Starting phenix.real_space_refine on Mon Jul 28 16:36:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghc_40040/07_2025/8ghc_40040.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghc_40040/07_2025/8ghc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ghc_40040/07_2025/8ghc_40040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghc_40040/07_2025/8ghc_40040.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghc_40040/07_2025/8ghc_40040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghc_40040/07_2025/8ghc_40040.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.75, per 1000 atoms: 0.64 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: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.06 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: 3.10 Time building geometry restraints manager: 2.78 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 663 or resid 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: 23.410 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.570 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.590 ------------------------------------------------------------------------------- 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 : 5.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.050 0.004 TRP B 197 HIS 0.014 0.003 HIS A 480 PHE 0.021 0.004 PHE A 278 TYR 0.023 0.003 TYR A 359 ARG 0.013 0.002 ARG B 5 Details of bonding type rmsd hydrogen bonds : bond 0.14419 ( 511) hydrogen bonds : angle 7.26456 ( 1428) covalent geometry : bond 0.00943 (10787) covalent geometry : angle 0.90735 (14663) *********************** 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 : 1.042 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: 0.7649 (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: 1.6371 time to fit residues: 310.1206 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 : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN B 406 GLN B 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103162 restraints weight = 12888.520| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.11 r_work: 0.3237 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1127 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 : 0.567 7.759 14663 Z= 0.295 Chirality : 0.041 0.138 1583 Planarity : 0.005 0.062 1906 Dihedral : 4.478 24.218 1425 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.42 % Allowed : 7.54 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1304 helix: 0.19 (0.20), residues: 587 sheet: -0.52 (0.42), residues: 134 loop : -0.17 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 25 HIS 0.006 0.001 HIS B 360 PHE 0.016 0.001 PHE A 386 TYR 0.022 0.002 TYR A 460 ARG 0.006 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 511) hydrogen bonds : angle 5.54331 ( 1428) covalent geometry : bond 0.00336 (10787) covalent geometry : angle 0.56710 (14663) *********************** 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 167 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.7444 (tpp-160) REVERT: A 7 ARG cc_start: 0.8204 (mtt90) cc_final: 0.7941 (mtt90) REVERT: A 169 GLU cc_start: 0.7943 (pm20) cc_final: 0.7219 (pm20) REVERT: A 184 GLU cc_start: 0.8316 (tt0) cc_final: 0.8111 (tt0) REVERT: A 394 ARG cc_start: 0.8252 (ptm-80) cc_final: 0.8005 (ptt180) REVERT: A 621 LYS cc_start: 0.7801 (mttm) cc_final: 0.7217 (tmmt) REVERT: B 7 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7451 (mtp85) REVERT: B 84 GLN cc_start: 0.8411 (tt0) cc_final: 0.8007 (mm-40) REVERT: B 91 GLU cc_start: 0.8049 (pt0) cc_final: 0.7477 (mt-10) REVERT: B 216 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 249 SER cc_start: 0.8884 (m) cc_final: 0.8667 (t) REVERT: B 394 ARG cc_start: 0.8024 (ttp-110) cc_final: 0.7771 (ttm-80) REVERT: B 473 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7924 (mtm110) REVERT: B 568 THR cc_start: 0.8129 (p) cc_final: 0.7913 (p) outliers start: 16 outliers final: 8 residues processed: 157 average time/residue: 1.5747 time to fit residues: 263.0206 Evaluate side-chains 146 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 16 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 0.0270 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.127996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.103278 restraints weight = 13054.476| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.12 r_work: 0.3239 rms_B_bonded: 2.39 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: 0.8499 moved from start: 0.1447 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= 0.138 Angle : 0.530 7.251 14663 Z= 0.270 Chirality : 0.040 0.136 1583 Planarity : 0.004 0.044 1906 Dihedral : 4.247 22.063 1425 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.77 % Allowed : 9.75 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1304 helix: 0.82 (0.21), residues: 586 sheet: -0.38 (0.43), residues: 134 loop : -0.02 