bonds : angle 4.23569 ( 1623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.350 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: B 341 PHE cc_start: 0.8138 (t80) cc_final: 0.7708 (t80) REVERT: B 404 PHE cc_start: 0.9110 (m-10) cc_final: 0.8651 (m-80) REVERT: B 410 MET cc_start: 0.8810 (tpt) cc_final: 0.8035 (tpt) REVERT: B 464 PHE cc_start: 0.9120 (p90) cc_final: 0.8433 (p90) REVERT: B 468 PHE cc_start: 0.9114 (m-10) cc_final: 0.8635 (m-80) REVERT: B 494 PHE cc_start: 0.9528 (t80) cc_final: 0.9124 (t80) REVERT: B 836 LYS cc_start: 0.9559 (mttt) cc_final: 0.9269 (mmtm) REVERT: A 250 MET cc_start: 0.8722 (mmm) cc_final: 0.8433 (mmm) REVERT: A 339 MET cc_start: 0.8925 (ptp) cc_final: 0.7905 (pmm) REVERT: A 341 PHE cc_start: 0.8281 (t80) cc_final: 0.7787 (t80) REVERT: A 410 MET cc_start: 0.9115 (tpt) cc_final: 0.8848 (tpt) REVERT: A 556 ILE cc_start: 0.9630 (pt) cc_final: 0.8804 (pt) REVERT: A 559 MET cc_start: 0.9673 (ppp) cc_final: 0.9327 (ppp) REVERT: A 560 MET cc_start: 0.9523 (mmp) cc_final: 0.8996 (mmm) REVERT: A 836 LYS cc_start: 0.9442 (mttt) cc_final: 0.9116 (tppt) REVERT: A 854 MET cc_start: 0.9400 (tmm) cc_final: 0.9065 (ppp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0787 time to fit residues: 20.5833 Evaluate side-chains 141 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 0.0070 chunk 20 optimal weight: 0.0870 chunk 104 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.066449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.051224 restraints weight = 62926.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.052928 restraints weight = 44232.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.054283 restraints weight = 33839.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.055343 restraints weight = 27164.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.056172 restraints weight = 22567.968| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9442 Z= 0.147 Angle : 0.801 9.248 12830 Z= 0.404 Chirality : 0.048 0.228 1518 Planarity : 0.005 0.042 1568 Dihedral : 5.844 26.644 1256 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.97 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.66 (0.25), residues: 1180 helix: 0.64 (0.19), residues: 774 sheet: 0.95 (1.09), residues: 20 loop : -2.82 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.018 0.002 TYR A 206 PHE 0.041 0.002 PHE B 488 TRP 0.055 0.002 TRP A 469 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9442) covalent geometry : angle 0.80066 (12830) hydrogen bonds : bond 0.04457 ( 555) hydrogen bonds : angle 4.10200 ( 1623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.352 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: B 227 ILE cc_start: 0.9450 (tp) cc_final: 0.8867 (tp) REVERT: B 235 PHE cc_start: 0.8905 (t80) cc_final: 0.8667 (t80) REVERT: B 341 PHE cc_start: 0.8049 (t80) cc_final: 0.7461 (t80) REVERT: B 400 VAL cc_start: 0.9132 (p) cc_final: 0.8923 (m) REVERT: B 401 ILE cc_start: 0.9697 (pt) cc_final: 0.9487 (pt) REVERT: B 427 LEU cc_start: 0.9609 (tp) cc_final: 0.9274 (tp) REVERT: B 490 LEU cc_start: 0.9181 (mm) cc_final: 0.8928 (mm) REVERT: B 494 PHE cc_start: 0.9400 (t80) cc_final: 0.9047 (t80) REVERT: A 122 VAL cc_start: 0.7963 (m) cc_final: 0.7546 (m) REVERT: A 227 ILE cc_start: 0.9292 (tp) cc_final: 0.9073 (tp) REVERT: A 235 PHE cc_start: 0.8876 (t80) cc_final: 0.8643 (t80) REVERT: A 307 PHE cc_start: 0.9284 (t80) cc_final: 0.9075 (t80) REVERT: A 339 MET cc_start: 0.8581 (ptp) cc_final: 0.7899 (pmm) REVERT: A 341 PHE cc_start: 0.8346 (t80) cc_final: 0.7858 (t80) REVERT: A 414 MET cc_start: 0.8630 (tmm) cc_final: 0.8071 (tmm) REVERT: A 427 LEU cc_start: 0.9171 (tp) cc_final: 0.8940 (tp) REVERT: A 449 TRP cc_start: 0.8327 (m100) cc_final: 0.7962 (m100) REVERT: A 556 ILE cc_start: 0.9153 (pt) cc_final: 0.8802 (pt) REVERT: A 559 MET cc_start: 0.9622 (ppp) cc_final: 0.9359 (ppp) REVERT: A 560 MET cc_start: 0.9663 (mmp) cc_final: 0.9428 (mmm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.0783 time to fit residues: 22.2364 Evaluate side-chains 149 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.064827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051546 restraints weight = 61222.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.052986 restraints weight = 45462.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.054136 restraints weight = 35875.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.054921 restraints weight = 29665.