Starting phenix.real_space_refine on Sun Aug 24 12:06:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ta5_41129/08_2025/8ta5_41129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ta5_41129/08_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_41129/08_2025/8ta5_41129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ta5_41129/08_2025/8ta5_41129.map" model { file = "/net/cci-nas-00/data/ceres_data/8ta5_41129/08_2025/8ta5_41129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ta5_41129/08_2025/8ta5_41129.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.41, per 1000 atoms: 0.17 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: 1.60 Conformation dependent library (CDL) restraints added in 696.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.37 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: 3.97 Time building geometry restraints manager: 2.17 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 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: 1.230 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: 0.130 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A 586 TYR 0.066 0.012 TYR A 23 PHE 0.064 0.012 PHE A 270 TRP 0.097 0.013 TRP A 106 HIS 0.009 0.003 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.01276 ( 9960) covalent geometry : angle 1.80134 (13530) hydrogen bonds : bond 0.23710 ( 601) hydrogen bonds : angle 6.46467 ( 1764) *********************** 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 : 0.545 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: 0.8162 (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: 1.0518 time to fit residues: 192.2686 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 : 0.428 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 356 ASN A 425 ASN A 796 GLN B 549 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.247052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.190409 restraints weight = 32909.055| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.46 r_work: 0.4084 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9960 Z= 0.196 Angle : 0.658 6.313 13530 Z= 0.362 Chirality : 0.042 0.144 1586 Planarity : 0.005 0.050 1676 Dihedral : 5.488 40.582 1348 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.03 % Allowed : 6.59 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.22), residues: 1230 helix: 1.26 (0.17), residues: 782 sheet: -1.52 (0.72), residues: 38 loop : -1.36 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 825 TYR 0.013 0.002 TYR B 275 PHE 0.014 0.002 PHE B 208 TRP 0.012 0.001 TRP A 295 HIS 0.006 0.002 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9960) covalent geometry : angle 0.65829 (13530) hydrogen bonds : bond 0.07071 ( 601) hydrogen bonds : angle 4.69661 ( 1764) *********************** 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 136 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.411 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 344 LYS cc_start: 0.8266 (tptp) cc_final: 0.7764 (tppt) REVERT: A 460 MET cc_start: 0.7855 (mmt) cc_final: 0.7646 (mmt) REVERT: B 101 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7721 (tpt) REVERT: B 266 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7308 (t) REVERT: B 395 GLU cc_start: 0.6355 (mm-30) cc_final: 0.6064 (mt-10) REVERT: B 401 PHE cc_start: 0.7785 (m-10) cc_final: 0.7558 (m-10) REVERT: B 450 THR cc_start: 0.7671 (m) cc_final: 0.7387 (p) REVERT: B 460 MET cc_start: 0.8160 (mmm) cc_final: 0.7762 (mmt) REVERT: B 538 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8062 (t) outliers start: 21 outliers final: 13 residues processed: 128 average time/residue: 0.7362 time to fit residues: 104.7818 Evaluate side-chains 113 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 119 optimal weight: 0.0970 chunk 67 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 425 ASN A 807 HIS B 153 GLN B 486 HIS B 530 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.213340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148546 restraints weight = 31721.933| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.42 r_work: 0.3613 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9960 Z= 0.230 Angle : 0.757 20.345 13530 Z= 0.402 Chirality : 0.043 0.163 1586 Planarity : 0.006 0.052 1676 Dihedral : 5.283 43.148 1344 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.94 % Allowed : 8.33 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.23), residues: 1230 helix: 1.50 (0.18), residues: 786 sheet: None (None), residues: 0 loop : -1.75 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 610 TYR 0.017 0.002 TYR B 275 PHE 0.023 0.003 PHE B 383 TRP 0.031 0.002 TRP A 276 HIS 0.009 0.002 HIS B 530 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 9960) covalent geometry : angle 0.75677 (13530) hydrogen bonds : bond 0.07204 ( 601) hydrogen bonds : angle 4.38676 ( 1764) *********************** 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: 20 poor density : 109 time to evaluate : 0.487 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: A 309 ARG cc_start: 0.8101 (mtm180) cc_final: 0.7817 (mmt90) REVERT: A 387 MET cc_start: 0.8824 (ptm) cc_final: 0.8536 (ptm) REVERT: A 395 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: A 460 MET cc_start: 0.7877 (mmt) cc_final: 0.7675 (mmt) REVERT: B 138 VAL cc_start: 0.8265 (t) cc_final: 0.8061 (m) REVERT: B 238 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6412 (mt-10) REVERT: B 395 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6981 (mt-10) REVERT: B 450 THR cc_start: 0.8305 (m) cc_final: 0.7736 (p) REVERT: B 460 MET cc_start: 0.8134 (mmm) cc_final: 0.7786 (mmt) REVERT: B 480 TRP cc_start: 0.7161 (t-100) cc_final: 0.5510 (t60) outliers start: 20 outliers final: 10 residues processed: 124 average time/residue: 1.1342 time to fit residues: 151.4604 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 493 ARG Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 266 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.207598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142759 restraints weight = 31525.265| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.39 r_work: 0.3543 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9960 Z= 0.194 Angle : 0.595 8.087 13530 Z= 0.321 Chirality : 0.041 0.163 1586 Planarity : 0.005 0.044 1676 Dihedral : 4.924 43.495 1344 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.52 % Allowed : 9.