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 176 HIS 0.005 0.001 HIS A 596 PHE 0.013 0.001 PHE A 386 TYR 0.019 0.002 TYR A 460 ARG 0.006 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 511) hydrogen bonds : angle 5.15309 ( 1428) covalent geometry : bond 0.00307 (10787) covalent geometry : angle 0.52956 (14663) *********************** 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 164 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 3.096 Fit side-chains REVERT: A 5 ARG cc_start: 0.7760 (tpp-160) cc_final: 0.7354 (tpp-160) REVERT: A 169 GLU cc_start: 0.7915 (pm20) cc_final: 0.7207 (pm20) REVERT: A 184 GLU cc_start: 0.8316 (tt0) cc_final: 0.8103 (tt0) REVERT: A 394 ARG cc_start: 0.8270 (ptm-80) cc_final: 0.8025 (ptt180) REVERT: A 621 LYS cc_start: 0.7780 (mttm) cc_final: 0.7248 (ttpt) REVERT: B 7 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7627 (mtm110) REVERT: B 21 ARG cc_start: 0.8225 (mpp80) cc_final: 0.8021 (mtm-85) REVERT: B 91 GLU cc_start: 0.8002 (pt0) cc_final: 0.7533 (tt0) REVERT: B 216 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 226 GLU cc_start: 0.8590 (pt0) cc_final: 0.7859 (pm20) REVERT: B 249 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8665 (t) REVERT: B 259 GLU cc_start: 0.7878 (tp30) cc_final: 0.7623 (tp30) REVERT: B 360 HIS cc_start: 0.8883 (t-170) cc_final: 0.8479 (t-170) REVERT: B 394 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7779 (ttm-80) REVERT: B 568 THR cc_start: 0.8080 (p) cc_final: 0.7859 (p) outliers start: 20 outliers final: 8 residues processed: 152 average time/residue: 2.0993 time to fit residues: 340.0840 Evaluate side-chains 146 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 257 MET 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 2 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.125234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100098 restraints weight = 12978.458| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.11 r_work: 0.3191 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10787 Z= 0.217 Angle : 0.575 7.129 14663 Z= 0.292 Chirality : 0.043 0.137 1583 Planarity : 0.005 0.048 1906 Dihedral : 4.374 21.996 1425 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.22 % Allowed : 10.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1304 helix: 0.89 (0.21), residues: 586 sheet: -0.22 (0.42), residues: 140 loop : 0.06 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 176 HIS 0.008 0.001 HIS B 51 PHE 0.018 0.002 PHE A 386 TYR 0.022 0.002 TYR A 460 ARG 0.008 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 511) hydrogen bonds : angle 5.15750 ( 1428) covalent geometry : bond 0.00500 (10787) covalent geometry : angle 0.57454 (14663) *********************** 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 165 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.214 Fit side-chains REVERT: A 5 ARG cc_start: 0.7823 (tpp-160) cc_final: 0.7465 (tpp-160) REVERT: A 7 ARG cc_start: 0.8247 (mtt90) cc_final: 0.7942 (mtt90) REVERT: A 169 GLU cc_start: 0.7916 (pm20) cc_final: 0.7230 (pm20) REVERT: A 184 GLU cc_start: 0.8326 (tt0) cc_final: 0.8115 (tt0) REVERT: A 394 ARG cc_start: 0.8271 (ptm-80) cc_final: 0.7986 (ptt180) REVERT: A 571 ASP cc_start: 0.8107 (m-30) cc_final: 0.7738 (m-30) REVERT: A 621 LYS cc_start: 0.7798 (mttm) cc_final: 0.7248 (ttpt) REVERT: B 7 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7405 (mtm-85) REVERT: B 21 ARG cc_start: 0.8196 (mpp80) cc_final: 0.7951 (mtm-85) REVERT: B 38 GLN cc_start: 0.8199 (mp10) cc_final: 0.7975 (mm-40) REVERT: B 216 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 226 GLU cc_start: 0.8526 (pt0) cc_final: 0.7841 (pm20) REVERT: B 249 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8707 (t) REVERT: B 394 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7758 (ttm-80) REVERT: B 644 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8441 (mm-40) outliers start: 25 outliers final: 10 residues processed: 153 average time/residue: 1.6906 time to fit residues: 274.8188 Evaluate side-chains 147 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 59 LEU Chi-restraints excluded: chain B residue 197 TRP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 85 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 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 = 0.3680 r_free = 0.3680 target = 0.127371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102704 restraints weight = 12974.927| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.11 r_work: 0.3230 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10787 Z= 0.127 Angle : 0.521 7.247 14663 Z= 0.265 Chirality : 0.040 0.155 1583 Planarity : 0.004 0.046 1906 Dihedral : 4.186 21.128 1425 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.60 % Allowed : 11.88 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1304 helix: 1.14 (0.21), residues: 586 sheet: -0.09 (0.43), residues: 140 loop : 0.08 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 176 HIS 0.005 0.001 HIS B 360 PHE 0.011 0.001 PHE A 482 TYR 0.018 0.002 TYR A 460 ARG 0.009 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 511) hydrogen bonds : angle 4.99645 ( 1428) covalent geometry : bond 0.00284 (10787) covalent geometry : angle 0.52064 (14663) *********************** 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 164 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 5 ARG cc_start: 0.7791 (tpp-160) cc_final: 0.7154 (ttm-80) REVERT: A 7 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7989 (mtt90) REVERT: A 48 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: A 169 GLU cc_start: 0.7882 (pm20) cc_final: 0.7204 (pm20) REVERT: A 394 ARG cc_start: 0.8242 (ptm-80) cc_final: 0.7967 (ptt180) REVERT: A 410 ASP cc_start: 0.8398 (t0) cc_final: 0.7944 (m-30) REVERT: A 621 LYS cc_start: 0.7774 (mttm) cc_final: 0.7236 (ttpt) REVERT: B 7 ARG cc_start: 0.7688 (mtm110) cc_final: 0.7478 (ttm-80) REVERT: B 21 ARG cc_start: 0.8185 (mpp80) cc_final: 0.7781 (mtm-85) REVERT: B 38 GLN cc_start: 0.8120 (mp10) cc_final: 0.7906 (mm-40) REVERT: B 91 GLU cc_start: 0.7940 (pt0) cc_final: 0.7606 (tt0) REVERT: B 216 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 259 GLU cc_start: 0.7896 (tp30) cc_final: 0.7620 (tp30) REVERT: B 360 HIS cc_start: 0.8808 (t-170) cc_final: 0.8475 (t-170) REVERT: B 394 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7774 (ttm-80) REVERT: B 644 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8449 (mm-40) outliers start: 18 outliers final: 7 residues processed: 156 average time/residue: 2.1465 time to fit residues: 358.2482 Evaluate side-chains 148 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 523 SER 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 109 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.127262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102547 restraints weight = 13044.739| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.11 r_work: 0.3228 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1749 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= 0.136 Angle : 0.530 7.961 14663 Z= 0.269 Chirality : 0.041 0.210 1583 Planarity : 0.004 0.046 1906 Dihedral : 4.143 20.343 1425 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.86 % Allowed : 12.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1304 helix: 1.27 (0.21), residues: 588 sheet: 0.01 (0.43), residues: 140 loop : 0.14 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 176 HIS 0.005 0.001 HIS B 360 PHE 0.011 0.001 PHE A 386 TYR 0.018 0.002 TYR A 460 ARG 0.009 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 511) hydrogen bonds : angle 4.92872 ( 1428) covalent geometry : bond 0.00308 (10787) covalent geometry : angle 0.53011 (14663) *********************** 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 163 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.358 Fit side-chains REVERT: A 5 ARG cc_start: 0.7771 (tpp-160) cc_final: 0.7119 (ttm-80) REVERT: A 48 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: A 51 HIS cc_start: 0.6095 (m-70) cc_final: 0.5843 (m-70) REVERT: A 169 GLU cc_start: 0.7897 (pm20) cc_final: 0.7218 (pm20) REVERT: A 394 ARG cc_start: 0.8254 (ptm-80) cc_final: 0.7956 (ptt180) REVERT: A 571 ASP cc_start: 0.8092 (m-30) cc_final: 0.7717 (m-30) REVERT: A 621 LYS cc_start: 0.7766 (mttm) cc_final: 0.7238 (ttpt) REVERT: B 21 ARG cc_start: 0.8170 (mpp80) cc_final: 0.7776 (mtm-85) REVERT: B 91 GLU cc_start: 0.8012 (pt0) cc_final: 0.7800 (tt0) REVERT: B 216 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7718 (mm-30) REVERT: B 259 GLU cc_start: 0.7910 (tp30) cc_final: 0.7626 (tp30) REVERT: B 360 HIS cc_start: 0.8784 (t-90) cc_final: 0.8493 (t-170) REVERT: B 394 ARG cc_start: 0.8064 (ttp-110) cc_final: 0.7752 (ttm-80) REVERT: B 644 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8457 (mm-40) outliers start: 21 outliers final: 11 residues processed: 152 average time/residue: 1.7079 time to fit residues: 276.9945 Evaluate side-chains 148 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 604 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100352 restraints weight = 13155.393| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.14 r_work: 0.3195 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10787 Z= 0.197 Angle : 0.568 8.090 14663 Z= 0.287 Chirality : 0.043 0.191 1583 Planarity : 0.005 0.048 1906 Dihedral : 4.282 20.245 1425 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.86 % Allowed : 12.15 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1304 helix: 1.17 (0.21), residues: 588 sheet: 0.10 (0.43), residues: 140 loop : 0.18 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 176 HIS 0.005 0.001 HIS B 360 PHE 0.017 0.002 PHE A 386 TYR 0.020 0.002 TYR A 460 ARG 0.009 