Starting phenix.real_space_refine on Tue Jun 17 08:36:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ta5_41129/06_2025/8ta5_41129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ta5_41129/06_2025/8ta5_41129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ta5_41129/06_2025/8ta5_41129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ta5_41129/06_2025/8ta5_41129.map" model { file = "/net/cci-nas-00/data/ceres_data/8ta5_41129/06_2025/8ta5_41129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ta5_41129/06_2025/8ta5_41129.cif" } resolution = 2.76 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= -0.002 sd= 0.155 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 56 5.16 5 Cl 2 4.86 5 C 6376 2.51 5 N 1634 2.21 5 O 1666 1.98 5 H 10041 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19775 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 9886 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 28, 'TRANS': 596} Chain breaks: 4 Chain: "B" Number of atoms: 9887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 9887 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 28, 'TRANS': 596} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.95, per 1000 atoms: 0.50 Number of scatterers: 19775 At special positions: 0 Unit cell: (118.25, 77.572, 117.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 56 16.00 O 1666 8.00 N 1634 7.00 C 6376 6.00 H 10041 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 67.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 89 through 124 Processing helix chain 'A' and resid 129 through 156 removed outlier: 3.770A pdb=" N TYR A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.589A pdb=" N VAL A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.510A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.913A pdb=" N MET A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 272 through 296 Processing helix chain 'A' and resid 320 through 352 removed outlier: 3.627A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 364 through 378 removed outlier: 3.525A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 388 removed outlier: 4.106A pdb=" N GLN A 385 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 388 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 420 through 425 removed outlier: 4.274A pdb=" N TRP A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 450 removed outlier: 3.914A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 removed outlier: 3.558A pdb=" N VAL A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.951A pdb=" N TYR A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 Processing helix chain 'A' and resid 530 through 547 removed outlier: 3.680A pdb=" N SER A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 572 through 578 removed outlier: 4.384A pdb=" N GLN A 575 " --> pdb=" O ARG A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.687A pdb=" N ILE A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.701A pdb=" N LEU A 602 " --> pdb=" O ARG A 598 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 641 removed outlier: 4.018A pdb=" N ALA A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 779 removed outlier: 4.303A pdb=" N LEU A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 779' Processing helix chain 'A' and resid 802 through 813 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'B' and resid 89 through 126 removed outlier: 3.584A pdb=" N PHE B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 160 removed outlier: 3.543A pdb=" N VAL B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 160' Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 181 through 198 Processing helix chain 'B' and resid 204 through 223 Processing helix chain 'B' and resid 231 through 253 removed outlier: 5.256A pdb=" N ALA B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA B 243 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 272 through 294 removed outlier: 3.599A pdb=" N VAL B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 320 through 352 removed outlier: 3.585A pdb=" N VAL B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 364 through 378 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.654A pdb=" N ALA B 388 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 430 through 450 