Starting phenix.real_space_refine on Wed Mar 4 03:30:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghc_40040/03_2026/8ghc_40040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghc_40040/03_2026/8ghc_40040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ghc_40040/03_2026/8ghc_40040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghc_40040/03_2026/8ghc_40040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ghc_40040/03_2026/8ghc_40040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghc_40040/03_2026/8ghc_40040.map" } resolution = 2.3 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= 0.004 sd= 1.385 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 67 5.16 5 C 6714 2.51 5 N 1830 2.21 5 O 1899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 10512 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5317 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 618} Chain: "B" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5193 Classifications: {'peptide': 648} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 606} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.21 Number of scatterers: 10512 At special positions: 0 Unit cell: (67.24, 121.36, 131.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 67 16.00 O 1899 8.00 N 1830 7.00 C 6714 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: 0.77 Conformation dependent library (CDL) restraints added in 449.6 milliseconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 49.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.675A pdb=" N GLN A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 167 through 192 Processing helix chain 'A' and resid 199 through 207 removed outlier: 3.588A pdb=" N ILE A 206 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 224 through 235 removed outlier: 4.144A pdb=" N PHE A 232 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.921A pdb=" N ARG A 394 " --> pdb=" O PRO A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 458 through 483 Processing helix chain 'A' and resid 485 through 491 removed outlier: 3.648A pdb=" N VAL A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 504 Processing helix chain 'A' and resid 509 through 514 removed outlier: 4.228A pdb=" N ASP A 512 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 537 Processing helix chain 'A' and resid 537 through 545 Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 583 through 599 Processing helix chain 'A' and resid 617 through 643 removed outlier: 3.722A pdb=" N LYS A 621 " --> pdb=" O GLY A 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 139 removed outlier: 3.555A pdb=" N GLN B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 194 removed outlier: 4.355A pdb=" N GLY B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.806A pdb=" N PHE B 203 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 224 through 235 removed outlier: 4.080A pdb=" N PHE B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'B' and resid 336 through 357 Processing helix chain 'B' and resid 364 through 379 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 395 through 406 Processing helix chain 'B' and resid 412 through 418 Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.543A pdb=" N GLN B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.951A pdb=" N ALA B 448 " --> pdb=" O PRO B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 483 removed outlier: 3.787A pdb=" N LEU B 481 " --> pdb=" O GLY B 477 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 491 removed outlier: 3.540A pdb=" N VAL B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 504 Processing helix chain 'B' and resid 509 through 514 removed outlier: 4.216A pdb=" N ASP B 512 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 537 Processing helix chain 'B' and resid 537 through 545 Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 573 through 581 Processing helix chain 'B' and resid 583 through 598 Processing helix chain 'B' and resid 617 through 643 removed outlier: 3.569A pdb=" N LYS B 621 " --> pdb=" O GLY B 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 52 removed outlier: 6.775A pdb=" N ILE A 6 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 83 