Starting phenix.real_space_refine on Tue May 20 08:31:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ta5_41129/05_2025/8ta5_41129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ta5_41129/05_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_41129/05_2025/8ta5_41129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ta5_41129/05_2025/8ta5_41129.map" model { file = "/net/cci-nas-00/data/ceres_data/8ta5_41129/05_2025/8ta5_41129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ta5_41129/05_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-5687/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: 8.94, per 1000 atoms: 0.45 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: 5.54 Conformation dependent library (CDL) restraints added in 1.6 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: 1.54 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: 6.95 Time building geometry restraints manager: 6.56 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: 0.820 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: 0.350 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 42.410 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.610 ------------------------------------------------------------------------------- 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 : 1.450 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: 2.3178 time to fit residues: 424.1985 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 : 1.314 ------------------------------------------------------------------------------- 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 = 0.251323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.196020 restraints weight = 33075.855| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.47 r_work: 0.4135 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 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 5.821 13530 Z= 0.364 Chirality : 0.041 0.137 1586 Planarity : 0.006 0.048 1676 Dihedral : 5.506 40.300 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 0.07421 ( 601) hydrogen bonds : angle 4.75157 ( 1764) covalent geometry : bond 0.00393 ( 9960) covalent geometry : angle 0.65538 (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 : 1.444 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: A 344 LYS cc_start: 0.8266 (tptp) cc_final: 0.7803 (tppt) REVERT: A 460 MET cc_start: 0.7874 (mmt) cc_final: 0.7621 (mmt) REVERT: B 101 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7813 (tpt) REVERT: B 266 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7291 (t) REVERT: B 450 THR cc_start: 0.7601 (m) cc_final: 0.7340 (p) REVERT: B 538 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8108 (t) outliers start: 20 outliers final: 13 residues processed: 125 average time/residue: 1.8134 time to fit residues: 252.5980 Evaluate side-chains 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4419 r_free = 0.4419 target = 0.219821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.154005 restraints weight = 31402.428| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.48 r_work: 0.3669 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9960 Z= 0.210 Angle : 0.674 11.999 13530 Z= 0.365 Chirality : 0.042 0.169 1586 Planarity : 0.006 0.059 1676 Dihedral : 5.242 42.943 1344 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.94 % Allowed : 7.85 % Favored : 90.21 % 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: 0.74 (0.23), residues: 1230 helix: 1.64 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -1.70 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 295 HIS 0.009 0.002 HIS B 530 PHE 0.015 0.002 PHE B 432 TYR 0.017 0.002 TYR B 275 ARG 0.009 0.001 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.06425 ( 601) hydrogen bonds : angle 4.35435 ( 1764) covalent geometry : bond 0.00444 ( 9960) covalent geometry : angle 0.67351 (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 130 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.428 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: 0.7861 (mtm180) cc_final: 0.7574 (mmt90) REVERT: A 395 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7191 (mt-10) REVERT: B 238 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6386 (mt-10) REVERT: B 450 THR cc_start: 0.8120 (m) cc_final: 0.7534 (p) REVERT: B 460 MET cc_start: 0.8081 (mmm) cc_final: 0.7726 (mmt) REVERT: B 480 TRP cc_start: 0.6949 (t-100) cc_final: 0.5399 (t60) outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 2.0681 time to fit residues: 275.9104 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 : 1.328 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.208943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143234 restraints weight = 31635.935| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.43 r_work: 0.3547 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9960 Z= 0.203 Angle : 0.598 6.193 13530 Z= 0.324 Chirality : 0.042 0.195 1586 Planarity : 0.005 0.046 1676 Dihedral : 4.953 43.151 1344 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.23 % Allowed : 9.59 % Favored : 88.18 % 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: 1.04 (0.23), residues: 1230 helix: 1.87 (0.18), residues: 782 sheet: -0.09 (1.23), residues: 18 loop : -1.59 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 295 HIS 0.006 0.001 HIS A 804 PHE 0.013 0.002 PHE B 379 TYR 0.011 0.002 TYR B 564 ARG 0.016 0.001 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.06566 ( 601) hydrogen bonds : angle 4.27703 ( 1764) covalent geometry : bond 0.00474 ( 9960) covalent geometry : angle 0.59792 (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: 23 poor density : 99 time to evaluate : 1.593 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: 0.6723 (t60) cc_final: 0.6365 (t60) REVERT: A 309 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7797 (mmt90) REVERT: A 344 LYS cc_start: 0.8287 (tptp) cc_final: 0.7775 (tppt) REVERT: A 387 MET cc_start: 0.8896 (ptm) cc_final: 0.8689 (ptm) REVERT: A 395 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 404 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.6931 (mtm180) REVERT: A 584 MET cc_start: 0.2839 (OUTLIER) cc_final: 0.2548 (ppp) REVERT: B 238 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6840 (mm-30) REVERT: B 450 THR cc_start: 0.8206 (m) cc_final: 0.7588 (p) REVERT: B 460 MET cc_start: 0.8086 (mmm) cc_final: 0.7785 (mmt) REVERT: B 480 TRP cc_start: 0.7304 (t-100) cc_final: 0.5584 (t60) REVERT: B 584 MET cc_start: -0.0376 (mmt) cc_final: -0.1674 (mmt) outliers start: 23 outliers final: 14 residues processed: 116 average time/residue: 2.0754 time to fit residues: 264.3779 Evaluate side-chains 102 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 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 348 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 542 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 356 ASN A 590 HIS A 807 HIS B 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.205596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145041 restraints weight = 31855.966| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.27 r_work: 0.3616 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9960 Z= 0.192 Angle : 0.602 10.156 13530 Z= 0.324 Chirality : 0.040 0.170 1586 Planarity : 0.005 0.044 1676 Dihedral : 4.863 44.433 1344 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.52 % Allowed : 10.37 % Favored : 87.11 % 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: 0.92 (0.23), residues: 1230 helix: 1.85 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -1.77 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 295 HIS 0.006 0.002 HIS A 804 PHE 0.023 0.002 PHE A 314 TYR 0.022 0.002 TYR A 492 ARG 0.006 0.001 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.06423 ( 601) hydrogen bonds : angle 4.18440 ( 1764) covalent geometry : bond 0.00435 ( 9960) covalent geometry : angle 0.60201 (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: 26 poor density : 102 time to evaluate : 1.384 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: 0.8191 (mtm180) cc_final: 0.7919 (mmt90) REVERT: A 404 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7403 (mtm180) REVERT: A 483 ASP cc_start: 0.8046 (m-30) cc_final: 0.7789 (m-30) REVERT: B 221 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6706 (ttpp) REVERT: B 365 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7324 (tp) REVERT: B 450 THR cc_start: 0.8443 (m) cc_final: 0.7936 (p) REVERT: B 460 MET cc_start: 0.8277 (mmm) cc_final: 0.7975 (mmt) REVERT: B 483 ASP cc_start: 0.7657 (t0) cc_final: 0.6594 (p0) outliers start: 26 outliers final: 14 residues processed: 122 average time/residue: 2.3061 time to fit residues: 305.3438 Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 354 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 584 MET Chi-restraints excluded: chain A residue 803 LEU 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 365 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 102 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 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 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.206079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146112 restraints weight = 31650.084| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.25 r_work: 0.3628 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.7093 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= 0.129 Angle : 0.505 5.214 13530 Z= 0.272 Chirality : 0.038 0.139 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.616 44.267 1344 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.55 % Allowed : 11.92 % Favored : 86.53 % 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: 1.30 (0.24), residues: 1230 helix: 2.16 (0.18), residues: 788 sheet: -0.88 (1.07), residues: 18 loop : -1.68 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 295 HIS 0.005 0.001 HIS B 573 PHE 0.009 0.001 PHE A 226 TYR 0.007 0.001 TYR A 819 ARG 0.004 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 601) hydrogen bonds : angle 4.02479 ( 1764) covalent geometry : bond 0.00281 ( 9960) covalent geometry : angle 0.50495 (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 110 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7937 (mmt90) REVERT: A 404 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7380 (mtm180) REVERT: A 816 ASP cc_start: 0.6666 (t0) cc_final: 0.6048 (p0) REVERT: B 101 MET cc_start: 0.8316 (mmm) cc_final: 0.8107 (tpt) REVERT: B 221 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6692 (ttpp) REVERT: B 450 THR cc_start: 0.8410 (m) cc_final: 0.7878 (p) REVERT: B 460 MET cc_start: 0.8191 (mmm) cc_final: 0.7958 (mmt) REVERT: B 584 MET cc_start: -0.0310 (mmt) cc_final: -0.2079 (mmt) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 2.3077 time to fit residues: 268.4600 Evaluate side-chains 102 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 430 ASN 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 220 SER Chi-restraints excluded: chain B residue 221 LYS 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: 0.9980 chunk 77 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 530 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.202011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141473 restraints weight = 31517.006| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.28 r_work: 0.3586 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.7414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9960 Z= 0.151 Angle : 0.525 5.170 13530 Z= 0.283 Chirality : 0.039 0.227 1586 Planarity : 0.005 0.044 1676 Dihedral : 4.560 45.067 1344 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.45 % Allowed : 12.31 % Favored : 86.24 % 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: 1.28 (0.24), residues: 1230 helix: 2.17 (0.18), residues: 790 sheet: -1.09 (1.06), residues: 18 loop : -1.75 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 121 HIS 0.003 0.001 HIS A 804 PHE 0.011 0.001 PHE B 270 TYR 0.010 0.001 TYR B 275 ARG 0.005 0.001 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 601) hydrogen bonds : angle 4.01135 ( 1764) covalent geometry : bond 0.00348 ( 9960) covalent geometry : angle 0.52514 (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 111 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.481 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 121 TRP cc_start: 0.6914 (t60) cc_final: 0.6426 (t60) REVERT: A 309 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7841 (mmt90) REVERT: A 404 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7296 (mtm180) REVERT: A 816 ASP cc_start: 0.6912 (t0) cc_final: 0.6506 (p0) REVERT: B 101 MET cc_start: 0.8288 (mmm) cc_final: 0.8073 (tpt) REVERT: B 221 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6614 (ttpp) REVERT: B 460 MET cc_start: 0.8175 (mmm) cc_final: 0.7962 (mmt) REVERT: B 584 MET cc_start: -0.0416 (mmt) cc_final: -0.2019 (mmt) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 2.3073 time to fit residues: 271.9660 Evaluate side-chains 101 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 430 ASN 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 220 SER Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 803 LEU 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: 5.9990 chunk 108 optimal weight: 2.9990 chunk 96 optimal weight: 0.0050 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.203587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142948 restraints weight = 31662.132| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.28 r_work: 0.3597 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.7538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9960 Z= 0.111 Angle : 0.479 5.038 13530 Z= 0.256 Chirality : 0.037 0.137 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.213 27.598 1342 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.07 % Allowed : 12.69 % Favored : 86.24 % 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: 1.56 (0.24), residues: 1230 helix: 2.44 (0.18), residues: 784 sheet: -1.36 (0.71), residues: 38 loop : -1.68 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 295 HIS 0.003 0.001 HIS B 573 PHE 0.009 0.001 PHE B 270 TYR 0.006 0.001 TYR B 275 ARG 0.003 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 601) hydrogen bonds : angle 3.91336 ( 1764) covalent geometry : bond 0.00237 ( 9960) covalent geometry : angle 0.47915 (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 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.499 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 121 TRP cc_start: 0.7019 (t60) cc_final: 0.6482 (t60) REVERT: A 309 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7843 (mmt90) REVERT: A 404 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7273 (mtm180) REVERT: A 816 ASP cc_start: 0.6941 (t0) cc_final: 0.6515 (p0) REVERT: B 221 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6544 (ttpp) REVERT: B 584 MET cc_start: -0.0373 (mmt) cc_final: -0.1797 (mmt) outliers start: 11 outliers final: 9 residues processed: 106 average time/residue: 2.2130 time to fit residues: 255.9138 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 : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 430 ASN 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 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 803 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.203465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142998 restraints weight = 31478.104| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.27 