removed outlier: 3.965A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 removed outlier: 3.562A pdb=" N VAL B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.834A pdb=" N TYR B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 530 through 547 removed outlier: 3.527A pdb=" N SER B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.543A pdb=" N ARG B 577 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 584 removed outlier: 3.849A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 606 Processing helix chain 'B' and resid 629 through 641 Processing helix chain 'B' and resid 802 through 813 Processing helix chain 'B' and resid 832 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.881A pdb=" N PHE A 270 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 270 " --> pdb=" O PHE A 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 592 removed outlier: 6.491A pdb=" N LEU A 612 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER A 626 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A 614 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 817 through 821 removed outlier: 3.566A pdb=" N GLY A 828 " --> pdb=" O VAL A 820 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 Processing sheet with id=AA6, first strand: chain 'B' and resid 590 through 592 removed outlier: 6.520A pdb=" N VAL B 591 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 612 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER B 626 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 614 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 817 through 822 removed outlier: 6.351A pdb=" N SER B 822 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1764 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: 7.13 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 10023 1.13 - 1.30: 1618 1.30 - 1.48: 3888 1.48 - 1.65: 4378 1.65 - 1.82: 94 Bond restraints: 20001 Sorted by residual: bond pdb=" N HIS A 804 " pdb=" H HIS A 804 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR A 450 " pdb=" H THR A 450 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ARG B 610 " pdb=" H ARG B 610 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N PHE A 261 " pdb=" H PHE A 261 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD1 PHE B 383 " pdb=" HD1 PHE B 383 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 19996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 30184 2.51 - 5.02: 4754 5.02 - 7.52: 1194 7.52 - 10.03: 65 10.03 - 12.54: 19 Bond angle restraints: 36216 Sorted by residual: angle pdb=" CA ASP A 402 " pdb=" CB ASP A 402 " pdb=" CG ASP A 402 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" CA ASP B 791 " pdb=" CB ASP B 791 " pdb=" CG ASP B 791 " ideal model delta sigma weight residual 112.60 118.16 -5.56 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA ASP B 313 " pdb=" CB ASP B 313 " pdb=" CG ASP B 313 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" CA ASP B 402 " pdb=" CB ASP B 402 " pdb=" CG ASP B 402 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.04e+01 angle pdb=" CA PHE B 401 " pdb=" CB PHE B 401 " pdb=" CG PHE B 401 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 ... (remaining 36211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 8512 17.73 - 35.47: 454 35.47 - 53.20: 160 53.20 - 70.93: 231 70.93 - 88.66: 18 Dihedral angle restraints: 9375 sinusoidal: 5044 harmonic: 4331 Sorted by residual: dihedral pdb=" CA GLY B 161 " pdb=" C GLY B 161 " pdb=" N SER B 162 " pdb=" CA SER B 162 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU B 176 " pdb=" C LEU B 176 " pdb=" N LYS B 177 " pdb=" CA LYS B 177 " ideal model delta harmonic sigma weight residual 180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP A 317 " pdb=" C ASP A 317 " pdb=" N LEU A 318 " pdb=" CA LEU A 318 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 9372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1000 0.078 - 0.155: 446 0.155 - 0.233: 122 0.233 - 0.310: 13 0.310 - 0.388: 5 Chirality restraints: 1586 Sorted by residual: chirality pdb=" CA PRO A 380 " pdb=" N PRO A 380 " pdb=" C PRO A 380 " pdb=" CB PRO A 380 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA PRO B 380 " pdb=" N PRO B 380 " pdb=" C PRO B 380 " pdb=" CB PRO B 380 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ASP