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.055349 restraints weight = 25349.140| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9442 Z= 0.158 Angle : 0.838 8.808 12830 Z= 0.419 Chirality : 0.049 0.223 1518 Planarity : 0.005 0.046 1568 Dihedral : 5.805 26.226 1256 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.14 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.70 (0.25), residues: 1180 helix: 0.54 (0.19), residues: 774 sheet: 1.15 (1.09), residues: 20 loop : -2.67 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.018 0.002 TYR A 146 PHE 0.025 0.002 PHE A 464 TRP 0.050 0.002 TRP A 469 HIS 0.004 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9442) covalent geometry : angle 0.83817 (12830) hydrogen bonds : bond 0.04548 ( 555) hydrogen bonds : angle 4.29932 ( 1623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.413 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: B 341 PHE cc_start: 0.8318 (t80) cc_final: 0.7843 (t80) REVERT: B 464 PHE cc_start: 0.9122 (p90) cc_final: 0.8644 (p90) REVERT: B 485 MET cc_start: 0.9454 (pmm) cc_final: 0.9115 (pmm) REVERT: B 494 PHE cc_start: 0.9473 (t80) cc_final: 0.9076 (t80) REVERT: B 559 MET cc_start: 0.9627 (ppp) cc_final: 0.9381 (ppp) REVERT: B 560 MET cc_start: 0.9582 (mmp) cc_final: 0.9110 (mmm) REVERT: B 609 MET cc_start: 0.9454 (mpp) cc_final: 0.9224 (mpp) REVERT: B 836 LYS cc_start: 0.9502 (mppt) cc_final: 0.9235 (tppt) REVERT: A 122 VAL cc_start: 0.9021 (m) cc_final: 0.8734 (m) REVERT: A 307 PHE cc_start: 0.9424 (t80) cc_final: 0.8951 (t80) REVERT: A 339 MET cc_start: 0.8923 (ptp) cc_final: 0.7904 (pmm) REVERT: A 341 PHE cc_start: 0.8369 (t80) cc_final: 0.7829 (t80) REVERT: A 400 VAL cc_start: 0.9290 (p) cc_final: 0.8927 (m) REVERT: A 410 MET cc_start: 0.9082 (tpt) cc_final: 0.8859 (tpt) REVERT: A 468 PHE cc_start: 0.8874 (m-80) cc_final: 0.8581 (m-80) REVERT: A 556 ILE cc_start: 0.9615 (pt) cc_final: 0.8718 (mt) REVERT: A 559 MET cc_start: 0.9633 (ppp) cc_final: 0.9196 (ppp) REVERT: A 560 MET cc_start: 0.9692 (mmp) cc_final: 0.9149 (mmm) REVERT: A 854 MET cc_start: 0.9374 (tmm) cc_final: 0.9132 (ppp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.0787 time to fit residues: 22.0433 Evaluate side-chains 143 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 84 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 0.0370 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.064451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051319 restraints weight = 62141.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052710 restraints weight = 46244.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.053781 restraints weight = 36940.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054574 restraints weight = 30617.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.055081 restraints weight = 26368.453| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9442 Z= 0.155 Angle : 0.822 9.421 12830 Z= 0.411 Chirality : 0.049 0.222 1518 Planarity : 0.005 0.040 1568 Dihedral : 5.723 26.257 1256 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.22 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1180 helix: 0.59 (0.19), residues: 774 sheet: 1.11 (1.08), residues: 20 loop : -2.66 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.018 0.002 TYR A 146 PHE 0.031 0.002 PHE B 288 TRP 0.057 0.002 TRP A 469 HIS 0.006 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9442) covalent geometry : angle 0.82236 (12830) hydrogen bonds : bond 0.04372 ( 555) hydrogen bonds : angle 4.16614 ( 1623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.375 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: B 227 ILE cc_start: 0.9004 (tp) cc_final: 0.8803 (tp) REVERT: B 341 PHE cc_start: 0.8319 (t80) cc_final: 0.7842 (t80) REVERT: B 400 VAL cc_start: 0.9256 (p) cc_final: 0.8914 (m) REVERT: B 410 MET cc_start: 0.8973 (tpt) cc_final: 0.8743 (tpt) REVERT: B 494 PHE cc_start: 0.9483 (t80) cc_final: 0.9100 (t80) REVERT: B 559 MET cc_start: 0.9617 (ppp) cc_final: 0.9318 (ppp) REVERT: B 560 MET cc_start: 0.9647 (mmp) cc_final: 0.9196 (mmm) REVERT: A 122 VAL cc_start: 0.9025 (m) cc_final: 0.8779 (m) REVERT: A 307 PHE cc_start: 0.9389 (t80) cc_final: 0.8925 (t80) REVERT: A 339 MET cc_start: 0.8908 (ptp) cc_final: 0.7904 (pmm) REVERT: A 341 PHE cc_start: 0.8326 (t80) cc_final: 0.7777 (t80) REVERT: A 368 LEU cc_start: 0.9241 (mm) cc_final: 0.9035 (pp) REVERT: A 400 VAL cc_start: 0.9309 (p) cc_final: 0.8957 (m) REVERT: A 468 PHE cc_start: 0.8781 (m-80) cc_final: 0.8465 (m-80) REVERT: A 485 MET cc_start: 0.9376 (pmm) cc_final: 0.8994 (pmm) REVERT: A 488 PHE cc_start: 0.9481 (m-10) cc_final: 0.9279 (m-80) REVERT: A 556 ILE cc_start: 0.9642 (pt) cc_final: 0.8754 (mt) REVERT: A 559 MET cc_start: 0.9621 (ppp) cc_final: 0.9148 (ppp) REVERT: A 560 MET cc_start: 0.9701 (mmp) cc_final: 0.9143 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.0790 time to fit residues: 21.7665 Evaluate side-chains 142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 98 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 HIS A 835 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.065671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.052220 restraints weight = 61405.