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.23), residues: 1230 helix: 1.80 (0.18), residues: 784 sheet: -0.49 (1.24), residues: 18 loop : -1.63 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 277 TYR 0.011 0.001 TYR B 564 PHE 0.014 0.002 PHE A 269 TRP 0.017 0.002 TRP A 295 HIS 0.006 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9960) covalent geometry : angle 0.59491 (13530) hydrogen bonds : bond 0.06319 ( 601) hydrogen bonds : angle 4.25767 ( 1764) *********************** 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 130 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.519 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: 0.6776 (t60) cc_final: 0.6407 (t60) REVERT: A 309 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7753 (mmt90) REVERT: A 395 GLU cc_start: 0.7792 (mp0) cc_final: 0.7440 (mt-10) REVERT: A 404 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7004 (mtm180) REVERT: A 460 MET cc_start: 0.7816 (mmt) cc_final: 0.7604 (mmt) REVERT: B 221 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6603 (ttpp) REVERT: B 349 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6796 (mtm) REVERT: B 365 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7117 (tp) REVERT: B 395 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7102 (mt-10) REVERT: B 450 THR cc_start: 0.8236 (m) cc_final: 0.7613 (p) REVERT: B 460 MET cc_start: 0.8083 (mmm) cc_final: 0.7757 (mmt) REVERT: B 480 TRP cc_start: 0.7380 (t-100) cc_final: 0.5652 (t60) REVERT: B 584 MET cc_start: -0.0780 (mmt) cc_final: -0.1200 (mmt) outliers start: 26 outliers final: 12 residues processed: 123 average time/residue: 0.9887 time to fit residues: 133.2099 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 348 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 365 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 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 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.206674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142665 restraints weight = 31400.145| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.36 r_work: 0.3538 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9960 Z= 0.134 Angle : 0.507 5.245 13530 Z= 0.274 Chirality : 0.038 0.145 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.669 43.428 1344 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.13 % Allowed : 10.08 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.24), residues: 1230 helix: 2.08 (0.18), residues: 786 sheet: -0.56 (1.20), residues: 18 loop : -1.74 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.008 0.001 TYR A 819 PHE 0.016 0.001 PHE A 279 TRP 0.011 0.001 TRP A 444 HIS 0.004 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9960) covalent geometry : angle 0.50741 (13530) hydrogen bonds : bond 0.05673 ( 601) hydrogen bonds : angle 4.08709 ( 1764) *********************** 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 116 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.427 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: 0.8139 (mtm180) cc_final: 0.7794 (mmt90) REVERT: A 395 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: A 404 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7041 (mtm180) REVERT: B 395 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7122 (mt-10) REVERT: B 450 THR cc_start: 0.8236 (m) cc_final: 0.7591 (p) REVERT: B 460 MET cc_start: 0.8050 (mmm) cc_final: 0.7821 (mmt) REVERT: B 480 TRP cc_start: 0.7440 (t-100) cc_final: 0.5697 (t60) REVERT: B 584 MET cc_start: -0.1125 (mmt) cc_final: -0.1636 (mmt) outliers start: 22 outliers final: 13 residues processed: 110 average time/residue: 1.0267 time to fit residues: 123.4013 Evaluate side-chains 104 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 395 GLU 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 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 349 MET 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 28 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 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 A 590 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.204189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.143438 restraints weight = 31659.688| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.26 r_work: 0.3603 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9960 Z= 0.176 Angle : 0.548 5.242 13530 Z= 0.295 Chirality : 0.040 0.147 1586 Planarity : 0.005 0.045 1676 Dihedral : 4.678 45.095 1344 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.13 % Allowed : 10.95 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.24), residues: 1230 helix: 2.00 (0.18), residues: 786 sheet: -0.85 (1.13), residues: 18 loop : -1.73 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 277 TYR 0.010 0.001 TYR B 275 PHE 0.013 0.002 PHE B 379 TRP 0.021 0.001 TRP A 121 HIS 0.006 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9960) covalent geometry : angle 0.54829 (13530) hydrogen bonds : bond 0.06142 ( 601) hydrogen bonds : angle 4.08553 ( 1764) *********************** 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 