B 402 " pdb=" N ASP B 402 " pdb=" C ASP B 402 " pdb=" CB ASP B 402 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1583 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 404 " 0.196 9.50e-02 1.11e+02 1.53e-01 4.32e+02 pdb=" NE ARG B 404 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 404 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 404 " -0.073 2.00e-02 2.50e+03 pdb=" NH2 ARG B 404 " 0.033 2.00e-02 2.50e+03 pdb="HH11 ARG B 404 " -0.177 2.00e-02 2.50e+03 pdb="HH12 ARG B 404 " 0.293 2.00e-02 2.50e+03 pdb="HH21 ARG B 404 " 0.056 2.00e-02 2.50e+03 pdb="HH22 ARG B 404 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 25 " 0.275 9.50e-02 1.11e+02 1.21e-01 1.46e+02 pdb=" NE ARG B 25 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG B 25 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG B 25 " 0.093 2.00e-02 2.50e+03 pdb=" NH2 ARG B 25 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 25 " -0.178 2.00e-02 2.50e+03 pdb="HH12 ARG B 25 " 0.068 2.00e-02 2.50e+03 pdb="HH21 ARG B 25 " -0.072 2.00e-02 2.50e+03 pdb="HH22 ARG B 25 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.142 2.00e-02 2.50e+03 5.11e-02 1.05e+02 pdb=" CG TRP A 106 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.050 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 TRP A 106 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP A 106 " 0.025 2.00e-02 2.50e+03 pdb=" HE3 TRP A 106 " 0.073 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 106 " -0.029 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 106 " -0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP A 106 " -0.069 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 914 2.18 - 2.79: 34141 2.79 - 3.39: 55064 3.39 - 4.00: 75504 4.00 - 4.60: 106702 Nonbonded interactions: 272325 Sorted by model distance: nonbonded pdb=" OE2 GLU B 264 " pdb=" HG SER B 516 " model vdw 1.580 2.450 nonbonded pdb=" OE2 GLU A 264 " pdb=" HG SER A 516 " model vdw 1.581 2.450 nonbonded pdb=" OE1 GLU B 320 " pdb=" HH TYR B 499 " model vdw 1.600 2.450 nonbonded pdb=" OE1 GLU A 238 " pdb=" HH TYR B 576 " model vdw 1.605 2.450 nonbonded pdb=" HG1 THR A 831 " pdb=" OE1 GLU A 834 " model vdw 1.607 2.450 ... (remaining 272320 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' selection = (chain 'B' and (resid 14 through 512 or (resid 513 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 514 through 841 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.340 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 42.780 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 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 : 0.013 0.041 9960 Z= 0.786 Angle : 1.801 8.204 13530 Z= 1.242 Chirality : 0.091 0.388 1586 Planarity : 0.013 0.134 1676 Dihedral : 13.219 88.665 3536 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 1.36 % Allowed : 2.62 % Favored : 96.03 % Cbeta Deviations : 0.17 % 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: -1.18 (0.20), residues: 1230 helix: -0.54 (0.15), residues: 776 sheet: -1.52 (1.16), residues: 20 loop : -0.93 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.013 TRP A 106 HIS 0.009 0.003 HIS A 513 PHE 0.064 0.012 PHE A 270 TYR 0.066 0.012 TYR A 23 ARG 0.008 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.23710 ( 601) hydrogen bonds : angle 6.46467 ( 1764) covalent geometry : bond 0.01276 ( 9960) covalent geometry : angle 1.80134 (13530) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8420 (tptp) cc_final: 0.8163 (tppt) REVERT: B 450 THR cc_start: 0.7582 (m) cc_final: 0.7254 (p) outliers start: 14 outliers final: 4 residues processed: 169 average time/residue: 2.2823 time to fit residues: 418.2485 Evaluate side-chains 108 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 425 ASN A 796 GLN B 542 ASN B 549 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.251327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.196024 restraints weight = 33077.860| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.47 r_work: 0.4136 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9960 Z= 0.188 Angle : 0.655 5.822 13530 Z= 0.364 Chirality : 0.041 0.137 1586 Planarity : 0.006 0.048 1676 Dihedral : 5.506 40.302 1348 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.94 % Allowed : 6.78 