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 511) hydrogen bonds : angle 4.98768 ( 1428) covalent geometry : bond 0.00454 (10787) covalent geometry : angle 0.56843 (14663) *********************** 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 161 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.183 Fit side-chains REVERT: A 5 ARG cc_start: 0.7788 (tpp-160) cc_final: 0.7413 (ttm-80) REVERT: A 48 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: A 51 HIS cc_start: 0.6124 (m-70) cc_final: 0.5852 (m-70) REVERT: A 169 GLU cc_start: 0.7900 (pm20) cc_final: 0.7215 (pm20) REVERT: A 394 ARG cc_start: 0.8289 (ptm-80) cc_final: 0.7988 (ptt180) REVERT: A 571 ASP cc_start: 0.8126 (m-30) cc_final: 0.7770 (m-30) REVERT: A 621 LYS cc_start: 0.7780 (mttm) cc_final: 0.7256 (ttpt) REVERT: B 21 ARG cc_start: 0.8139 (mpp80) cc_final: 0.7763 (mtm-85) REVERT: B 91 GLU cc_start: 0.8120 (pt0) cc_final: 0.7772 (tt0) REVERT: B 216 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7743 (mm-30) REVERT: B 394 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7767 (ttm-80) REVERT: B 644 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8479 (mm-40) outliers start: 21 outliers final: 14 residues processed: 151 average time/residue: 1.6443 time to fit residues: 264.6686 Evaluate side-chains 152 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 604 MET 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 226 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 51 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 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 = 0.3662 r_free = 0.3662 target = 0.125926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101154 restraints weight = 12944.648| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.11 r_work: 0.3206 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10787 Z= 0.165 Angle : 0.562 10.864 14663 Z= 0.283 Chirality : 0.042 0.175 1583 Planarity : 0.005 0.048 1906 Dihedral : 4.274 20.186 1425 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1304 helix: 1.22 (0.21), residues: 588 sheet: 0.18 (0.43), residues: 134 loop : 0.15 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 176 HIS 0.009 0.001 HIS B 596 PHE 0.014 0.001 PHE A 386 TYR 0.019 0.002 TYR A 460 ARG 0.009 0.001 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 511) hydrogen bonds : angle 4.96084 ( 1428) covalent geometry : bond 0.00378 (10787) covalent geometry : angle 0.56184 (14663) *********************** 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 151 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.427 Fit side-chains REVERT: A 5 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7283 (ttm-80) REVERT: A 48 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: A 51 HIS cc_start: 0.6022 (m-70) cc_final: 0.5742 (m-70) REVERT: A 169 GLU cc_start: 0.7877 (pm20) cc_final: 0.7172 (pm20) REVERT: A 394 ARG cc_start: 0.8265 (ptm-80) cc_final: 0.7975 (ptt180) REVERT: A 410 ASP cc_start: 0.8417 (t0) cc_final: 0.7931 (m-30) REVERT: A 621 LYS cc_start: 0.7760 (mttm) cc_final: 0.7238 (ttpt) REVERT: B 21 ARG cc_start: 0.8164 (mpp80) cc_final: 0.7799 (mtm-85) REVERT: B 91 GLU cc_start: 0.8162 (pt0) cc_final: 0.7811 (tt0) REVERT: B 216 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 259 GLU cc_start: 0.7937 (tp30) cc_final: 0.7720 (tp30) REVERT: B 394 ARG cc_start: 0.8065 (ttp-110) cc_final: 0.7738 (ttm-80) REVERT: B 644 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8472 (mm-40) outliers start: 17 outliers final: 13 residues processed: 143 average time/residue: 2.2007 time to fit residues: 335.3722 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 : 1.076 ------------------------------------------------------------------------------- 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 214 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 604 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 121 optimal weight: 0.0060 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101929 restraints weight = 13228.562| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.14 r_work: 0.3218 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1903 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= 0.143 Angle : 0.550 10.038 14663 Z= 0.276 Chirality : 0.041 0.197 1583 Planarity : 0.004 0.047 1906 Dihedral : 4.209 19.809 1425 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.68 % Allowed : 12.85 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1304 helix: 1.30 (0.21), residues: 588 sheet: 0.13 (0.42), residues: 140 loop : 0.19 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 176 HIS 0.008 0.001 HIS B 596 PHE 0.011 0.001 PHE A 482 TYR 0.017 0.002 TYR A 460 ARG 0.009 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 511) hydrogen bonds : angle 4.90622 ( 1428) covalent geometry : bond 0.00326 (10787) covalent geometry : angle 0.55045 (14663) *********************** 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 155 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.333 Fit side-chains REVERT: A 5 ARG cc_start: 0.7790 (tpp-160) cc_final: 0.7287 (ttm-80) REVERT: A 48 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: A 169 GLU cc_start: 0.7973 (pm20) cc_final: 0.7241 (pm20) REVERT: A 394 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.7966 (ptt180) REVERT: A 410 ASP cc_start: 0.8414 (t0) cc_final: 0.7944 (m-30) REVERT: A 621 LYS cc_start: 0.7758 (mttm) cc_final: 0.7224 (ttpt) REVERT: B 21 ARG cc_start: 0.8135 (mpp80) cc_final: 0.7780 (mtm-85) REVERT: B 91 GLU cc_start: 0.8160 (pt0) cc_final: 0.7899 (tt0) REVERT: B 216 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 226 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: B 259 GLU cc_start: 0.7940 (tp30) cc_final: 0.7706 (tp30) REVERT: B 360 HIS cc_start: 0.8785 (t-90) cc_final: 0.8475 (t-170) REVERT: B 394 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7745 (ttm-80) REVERT: B 500 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7771 (mtm110) REVERT: B 644 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8470 (mm-40) outliers start: 19 outliers final: 11 residues processed: 145 average time/residue: 2.1014 time to fit residues: 323.9431 Evaluate side-chains 147 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 226 GLU 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 563 MET 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 83 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.127083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102413 restraints weight = 13051.030| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.11 r_work: 0.3228 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10787 Z= 0.137 Angle : 0.556 12.552 14663 Z= 0.276 Chirality : 0.040 0.169 1583 Planarity : 0.004 0.047 1906 Dihedral : 4.193 19.087 1425 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.15 % Allowed : 13.48 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1304 helix: 1.35 (0.21), residues: 588 sheet: 0.15 (0.42), residues: 140 loop : 0.23 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 176 HIS 0.008 0.001 HIS B 596 PHE 0.011 0.001 PHE A 482 TYR 0.017 0.002 TYR B 460 ARG 0.011 0.001 ARG A 7 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 511) hydrogen bonds : angle 4.87282 ( 1428) covalent geometry : bond 0.00312 (10787) covalent geometry : angle 0.55611 (14663) ********************** 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 151 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.165 Fit side-chains REVERT: A 5 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.7236 (ttm-80) REVERT: A 48 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: A 169 GLU cc_start: 0.7959 (pm20) cc_final: 0.7238 (pm20) REVERT: A 394 ARG cc_start: 0.8264 (ptm-80) cc_final: 0.7964 (ptt180) REVERT: A 410 ASP cc_start: 0.8391 (t0) cc_final: 0.7948 (m-30) REVERT: A 621 LYS cc_start: 0.7761 (mttm) cc_final: 0.7225 (ttpt) REVERT: B 21 ARG cc_start: 0.8127 (mpp80) cc_final: 0.7798 (mtm-85) REVERT: B 91 GLU cc_start: 0.8165 (pt0) cc_final: 0.7910 (tt0) REVERT: B 216 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 259 GLU cc_start: 0.7954 (tp30) cc_final: 0.7717 (tp30) REVERT: B 360 HIS cc_start: 0.8756 (t-90) cc_final: 0.8473 (t-170) REVERT: B 394 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7753 (ttm-80) REVERT: B 500 ARG cc_start: 0.8031 (ttp-110) cc_final: 0.7763 (mtm110) REVERT: B 644 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8465 (mm-40) outliers start: 13 outliers final: 11 residues processed: 144 average time/residue: 1.6249 time to fit residues: 249.8489 Evaluate side-chains 145 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 563 MET 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 68 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101930 restraints weight = 12983.782| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.11 r_work: 0.3219 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10787 Z= 0.149 Angle : 0.557 12.158 14663 Z= 0.279 Chirality : 0.041 0.166 1583 Planarity : 0.004 0.047 1906 Dihedral : 4.216 18.810 1425 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.15 % Allowed : 13.48 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1304 helix: 1.33 (0.21), residues: 588 sheet: 0.16 (0.42), residues: 140 loop : 0.24 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 176 HIS 0.008 0.001 HIS B 596 PHE 0.012 0.001 PHE A 386 TYR 0.017 0.002 TYR A 460 ARG 0.010 0.001 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 511) hydrogen bonds : angle 4.87412 ( 1428) covalent geometry : bond 0.00342 (10787) covalent geometry : angle 0.55743 (14663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10193.86 seconds wall clock time: 186 minutes 20.16 seconds (11180.16 seconds total)