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 8 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE A 81 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A 10 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP A 79 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA A 75 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 100 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE A 77 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ARG A 98 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP A 79 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.547A pdb=" N ASN A 20 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG A 21 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS A 67 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN A 23 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 65 " --> pdb=" O GLN A 23 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TRP A 25 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 63 " --> pdb=" O TRP A 25 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 removed outlier: 6.409A pdb=" N LEU A 300 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A 316 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET A 302 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.746A pdb=" N ILE B 6 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 83 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 8 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 81 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B 10 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP B 79 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B 77 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG B 98 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 79 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 39 removed outlier: 4.410A pdb=" N ARG B 21 " --> pdb=" O HIS B 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 243 removed outlier: 6.412A pdb=" N LEU B 300 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE B 316 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N MET B 302 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 288 through 289 511 hydrogen bonds defined for protein. 1428 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: 1.73 Time building geometry restraints manager: 1.05 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: 2049 1.32 - 1.45: 2673 1.45 - 1.57: 5965 1.57 - 1.69: 0 1.69 - 1.82: 100 Bond restraints: 10787 Sorted by residual: bond pdb=" CB VAL B 584 " pdb=" CG1 VAL B 584 " ideal model delta sigma weight residual 1.521 1.425 0.096 3.30e-02 9.18e+02 8.45e+00 bond pdb=" CB ILE B 413 " pdb=" CG2 ILE B 413 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.71e+00 bond pdb=" CG LEU B 362 " pdb=" CD2 LEU B 362 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.00e+00 bond pdb=" CG LEU A 240 " pdb=" CD2 LEU A 240 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.21e+00 bond pdb=" CB VAL B 92 " pdb=" CG1 VAL B 92 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 4.98e+00 ... (remaining 10782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 14104 2.15 - 4.31: 480 4.31 - 6.46: 59 6.46 - 8.61: 15 8.61 - 10.77: 5 Bond angle restraints: 14663 Sorted by residual: angle pdb=" N PRO B 443 " pdb=" CA PRO B 443 " pdb=" C PRO B 443 " ideal model delta sigma weight residual 110.70 115.61 -4.91 1.22e+00 6.72e-01 1.62e+01 angle pdb=" N PRO A 443 " pdb=" CA PRO A 443 " pdb=" C PRO A 443 " ideal model delta sigma weight residual 110.70 115.41 -4.71 1.22e+00 6.72e-01 1.49e+01 angle pdb=" CA PRO B 443 " pdb=" C PRO B 443 " pdb=" N PRO B 444 " ideal model delta sigma weight residual 117.93 122.39 -4.46 1.20e+00 6.94e-01 1.38e+01 angle pdb=" CA PRO A 443 " pdb=" C PRO A 443 " pdb=" N PRO A 444 " ideal model delta sigma weight residual 117.93 122.31 -4.38 1.20e+00 6.94e-01 1.33e+01 angle pdb=" CA PRO A 391 " pdb=" N PRO A 391 " pdb=" CD PRO A 391 " ideal model delta sigma weight residual 112.00 106.92 5.08 1.40e+00 5.10e-01 1.32e+01 ... (remaining 14658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5955 17.34 - 34.67: 418 34.67 - 52.01: 67 52.01 - 69.35: 28 69.35 - 86.68: 8 Dihedral angle restraints: 6476 sinusoidal: 2671 harmonic: 