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.22), residues: 1230 helix: 1.23 (0.17), residues: 784 sheet: -2.00 (0.90), residues: 20 loop : -1.25 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 295 HIS 0.007 0.002 HIS A 513 PHE 0.014 0.001 PHE A 358 TYR 0.012 0.001 TYR B 275 ARG 0.004 0.000 ARG B 277 Details of bonding type rmsd hydrogen bonds : bond 0.07422 ( 601) hydrogen bonds : angle 4.75161 ( 1764) covalent geometry : bond 0.00393 ( 9960) covalent geometry : angle 0.65539 (13530) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.8259 (tptp) cc_final: 0.7794 (tppt) REVERT: A 460 MET cc_start: 0.7881 (mmt) cc_final: 0.7629 (mmt) REVERT: B 101 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7802 (tpt) REVERT: B 266 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7287 (t) REVERT: B 395 GLU cc_start: 0.6142 (mm-30) cc_final: 0.5941 (mt-10) REVERT: B 450 THR cc_start: 0.7599 (m) cc_final: 0.7334 (p) REVERT: B 538 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8110 (t) outliers start: 20 outliers final: 13 residues processed: 125 average time/residue: 1.8931 time to fit residues: 265.0336 Evaluate side-chains 111 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 425 ASN B 153 GLN B 486 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.216819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151845 restraints weight = 31357.722| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.42 r_work: 0.3633 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9960 Z= 0.228 Angle : 0.705 11.444 13530 Z= 0.384 Chirality : 0.043 0.169 1586 Planarity : 0.006 0.056 1676 Dihedral : 5.427 43.861 1344 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.84 % Allowed : 8.14 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.52 (0.23), residues: 1230 helix: 1.46 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 295 HIS 0.009 0.002 HIS B 530 PHE 0.016 0.002 PHE B 432 TYR 0.017 0.002 TYR A 819 ARG 0.011 0.001 ARG A 610 Details of bonding type rmsd hydrogen bonds : bond 0.07241 ( 601) hydrogen bonds : angle 4.43537 ( 1764) covalent geometry : bond 0.00505 ( 9960) covalent geometry : angle 0.70499 (13530) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.7963 (mtm180) cc_final: 0.7713 (mmt90) REVERT: A 395 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 101 MET cc_start: 0.8113 (mmm) cc_final: 0.7807 (tpt) REVERT: B 238 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6523 (mt-10) REVERT: B 395 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6973 (mt-10) REVERT: B 450 THR cc_start: 0.8174 (m) cc_final: 0.7598 (p) REVERT: B 460 MET cc_start: 0.8139 (mmm) cc_final: 0.7765 (mmt) REVERT: B 480 TRP cc_start: 0.7054 (t-100) cc_final: 0.5411 (t60) outliers start: 19 outliers final: 11 residues processed: 122 average time/residue: 2.0749 time to fit residues: 277.4709 Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN B 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.214752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149101 restraints weight = 31647.006| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.46 r_work: 0.3624 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9960 Z= 0.140 Angle : 0.528 5.331 13530 Z= 0.284 Chirality : 0.038 0.151 1586 Planarity : 0.005 0.045 1676 Dihedral : 4.876 42.273 1344 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.94 % Allowed : 9.50 % Favored : 88.57 % 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: 1.08 (0.23), residues: 1230 helix: 1.95 (0.18), residues: 786 sheet: -0.31 (1.20), residues: 18 loop : -1.70 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 295 HIS 0.004 0.001 HIS A 804 PHE 0.011 0.001 PHE B 314 TYR 0.006 0.001 TYR B 564 ARG 0.004 0.001 ARG A 610 Details of bonding type rmsd hydrogen bonds : bond 0.05731 ( 601) hydrogen bonds : angle 4.20936 ( 1764) covalent geometry : bond 0.00293 ( 9960) covalent geometry : angle 0.52822 (13530) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.6692 (t60) cc_final: 0.6357 (t60) REVERT: A 296 ASN cc_start: 0.6610 (m-40) cc_final: 0.6410 (m-40) REVERT: A 309 ARG cc_start: 0.7956 (mtm180) cc_final: 0.7681 (mmt90) REVERT: A 395 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 101 MET cc_start: 0.8013 (mmm) cc_final: 0.7759 (tpt) REVERT: B 395 