r_work: 0.3600 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.7592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9960 Z= 0.112 Angle : 0.479 5.026 13530 Z= 0.257 Chirality : 0.037 0.181 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.161 27.735 1342 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.16 % Allowed : 12.98 % Favored : 85.85 % 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: 1.65 (0.24), residues: 1230 helix: 2.52 (0.18), residues: 784 sheet: -1.30 (0.72), residues: 38 loop : -1.67 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 121 HIS 0.003 0.001 HIS B 573 PHE 0.010 0.001 PHE B 270 TYR 0.007 0.001 TYR B 275 ARG 0.003 0.000 ARG A 277 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 601) hydrogen bonds : angle 3.89051 ( 1764) covalent geometry : bond 0.00239 ( 9960) covalent geometry : angle 0.47929 (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 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.562 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 121 TRP cc_start: 0.6970 (t60) cc_final: 0.6455 (t60) REVERT: A 166 GLU cc_start: 0.8269 (mp0) cc_final: 0.7854 (mp0) REVERT: A 309 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7826 (mmt90) REVERT: A 404 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7241 (mtm180) REVERT: A 816 ASP cc_start: 0.6958 (t0) cc_final: 0.6529 (p0) REVERT: B 221 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6559 (ttpp) REVERT: B 584 MET cc_start: -0.0391 (mmt) cc_final: -0.1803 (mmt) outliers start: 12 outliers final: 10 residues processed: 105 average time/residue: 2.0977 time to fit residues: 241.7501 Evaluate side-chains 104 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 430 ASN 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 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR 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: 3.9990 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 43 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.201247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.141280 restraints weight = 31558.558| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.26 r_work: 0.3576 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.7708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9960 Z= 0.145 Angle : 0.503 5.070 13530 Z= 0.271 Chirality : 0.038 0.198 1586 Planarity : 0.004 0.044 1676 Dihedral : 4.198 27.498 1342 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.16 % Allowed : 13.37 % Favored : 85.47 % 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: 1.56 (0.24), residues: 1230 helix: 2.44 (0.18), residues: 784 sheet: -1.28 (0.73), residues: 38 loop : -1.69 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 121 HIS 0.003 0.001 HIS A 804 PHE 0.009 0.001 PHE B 270 TYR 0.009 0.001 TYR B 275 ARG 0.009 0.000 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.05283 ( 601) hydrogen bonds : angle 3.93292 ( 1764) covalent geometry : bond 0.00329 ( 9960) covalent geometry : angle 0.50271 (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 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.564 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 121 TRP cc_start: 0.7031 (t60) cc_final: 0.6479 (t60) REVERT: A 404 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7314 (mtm180) REVERT: A 816 ASP cc_start: 0.6986 (t0) cc_final: 0.6589 (p0) REVERT: B 221 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6541 (ttpp) REVERT: B 584 MET cc_start: -0.0439 (mmt) cc_final: -0.1795 (mmt) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 2.0002 time to fit residues: 231.7294 Evaluate side-chains 106 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 430 ASN 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 221 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR 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: 3.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 84 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 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: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.201448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141680 restraints weight = 31492.626| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.26 r_work: 0.3578 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.7862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9960 Z= 0.120 Angle : 0.484 5.000 13530 Z= 0.259 Chirality : 0.038 0.189 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.097 27.444 1342 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.97 % Allowed : 13.57 % Favored : 85.47 % 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: 1.67 (0.24), residues: 1230 helix: 2.55 (0.18), residues: 784 sheet: -1.19 (0.74), residues: 38 loop : -1.70 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 121 HIS 0.003 0.001 HIS A 804 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 0.04872 ( 601) hydrogen bonds : angle 3.87136 ( 1764) covalent geometry : bond 0.00268 ( 9960) covalent geometry : angle 0.48404 (13530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13042.21 seconds wall clock time: 222 minutes 58.97 seconds (13378.97 seconds total)