3805 Sorted by residual: dihedral pdb=" CA ASP A 335 " pdb=" C ASP A 335 " pdb=" N PRO A 336 " pdb=" CA PRO A 336 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ALA A 417 " pdb=" C ALA A 417 " pdb=" N VAL A 418 " pdb=" CA VAL A 418 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ALA B 417 " pdb=" C ALA B 417 " pdb=" N VAL B 418 " pdb=" CA VAL B 418 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1173 0.062 - 0.124: 346 0.124 - 0.185: 52 0.185 - 0.247: 8 0.247 - 0.309: 4 Chirality restraints: 1583 Sorted by residual: chirality pdb=" CG LEU B 362 " pdb=" CB LEU B 362 " pdb=" CD1 LEU B 362 " pdb=" CD2 LEU B 362 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB THR B 327 " pdb=" CA THR B 327 " pdb=" OG1 THR B 327 " pdb=" CG2 THR B 327 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CG LEU B 240 " pdb=" CB LEU B 240 " pdb=" CD1 LEU B 240 " pdb=" CD2 LEU B 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1580 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 94 " -0.020 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C PHE B 94 " 0.067 2.00e-02 2.50e+03 pdb=" O PHE B 94 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO B 95 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 197 " 0.005 2.00e-02 2.50e+03 2.30e-02 1.33e+01 pdb=" CG TRP B 197 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 197 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP B 197 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 197 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP B 197 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP B 197 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 197 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 197 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 197 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 349 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" CG ASN A 349 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN A 349 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 349 " -0.019 2.00e-02 2.50e+03 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 148 2.63 - 3.20: 9035 3.20 - 3.77: 18664 3.77 - 4.33: 25654 4.33 - 4.90: 40849 Nonbonded interactions: 94350 Sorted by model distance: nonbonded pdb=" OXT ILE B 663 " pdb="FE FE2 B 901 " model vdw 2.067 3.000 nonbonded pdb=" NE2 HIS B 360 " pdb="FE FE2 B 901 " model vdw 2.099 3.080 nonbonded pdb=" NE2 HIS A 365 " pdb="FE FE2 A 901 " model vdw 2.131 3.080 nonbonded pdb=" NE2 HIS B 540 " pdb="FE FE2 B 901 " model vdw 2.131 3.080 nonbonded pdb=" NE2 HIS A 360 " pdb="FE FE2 A 901 " model vdw 2.131 3.080 ... (remaining 94345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 155 or resid 170 through 901)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.710 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.009 0.115 10787 Z= 0.389 Angle : 0.907 10.765 14663 Z= 0.478 Chirality : 0.060 0.309 1583 Planarity : 0.008 0.068 1906 Dihedral : 12.960 86.684 4012 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.09 % Allowed : 2.39 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1304 helix: -1.14 (0.18), residues: 578 sheet: -0.50 (0.42), residues: 128 loop : -0.65 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 5 TYR 0.023 0.003 TYR A 359 PHE 0.021 0.004 PHE A 278 TRP 0.050 0.004 TRP B 197 HIS 0.014 0.003 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00943 (10787) covalent geometry : angle 0.90735 (14663) hydrogen bonds : bond 0.14419 ( 511) hydrogen bonds : angle 7.26456 ( 1428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7526 (tpp-160) cc_final: 0.7212 (tpp-160) REVERT: A 7 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7648 (mtt90) REVERT: A 169 GLU cc_start: 0.7886 (pm20) cc_final: 0.7221 (pm20) REVERT: A 184 GLU cc_start: 0.8182 (tt0) cc_final: 0.7973 (tt0) REVERT: A 394 ARG cc_start: 0.8108 (ptm-80) cc_final: 0.7865 (ppt170) REVERT: A 571 ASP cc_start: 0.7948 (m-30) cc_final: 0.7675 (m-30) REVERT: A 621 LYS cc_start: 0.7934 (mttm) cc_final: 0.7636 (ttpt) REVERT: B 84 GLN cc_start: 0.7882 (tt0) cc_final: 0.7286 (mm-40) REVERT: B 216 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6924 (mm-30) REVERT: B 239 MET cc_start: 0.8980 (mmm) cc_final: 0.8724 (mmm) REVERT: B 305 MET cc_start: 0.8630 (tpt) cc_final: 0.8305 (tpp) REVERT: B 394 ARG cc_start: 0.7823 (ttp-110) cc_final: 0.7391 (ttm-80) REVERT: B 568 THR cc_start: 0.8340 (p) cc_final: 0.8114 (p) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.7170 time to fit residues: 135.2022 Evaluate side-chains 141 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.0070 chunk 129 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN B 358 GLN B 406 GLN B 435 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103408 restraints weight = 12987.683| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.12 r_work: 0.3239 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10787 Z= 0.154 Angle : 0.566 7.489 14663 Z= 0.294 Chirality : 0.041 0.144 1583 Planarity : 0.005 0.062 1906 Dihedral : 4.453 24.035 1425 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.33 % Allowed : 7.71 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.22), residues: 1304 helix: 0.18 (0.20), residues: 587 sheet: -0.51 (0.42), residues: 134 loop : -0.16 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 156 TYR 0.022 0.002 TYR A 460 PHE 0.015 0.001 PHE A 386 TRP 0.011 0.001 TRP B 25 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00335 (10787) covalent geometry : angle 0.56590 (14663) hydrogen bonds : bond 0.04427 ( 511) hydrogen bonds : angle 5.53668 ( 1428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7731 (tpp-160) cc_final: 0.7445 (tpp-160) REVERT: A 7 ARG cc_start: 0.8204 (mtt90) cc_final: 0.7943 (mtt90) REVERT: A 169 GLU cc_start: 0.7955 (pm20) cc_final: 0.7234 (pm20) REVERT: A 184 GLU cc_start: 0.8321 (tt0) cc_final: 0.8111 (tt0) REVERT: A 394 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.7896 (ptt180) REVERT: A 621 LYS cc_start: 0.7795 (mttm) cc_final: 0.7213 (tmmt) REVERT: B 7 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7470 (mtp85) REVERT: B 84 GLN cc_start: 0.8405 (tt0) cc_final: 0.8015 (mm-40) REVERT: B 91 GLU cc_start: 0.8052 (pt0) cc_final: 0.7447 (mt-10) REVERT: B 216 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 249 SER cc_start: 0.8886 (m) cc_final: 0.8668 (t) REVERT: B 394 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7777 (ttm-80) REVERT: B 568 THR cc_start: 0.8115 (p) cc_final: 0.7880 (p) outliers start: 15 outliers final: 7 residues processed: 160 average time/residue: 0.7767 time to fit residues: 131.7533 Evaluate side-chains 146 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 105 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 106 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103011 restraints weight = 13096.184| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.12 r_work: 0.3236 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10787 Z= 0.140 Angle : 0.529 7.245 14663 Z= 0.270 Chirality : 0.040 0.142 1583 Planarity : 0.004 0.045 1906 Dihedral : 4.256 22.153 1425 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.86 % Allowed : 9.93 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.22), residues: 1304 helix: 0.81 (0.21), residues: 586 sheet: -0.36 (0.43), residues: 134 loop : -0.01 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 40 TYR 0.019 0.002 TYR A 460 PHE 0.014 0.001 PHE A 386 TRP 0.009 0.001 TRP B 176 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00313 (10787) covalent geometry : angle 0.52936 (14663) hydrogen bonds : bond 0.03971 ( 511) hydrogen bonds : angle 5.16716 ( 1428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7362 (tpp-160) REVERT: A 169 GLU cc_start: 0.7909 (pm20) cc_final: 0.7211 (pm20) REVERT: A 184 GLU cc_start: 0.8320 (tt0) cc_final: 0.8108 (tt0) REVERT: A 394 ARG cc_start: 0.8267 (ptm-80) cc_final: 0.8023 (ptt180) REVERT: A 621 LYS cc_start: 0.7772 (mttm) cc_final: 0.7237 (ttpt) REVERT: B 7 ARG cc_start: 0.7884 (mtm110) cc_final: 0.7627 (mtm110) REVERT: B 21 ARG cc_start: 0.8233 (mpp80) cc_final: 0.7983 (mtm-85) REVERT: B 38 GLN cc_start: 0.8131 (mp10) cc_final: 0.7924 (mm-40) REVERT: B 91 GLU cc_start: 0.7995 (pt0) cc_final: 0.7556 (tt0) REVERT: B 216 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 226 GLU cc_start: 0.8593 (pt0) cc_final: 0.7863 (pm20) REVERT: B 249 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8665 (t) REVERT: B 259 GLU cc_start: 0.7900 (tp30) cc_final: 0.7642 (tp30) REVERT: B 394 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7774 (ttm-80) REVERT: B 568 THR cc_start: 0.8076 (p) cc_final: 0.7855 (p) outliers start: 21 outliers final: 8 residues processed: 150 average time/residue: 0.7806 time to fit residues: 123.9891 Evaluate side-chains 145 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 0.0010 chunk 3 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101002 restraints weight = 13167.603| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.13 r_work: 0.3203 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10787 Z= 0.187 Angle : 0.553 7.087 14663 Z= 0.282 Chirality : 0.042 0.140 1583 Planarity : 0.005 0.048 1906 Dihedral : 4.303 21.714 1425 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.95 % Allowed : 10.46 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1304 helix: 0.95 (0.21), residues: 587 sheet: -0.20 (0.43), residues: 140 loop : 0.08 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 156 TYR 0.021 0.002 TYR A 460 PHE 0.017 0.002 PHE A 386 TRP 0.011 0.002 TRP B 176 HIS 0.011 0.001 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00429 (10787) covalent geometry : angle 0.55291 (14663) hydrogen bonds : bond 0.04118 ( 511) hydrogen bonds : angle 5.11887 ( 1428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.7537 (tpp-160) REVERT: A 7 ARG cc_start: 0.8225 (mtt90) cc_final: 0.7913 (mtt90) REVERT: A 169 GLU cc_start: 0.7926 (pm20) cc_final: 0.7229 (pm20) REVERT: A 184 GLU cc_start: 0.8310 (tt0) cc_final: 0.8101 (tt0) REVERT: A 394 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.7979 (ptt180) REVERT: A 621 LYS cc_start: 0.7787 (mttm) cc_final: 0.7244 (ttpt) REVERT: B 7 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7336 (mtm-85) REVERT: B 21 ARG cc_start: 0.8220 (mpp80) cc_final: 0.7806 (mtm-85) REVERT: B 38 GLN cc_start: 0.8181 (mp10) cc_final: 0.7961 (mm-40) REVERT: B 216 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 226 GLU cc_start: 0.8553 (pt0) cc_final: 0.7836 (pm20) REVERT: B 249 SER cc_start: 0.8905 (m) cc_final: 0.8696 (t) REVERT: B 394 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7757 (ttm-80) REVERT: B 644 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8447 (mm-40) outliers start: 22 outliers final: 10 residues processed: 152 average time/residue: 0.7684 time to fit residues: 123.7158 Evaluate side-chains 148 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 7 ARG Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.126140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.101278 restraints weight = 13079.300| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.12 r_work: 0.3209 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10787 Z= 0.165 Angle : 0.544 6.944 14663 Z= 0.277 Chirality : 0.041 0.147 1583 Planarity : 0.004 0.047 1906 Dihedral : 4.257 21.286 1425 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.68 % Allowed : 11.52 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.22), residues: 1304 helix: 1.07 (0.21), residues: 587 sheet: -0.06 (0.43), residues: 140 loop : 0.09 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 156 TYR 0.020 0.002 TYR A 460 PHE 0.014 0.001 PHE A 386 TRP 0.012 0.001 TRP B 176 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00375 (10787) covalent geometry : angle 0.54428 (14663) hydrogen bonds : bond 0.03982 ( 511) hydrogen bonds : angle 5.04178 ( 1428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7796 (tpp-160) cc_final: 0.7401 (tpp-160) REVERT: A 7 ARG cc_start: 0.8221 (mtt90) cc_final: 0.7963 (mtt90) REVERT: A 48 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: A 169 GLU cc_start: 0.7904 (pm20) cc_final: 0.7217 (pm20) REVERT: A 184 GLU cc_start: 0.8307 (tt0) cc_final: 0.8096 (tt0) REVERT: A 394 ARG cc_start: 0.8244 (ptm-80) cc_final: 0.7964 (ptt180) REVERT: A 621 LYS cc_start: 0.7783 (mttm) cc_final: 0.7236 (ttpt) REVERT: B 7 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7503 (ttm-80) REVERT: B 21 ARG cc_start: 0.8194 (mpp80) cc_final: 0.7787 (mtm-85) REVERT: B 38 GLN cc_start: 0.8136 (mp10) cc_final: 0.7930 (mm-40) REVERT: B 91 GLU cc_start: 0.7991 (pt0) cc_final: 0.7738 (tt0) REVERT: B 216 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 249 SER cc_start: 0.8901 (m) cc_final: 0.8700 (t) REVERT: B 259 GLU cc_start: 0.7882 (tp30) cc_final: 0.7606 (tp30) REVERT: B 394 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7779 (ttm-80) REVERT: B 644 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8463 (mm-40) outliers start: 19 outliers final: 8 residues processed: 151 average time/residue: 0.7828 time to fit residues: 125.5419 Evaluate side-chains 147 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 124 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.124562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099453 restraints weight = 13107.561| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.12 r_work: 0.3177 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10787 Z= 0.222 Angle : 0.588 8.697 14663 Z= 0.298 Chirality : 0.043 0.221 1583 Planarity : 0.005 0.049 1906 Dihedral : 4.399 21.206 1425 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.68 % Allowed : 12.23 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1304 helix: 1.00 (0.21), residues: 587 sheet: -0.00 (0.43), residues: 137 loop : 0.15 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 156 TYR 0.021 0.002 TYR A 460 PHE 0.017 0.002 PHE A 386 TRP 0.014 0.002 TRP B 176 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00510 (10787) covalent geometry : angle 0.58809 (14663) hydrogen bonds : bond 0.04275 ( 511) hydrogen bonds : angle 5.10093 ( 1428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7153 (ttm-80) REVERT: A 48 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: A 169 GLU cc_start: 0.7882 (pm20) cc_final: 0.7208 (pm20) REVERT: A 184 GLU cc_start: 0.8316 (tt0) cc_final: 0.8104 (tt0) REVERT: A 394 ARG cc_start: 0.8274 (ptm-80) cc_final: 0.7970 (ptt180) REVERT: A 621 LYS cc_start: 0.7785 (mttm) cc_final: 0.7233 (ttpt) REVERT: B 7 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7449 (ttm-80) REVERT: B 21 ARG cc_start: 0.8178 (mpp80) cc_final: 0.7761 (mtm-85) REVERT: B 38 GLN cc_start: 0.8183 (mp10) cc_final: 0.7926 (mm-40) REVERT: B 91 GLU cc_start: 0.8069 (pt0) cc_final: 0.7774 (tt0) REVERT: B 216 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7787 (mm-30) REVERT: B 249 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8721 (t) REVERT: B 394 ARG cc_start: 0.8077 (ttp-110) cc_final: 0.7766 (ttm-80) REVERT: B 644 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8480 (mm-40) outliers start: 19 outliers final: 11 residues processed: 152 average time/residue: 0.7784 time to fit residues: 125.4417 Evaluate side-chains 149 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** 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 = 0.3673 r_free = 0.3673 target = 0.126852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102203 restraints weight = 13019.016| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.11 r_work: 0.3223 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10787 Z= 0.131 Angle : 0.532 8.279 14663 Z= 0.270 Chirality : 0.040 0.176 1583 Planarity : 0.004 0.047 1906 Dihedral : 4.201 20.742 1425 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.51 % Allowed : 12.68 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.22), residues: 1304 helix: 1.25 (0.21), residues: 587 sheet: 0.12 (0.43), residues: 140 loop : 0.15 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 156 TYR 0.016 0.002 TYR A 460 PHE 0.011 0.001 PHE A 482 TRP 0.016 0.001 TRP A 176 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00295 (10787) covalent geometry : angle 0.53159 (14663) hydrogen bonds : bond 0.03736 ( 511) hydrogen bonds : angle 4.94746 ( 1428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.429 Fit side-chains REVERT: A 5 ARG cc_start: 0.7836 (tpp-160) cc_final: 0.7470 (ttm-80) REVERT: A 7 ARG cc_start: 0.8269 (mtt90) cc_final: 0.8048 (mtt90) REVERT: A 48 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: A 51 HIS cc_start: 0.6080 (m-70) cc_final: 0.5775 (m-70) REVERT: A 169 GLU cc_start: 0.7878 (pm20) cc_final: 0.7212 (pm20) REVERT: A 394 ARG cc_start: 0.8267 (ptm-80) cc_final: 0.8050 (ptt180) REVERT: A 410 ASP cc_start: 0.8402 (t0) cc_final: 0.7925 (m-30) REVERT: A 571 ASP cc_start: 0.8112 (m-30) cc_final: 0.7754 (m-30) REVERT: A 621 LYS cc_start: 0.7761 (mttm) cc_final: 0.7223 (ttpt) REVERT: B 7 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7369 (ttm-80) REVERT: B 21 ARG cc_start: 0.8157 (mpp80) cc_final: 0.7775 (mtm-85) REVERT: B 38 GLN cc_start: 0.8096 (mp10) cc_final: 0.7844 (mm-40) REVERT: B 91 GLU cc_start: 0.8073 (pt0) cc_final: 0.7871 (tt0) REVERT: B 216 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 394 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7742 (ttm-80) REVERT: B 644 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8469 (mm-40) outliers start: 17 outliers final: 9 residues processed: 149 average time/residue: 0.7427 time to fit residues: 117.4815 Evaluate side-chains 144 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101571 restraints weight = 12964.932| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.11 r_work: 0.3213 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10787 Z= 0.154 Angle : 0.551 9.077 14663 Z= 0.277 Chirality : 0.041 0.176 1583 Planarity : 0.004 0.048 1906 Dihedral : 4.217 20.215 1425 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.42 % Allowed : 12.94 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.22), residues: 1304 helix: 1.27 (0.21), residues: 588 sheet: 0.19 (0.42), residues: 140 loop : 0.18 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 156 TYR 0.018 0.002 TYR A 460 PHE 0.012 0.001 PHE A 386 TRP 0.021 0.001 TRP A 176 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00351 (10787) covalent geometry : angle 0.55060 (14663) hydrogen bonds : bond 0.03824 ( 511) hydrogen bonds : angle 4.94321 ( 1428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.385 Fit side-chains REVERT: A 5 ARG cc_start: 0.7826 (tpp-160) cc_final: 0.7463 (ttm-80) REVERT: A 7 ARG cc_start: 0.8283 (mtt90) cc_final: 0.8079 (mtt90) REVERT: A 48 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: A 51 HIS cc_start: 0.6095 (m-70) cc_final: 0.5802 (m-70) REVERT: A 169 GLU cc_start: 0.7962 (pm20) cc_final: 0.7239 (pm20) REVERT: A 394 ARG cc_start: 0.8260 (ptm-80) cc_final: 0.7970 (ptt180) REVERT: A 571 ASP cc_start: 0.8093 (m-30) cc_final: 0.7741 (m-30) REVERT: A 621 LYS cc_start: 0.7764 (mttm) cc_final: 0.7237 (ttpt) REVERT: B 7 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7518 (ttm-80) REVERT: B 21 ARG cc_start: 0.8143 (mpp80) cc_final: 0.7765 (mtm-85) REVERT: B 38 GLN cc_start: 0.8027 (mp10) cc_final: 0.7797 (mm-40) REVERT: B 216 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 394 ARG cc_start: 0.8051 (ttp-110) cc_final: 0.7737 (ttm-80) REVERT: B 500 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7753 (mtm110) REVERT: B 644 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8464 (mm-40) outliers start: 16 outliers final: 9 residues processed: 146 average time/residue: 0.7246 time to fit residues: 112.3926 Evaluate side-chains 144 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.126123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101290 restraints weight = 12998.143| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.11 r_work: 0.3210 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10787 Z= 0.161 Angle : 0.564 9.819 14663 Z= 0.282 Chirality : 0.042 0.192 1583 Planarity : 0.004 0.048 1906 Dihedral : 4.242 19.995 1425 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.98 % Allowed : 13.48 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.22), residues: 1304 helix: 1.27 (0.21), residues: 588 sheet: 0.20 (0.42), residues: 140 loop : 0.20 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 156 TYR 0.018 0.002 TYR A 460 PHE 0.013 0.001 PHE A 386 TRP 0.026 0.001 TRP A 176 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00370 (10787) covalent geometry : angle 0.56387 (14663) hydrogen bonds : bond 0.03845 ( 511) hydrogen bonds : angle 4.93913 ( 1428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.408 Fit side-chains REVERT: A 5 ARG cc_start: 0.7784 (tpp-160) cc_final: 0.7185 (ttm-80) REVERT: A 48 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6739 (mp0) REVERT: A 51 HIS cc_start: 0.6062 (m-70) cc_final: 0.5743 (m-70) REVERT: A 169 GLU cc_start: 0.7964 (pm20) cc_final: 0.7240 (pm20) REVERT: A 394 ARG cc_start: 