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6889 (mt-10) REVERT: B 450 THR cc_start: 0.8152 (m) cc_final: 0.7573 (p) REVERT: B 460 MET cc_start: 0.8027 (mmm) cc_final: 0.7723 (mmt) REVERT: B 480 TRP cc_start: 0.7084 (t-100) cc_final: 0.5428 (t60) REVERT: B 584 MET cc_start: -0.0521 (mmt) cc_final: -0.1673 (mmt) outliers start: 20 outliers final: 11 residues processed: 116 average time/residue: 2.0375 time to fit residues: 259.6244 Evaluate side-chains 105 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN A 807 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.204777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143860 restraints weight = 31860.749| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.28 r_work: 0.3597 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.6671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9960 Z= 0.203 Angle : 0.624 5.497 13530 Z= 0.340 Chirality : 0.042 0.157 1586 Planarity : 0.006 0.047 1676 Dihedral : 4.996 45.303 1344 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.33 % Allowed : 9.59 % Favored : 88.08 % 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: 0.73 (0.23), residues: 1230 helix: 1.71 (0.18), residues: 782 sheet: -0.58 (1.17), residues: 18 loop : -1.87 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 444 HIS 0.008 0.002 HIS A 804 PHE 0.024 0.002 PHE B 481 TYR 0.014 0.002 TYR B 275 ARG 0.006 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.07117 ( 601) hydrogen bonds : angle 4.28688 ( 1764) covalent geometry : bond 0.00471 ( 9960) covalent geometry : angle 0.62374 (13530) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.8265 (mtm180) cc_final: 0.7998 (mmt90) REVERT: A 404 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7418 (mtm180) REVERT: B 221 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6728 (ttpp) REVERT: B 395 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7487 (mt-10) REVERT: B 450 THR cc_start: 0.8491 (m) cc_final: 0.7991 (p) REVERT: B 460 MET cc_start: 0.8353 (mmm) cc_final: 0.8029 (mmt) REVERT: B 480 TRP cc_start: 0.7667 (t-100) cc_final: 0.5880 (t60) REVERT: B 483 ASP cc_start: 0.7616 (t0) cc_final: 0.6555 (p0) REVERT: B 584 MET cc_start: -0.0256 (mmt) cc_final: -0.1774 (mmt) outliers start: 24 outliers final: 13 residues processed: 121 average time/residue: 2.3418 time to fit residues: 307.9131 Evaluate side-chains 108 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 590 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.203410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139437 restraints weight = 31559.731| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.37 r_work: 0.3509 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9960 Z= 0.131 Angle : 0.509 5.194 13530 Z= 0.275 Chirality : 0.038 0.167 1586 Planarity : 0.005 0.042 1676 Dihedral : 4.642 44.063 1344 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.65 % Allowed : 11.34 % Favored : 87.02 % 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: 1.16 (0.24), residues: 1230 helix: 2.09 (0.18), residues: 788 sheet: -0.76 (1.07), residues: 18 loop : -1.84 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 444 HIS 0.003 0.001 HIS A 804 PHE 0.012 0.001 PHE A 279 TYR 0.007 0.001 TYR A 819 ARG 0.009 0.000 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.05496 ( 601) hydrogen bonds : angle 4.08922 ( 1764) covalent geometry : bond 0.00275 ( 9960) covalent geometry : angle 0.50865 (13530) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.6921 (t60) cc_final: 0.6415 (t60) REVERT: A 309 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7743 (mmt90) REVERT: A 404 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7179 (mtm180) REVERT: A 428 ARG cc_start: 0.6629 (mtm180) cc_final: 0.6382 (mtt-85) REVERT: A 816 ASP cc_start: 0.6676 (t0) cc_final: 0.5935 (p0) REVERT: B 395 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7162 (mt-10) REVERT: B 450 THR cc_start: 0.8269 (m) cc_final: 0.7652 (p) REVERT: B 460 MET cc_start: 0.8008 (mmm) cc_final: 0.7766 (mmt) REVERT: B 480 TRP cc_start: 0.7655 (t-100) cc_final: 0.5726 (t60) REVERT: B 483 ASP cc_start: 0.7430 (t0) cc_final: 0.6421 (p0) REVERT: B 584 MET cc_start: -0.0461 (mmt) cc_final: -0.1968 (mmt) outliers start: 17 outliers final: 10 residues processed: 115 average time/residue: 2.2962 