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.053700 restraints weight = 45373.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054806 restraints weight = 35759.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.055657 restraints weight = 29444.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.056118 restraints weight = 25103.451| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9442 Z= 0.149 Angle : 0.834 9.692 12830 Z= 0.412 Chirality : 0.049 0.220 1518 Planarity : 0.005 0.042 1568 Dihedral : 5.601 27.227 1256 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.22 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1180 helix: 0.61 (0.19), residues: 772 sheet: 1.14 (1.04), residues: 20 loop : -2.66 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 663 TYR 0.017 0.001 TYR A 146 PHE 0.026 0.002 PHE B 235 TRP 0.077 0.003 TRP B 469 HIS 0.005 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9442) covalent geometry : angle 0.83404 (12830) hydrogen bonds : bond 0.04255 ( 555) hydrogen bonds : angle 4.13411 ( 1623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.359 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: B 341 PHE cc_start: 0.8278 (t80) cc_final: 0.7798 (t80) REVERT: B 400 VAL cc_start: 0.9296 (p) cc_final: 0.8953 (m) REVERT: B 410 MET cc_start: 0.8944 (tpt) cc_final: 0.8687 (tpt) REVERT: B 494 PHE cc_start: 0.9445 (t80) cc_final: 0.9105 (t80) REVERT: B 559 MET cc_start: 0.9610 (ppp) cc_final: 0.9304 (ppp) REVERT: B 560 MET cc_start: 0.9625 (mmp) cc_final: 0.9143 (mmm) REVERT: B 646 MET cc_start: 0.9168 (mtm) cc_final: 0.8896 (mmm) REVERT: B 836 LYS cc_start: 0.9459 (mppt) cc_final: 0.9157 (tppt) REVERT: A 122 VAL cc_start: 0.8936 (m) cc_final: 0.8688 (m) REVERT: A 307 PHE cc_start: 0.9344 (t80) cc_final: 0.8905 (t80) REVERT: A 339 MET cc_start: 0.8804 (ptp) cc_final: 0.7862 (pmm) REVERT: A 341 PHE cc_start: 0.8324 (t80) cc_final: 0.7796 (t80) REVERT: A 368 LEU cc_start: 0.9239 (mm) cc_final: 0.9030 (pp) REVERT: A 400 VAL cc_start: 0.9343 (p) cc_final: 0.8997 (m) REVERT: A 468 PHE cc_start: 0.8868 (m-80) cc_final: 0.8569 (m-80) REVERT: A 485 MET cc_start: 0.9408 (pmm) cc_final: 0.9015 (pmm) REVERT: A 488 PHE cc_start: 0.9437 (m-10) cc_final: 0.9231 (m-80) REVERT: A 556 ILE cc_start: 0.9649 (pt) cc_final: 0.8722 (mt) REVERT: A 557 LEU cc_start: 0.9727 (mp) cc_final: 0.9108 (tt) REVERT: A 559 MET cc_start: 0.9626 (ppp) cc_final: 0.9151 (ppp) REVERT: A 560 MET cc_start: 0.9708 (mmp) cc_final: 0.9170 (mmm) REVERT: A 836 LYS cc_start: 0.9622 (tptp) cc_final: 0.9419 (mmtm) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.0775 time to fit residues: 21.6989 Evaluate side-chains 145 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.064751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051740 restraints weight = 61438.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.053131 restraints weight = 45622.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054169 restraints weight = 36247.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054984 restraints weight = 29903.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.055619 restraints weight = 25642.087| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9442 Z= 0.154 Angle : 0.840 10.429 12830 Z= 0.420 Chirality : 0.048 0.219 1518 Planarity : 0.005 0.040 1568 Dihedral : 5.636 29.433 1256 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.14 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: -0.63 (0.25), residues: 1180 helix: 0.58 (0.19), residues: 774 sheet: 1.33 (1.06), residues: 20 loop : -2.62 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 317 TYR 0.019 0.001 TYR A 146 PHE 0.027 0.002 PHE B 288 TRP 0.074 0.003 TRP B 469 HIS 0.007 0.001 HIS A 436 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9442) covalent geometry : angle 0.83973 (12830) hydrogen bonds : bond 0.04288 ( 555) hydrogen bonds : angle 4.19420 ( 1623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.49 seconds wall clock time: 26 minutes 3.48 seconds (1563.48 seconds total)