0.8270 (ptm-80) cc_final: 0.7984 (ptt180) REVERT: A 410 ASP cc_start: 0.8409 (t0) cc_final: 0.7940 (m-30) REVERT: A 621 LYS cc_start: 0.7763 (mttm) cc_final: 0.7234 (ttpt) REVERT: B 7 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7491 (ttm-80) REVERT: B 21 ARG cc_start: 0.8159 (mpp80) cc_final: 0.7785 (mtm-85) REVERT: B 38 GLN cc_start: 0.8019 (mp10) cc_final: 0.7817 (mm-40) REVERT: B 216 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 394 ARG cc_start: 0.8057 (ttp-110) cc_final: 0.7746 (ttm-80) REVERT: B 500 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7745 (mtm110) REVERT: B 644 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8469 (mm-40) outliers start: 11 outliers final: 9 residues processed: 142 average time/residue: 0.7459 time to fit residues: 112.4964 Evaluate side-chains 144 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 95 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102070 restraints weight = 12911.725| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.11 r_work: 0.3220 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10787 Z= 0.145 Angle : 0.561 11.867 14663 Z= 0.278 Chirality : 0.041 0.174 1583 Planarity : 0.004 0.047 1906 Dihedral : 4.209 19.682 1425 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.24 % Allowed : 13.48 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.22), residues: 1304 helix: 1.31 (0.21), residues: 588 sheet: 0.21 (0.42), residues: 140 loop : 0.23 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 98 TYR 0.017 0.002 TYR A 460 PHE 0.011 0.001 PHE A 482 TRP 0.031 0.002 TRP A 176 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00331 (10787) covalent geometry : angle 0.56076 (14663) hydrogen bonds : bond 0.03749 ( 511) hydrogen bonds : angle 4.89967 ( 1428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.406 Fit side-chains REVERT: A 5 ARG cc_start: 0.7825 (tpp-160) cc_final: 0.7234 (ttm-80) REVERT: A 7 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7963 (mtt90) REVERT: A 48 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: A 169 GLU cc_start: 0.7955 (pm20) cc_final: 0.7229 (pm20) REVERT: A 394 ARG cc_start: 0.8265 (ptm-80) cc_final: 0.7971 (ptt180) REVERT: A 410 ASP cc_start: 0.8389 (t0) cc_final: 0.7943 (m-30) REVERT: A 621 LYS cc_start: 0.7761 (mttm) cc_final: 0.7229 (ttpt) REVERT: B 7 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7467 (ttm-80) REVERT: B 21 ARG cc_start: 0.8137 (mpp80) cc_final: 0.7754 (mtm-85) REVERT: B 38 GLN cc_start: 0.7986 (mp10) cc_final: 0.7780 (mm-40) REVERT: B 216 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 394 ARG cc_start: 0.8032 (ttp-110) cc_final: 0.7722 (ttm-80) REVERT: B 500 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7751 (mtm110) REVERT: B 644 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8447 (mm-40) outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 0.7298 time to fit residues: 109.3672 Evaluate side-chains 143 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain B residue 512 ASP Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 584 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 7.9990 chunk 113 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.126344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.101474 restraints weight = 13021.701| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.11 r_work: 0.3210 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10787 Z= 0.164 Angle : 0.567 11.967 14663 Z= 0.283 Chirality : 0.041 0.175 1583 Planarity : 0.004 0.048 1906 Dihedral : 4.251 19.248 1425 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.98 % Allowed : 13.48 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1304 helix: 1.28 (0.21), residues: 588 sheet: 0.28 (0.43), residues: 140 loop : 0.24 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 98 TYR 0.018 0.002 TYR A 460 PHE 0.013 0.001 PHE A 386 TRP 0.032 0.002 TRP A 176 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00377 (10787) covalent geometry : angle 0.56717 (14663) hydrogen bonds : bond 0.03845 ( 511) hydrogen bonds : angle 4.92632 ( 1428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4591.26 seconds wall clock time: 78 minutes 45.44 seconds (4725.44 seconds total)