time to fit residues: 287.9584 Evaluate side-chains 103 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 92 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.200384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.140275 restraints weight = 31624.909| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.25 r_work: 0.3556 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9960 Z= 0.180 Angle : 0.558 5.322 13530 Z= 0.301 Chirality : 0.040 0.146 1586 Planarity : 0.005 0.045 1676 Dihedral : 4.664 45.901 1344 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.74 % Allowed : 11.82 % Favored : 86.43 % 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: 1.11 (0.24), residues: 1230 helix: 2.06 (0.18), residues: 784 sheet: -0.90 (1.10), residues: 18 loop : -1.83 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 444 HIS 0.004 0.001 HIS A 486 PHE 0.015 0.002 PHE B 270 TYR 0.013 0.001 TYR B 275 ARG 0.007 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.06319 ( 601) hydrogen bonds : angle 4.08862 ( 1764) covalent geometry : bond 0.00427 ( 9960) covalent geometry : angle 0.55755 (13530) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ARG cc_start: 0.5385 (tpt170) cc_final: 0.4281 (tmt-80) REVERT: A 309 ARG cc_start: 0.8187 (mtm180) cc_final: 0.7850 (mmt90) REVERT: A 404 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7404 (mtm180) REVERT: A 428 ARG cc_start: 0.6725 (mtm180) cc_final: 0.6514 (mtt-85) REVERT: A 805 LYS cc_start: 0.5466 (tptm) cc_final: 0.5211 (ttmt) REVERT: A 808 THR cc_start: 0.8183 (m) cc_final: 0.7975 (m) REVERT: A 816 ASP cc_start: 0.6983 (t0) cc_final: 0.6600 (p0) REVERT: B 221 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6563 (ttpp) REVERT: B 460 MET cc_start: 0.8252 (mmm) cc_final: 0.8038 (mmt) REVERT: B 483 ASP cc_start: 0.7732 (t0) cc_final: 0.6838 (p0) REVERT: B 584 MET cc_start: -0.0356 (mmt) cc_final: -0.1977 (mmt) outliers start: 18 outliers final: 11 residues processed: 113 average time/residue: 2.4117 time to fit residues: 296.3668 Evaluate side-chains 104 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 809 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 117 optimal weight: 0.0980 chunk 113 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.201357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141128 restraints weight = 31820.591| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.29 r_work: 0.3571 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.7527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9960 Z= 0.130 Angle : 0.502 5.114 13530 Z= 0.271 Chirality : 0.038 0.177 1586 Planarity : 0.005 0.043 1676 Dihedral : 4.354 26.838 1342 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.36 % Allowed : 12.31 % Favored : 86.34 % 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: 1.32 (0.24), residues: 1230 helix: 2.23 (0.18), residues: 788 sheet: -0.97 (1.08), residues: 18 loop : -1.80 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 444 HIS 0.006 0.001 HIS B 573 PHE 0.010 0.001 PHE B 270 TYR 0.007 0.001 TYR B 275 ARG 0.004 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.05403 ( 601) hydrogen bonds : angle 4.01158 ( 1764) covalent geometry : bond 0.00281 ( 9960) covalent geometry : angle 0.50206 (13530) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7410 (mtm180) REVERT: A 428 ARG cc_start: 0.6697 (mtm180) cc_final: 0.6484 (mtt-85) REVERT: A 816 ASP cc_start: 0.6981 (t0) cc_final: 0.6604 (p0) REVERT: B 101 MET cc_start: 0.8288 (mmm) cc_final: 0.8070 (tpt) REVERT: B 460 MET cc_start: 0.8167 (mmm) cc_final: 0.7940 (mmt) REVERT: B 483 ASP cc_start: 0.7779 (t0) cc_final: 0.6966 (p0) REVERT: B 584 MET cc_start: -0.0328 (mmt) cc_final: -0.1843 (mmt) outliers start: 14 outliers final: 13 residues processed: 108 average time/residue: 2.1607 time to fit residues: 256.3694 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 809 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 109 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.202335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142561 restraints weight = 31508.528| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.26 r_work: 0.3580 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.7629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9960 Z= 0.113 Angle : 0.486 5.051 13530 Z= 0.259 Chirality : 0.037 0.190 1586 Planarity : 0.004 0.042 1676 Dihedral : 4.228 27.204 1342 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.26 % Allowed : 12.79 % Favored : 85.95 % 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: 1.53 (0.24), residues: 1230 helix: 2.43 (0.18), residues: 786 sheet: -1.30 (0.75), residues: 38 loop : -1.73 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 444 HIS 0.003 0.001 HIS B 573 PHE 0.011 0.001 PHE B 270 TYR 0.007 0.001 TYR B 275 ARG 0.006 0.000 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 601) hydrogen bonds : angle 3.93729 ( 1764) covalent geometry : bond 0.00241 ( 9960) covalent geometry : angle 0.48594 (13530) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.8213 (mtm180) cc_final: 0.7806 (mmt90) REVERT: A 404 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7302 (mtm180) REVERT: A 428 ARG cc_start: 0.6707 (mtm180) cc_final: 0.6501 (mtt-85) REVERT: A 816 ASP cc_start: 0.6968 (t0) cc_final: 0.6602 (p0) REVERT: B 221 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6544 (ttpp) REVERT: B 460 MET cc_start: 0.8067 (mmm) cc_final: 0.7865 (mmt) REVERT: B 483 ASP cc_start: 0.7761 (t0) cc_final: 0.6960 (p0) REVERT: B 584 MET cc_start: -0.0405 (mmt) cc_final: -0.1871 (mmt) outliers start: 13 outliers final: 11 residues processed: 109 average time/residue: 2.3136 time to fit residues: 274.2725 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.201810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142107 restraints weight = 31506.351| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.27 r_work: 0.3584 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.7752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9960 Z= 0.113 Angle : 0.483 4.982 13530 Z= 0.258 Chirality : 0.037 0.193 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.157 27.505 1342 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.45 % Allowed : 12.79 % Favored : 85.76 % 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: 1.63 (0.24), residues: 1230 helix: 2.50 (0.18), residues: 786 sheet: -1.24 (0.76), residues: 38 loop : -1.70 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 444 HIS 0.003 0.001 HIS B 573 PHE 0.009 0.001 PHE B 270 TYR 0.007 0.001 TYR B 275 ARG 0.004 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 601) hydrogen bonds : angle 3.88557 ( 1764) covalent geometry : bond 0.00246 ( 9960) covalent geometry : angle 0.48335 (13530) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7315 (mtm180) REVERT: A 428 ARG cc_start: 0.6698 (mtm180) cc_final: 0.6495 (mtt-85) REVERT: A 816 ASP cc_start: 0.7005 (t0) cc_final: 0.6645 (p0) REVERT: B 221 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6554 (ttpp) REVERT: B 483 ASP cc_start: 0.7803 (t0) cc_final: 0.6993 (p0) REVERT: B 584 MET cc_start: -0.0460 (mmt) cc_final: -0.1714 (mmt) outliers start: 15 outliers final: 11 residues processed: 112 average time/residue: 2.1913 time to fit residues: 268.4979 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 119 optimal weight: 0.0980 chunk 86 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 527 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.200778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.140969 restraints weight = 31555.461| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.27 r_work: 0.3573 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9960 Z= 0.122 Angle : 0.488 5.025 13530 Z= 0.260 Chirality : 0.038 0.195 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.131 27.414 1342 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.26 % Allowed : 13.47 % Favored : 85.27 % 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: 1.64 (0.24), residues: 1230 helix: 2.53 (0.18), residues: 784 sheet: -1.22 (0.77), residues: 38 loop : -1.72 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 444 HIS 0.003 0.001 HIS A 807 PHE 0.009 0.001 PHE B 270 TYR 0.008 0.001 TYR B 275 ARG 0.005 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04938 ( 601) hydrogen bonds : angle 3.88536 ( 1764) covalent geometry : bond 0.00270 ( 9960) covalent geometry : angle 0.48803 (13530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13526.28 seconds wall clock time: 228 minutes 55.73 seconds (13735.73 seconds total)