120 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.6838 (t60) cc_final: 0.6386 (t60) REVERT: A 309 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7950 (mmt90) REVERT: A 395 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: A 404 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7430 (mtm180) REVERT: A 799 GLU cc_start: 0.5646 (OUTLIER) cc_final: 0.5088 (mm-30) REVERT: A 816 ASP cc_start: 0.6835 (t0) cc_final: 0.6213 (p0) REVERT: B 395 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7479 (mt-10) REVERT: B 450 THR cc_start: 0.8465 (m) cc_final: 0.7932 (p) REVERT: B 460 MET cc_start: 0.8284 (mmm) cc_final: 0.8040 (mmt) REVERT: B 584 MET cc_start: -0.0524 (mmt) cc_final: -0.1085 (mmt) outliers start: 22 outliers final: 14 residues processed: 113 average time/residue: 1.0789 time to fit residues: 132.4274 Evaluate side-chains 109 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 395 GLU 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 799 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 542 ASN 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 81 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.205157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.145750 restraints weight = 31887.606| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.24 r_work: 0.3622 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.7250 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= 0.128 Angle : 0.498 5.073 13530 Z= 0.268 Chirality : 0.037 0.137 1586 Planarity : 0.005 0.043 1676 Dihedral : 4.366 27.659 1342 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.94 % Allowed : 11.34 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.24), residues: 1230 helix: 2.21 (0.18), residues: 790 sheet: -1.07 (1.07), residues: 18 loop : -1.68 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.008 0.001 TYR B 275 PHE 0.009 0.001 PHE B 269 TRP 0.010 0.001 TRP A 444 HIS 0.007 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9960) covalent geometry : angle 0.49826 (13530) hydrogen bonds : bond 0.05346 ( 601) hydrogen bonds : angle 3.98278 ( 1764) *********************** 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 114 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.391 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: 0.6979 (t60) cc_final: 0.6486 (t60) REVERT: A 309 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7853 (mmt90) REVERT: A 395 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: A 404 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7282 (mtm180) REVERT: A 816 ASP cc_start: 0.6888 (t0) cc_final: 0.6380 (p0) REVERT: B 101 MET cc_start: 0.8261 (mmm) cc_final: 0.8055 (tpt) REVERT: B 395 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7381 (mt-10) REVERT: B 450 THR cc_start: 0.8406 (m) cc_final: 0.7848 (p) REVERT: B 460 MET cc_start: 0.8173 (mmm) cc_final: 0.7954 (mmt) REVERT: B 584 MET cc_start: -0.0630 (mmt) cc_final: -0.1235 (mmt) outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 1.0138 time to fit residues: 118.8613 Evaluate side-chains 107 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 395 GLU 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 803 LEU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 542 ASN 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 81 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 113 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.198473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.138791 restraints weight = 31653.040| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.24 r_work: 0.3552 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9960 Z= 0.172 Angle : 0.555 5.231 13530 Z= 0.300 Chirality : 0.040 0.146 1586 Planarity : 0.005 0.045 1676 Dihedral : 4.465 27.005 1342 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.23 % Allowed : 11.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.24), residues: 1230 helix: 2.07 (0.18), residues: 788 sheet: -0.95 (1.09), residues: 18 loop : -1.81 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 277 TYR 0.012 0.001 TYR A 275 PHE 0.014 0.002 PHE B 270 TRP 0.011 0.001 TRP A 121 HIS 0.005 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9960) covalent geometry : angle 0.55487 (13530) hydrogen bonds : bond 0.06266 ( 601) hydrogen bonds : angle 4.07943 ( 1764) *********************** 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 121 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.492 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: 0.7102 (t60) cc_final: 0.6549 (t60) REVERT: A 279 PHE cc_start: 0.6770 (t80) cc_final: 0.6509 (t80) REVERT: A 395 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: A 404 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7359 (mtm180) REVERT: A 816 ASP cc_start: 0.7079 (t0) cc_final: 0.6772 (p0) REVERT: B 221 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6598 (ttpp) REVERT: B 460 MET cc_start: 0.8271 (mmm) cc_final: 0.8050 (mmt) REVERT: B 483 ASP cc_start: 0.7882 (t0) cc_final: 0.7019 (p0) REVERT: B 584 MET cc_start: -0.0695 (mmt) cc_final: -0.1269 (mmt) outliers start: 23 outliers final: 16 residues processed: 114 average time/residue: 1.0981 time to fit residues: 136.1368 Evaluate side-chains 113 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 395 GLU 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 627 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 348 VAL Chi-restraints excluded: chain B residue 349 MET 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 50 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.198027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138371 restraints weight = 31579.311| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.25 r_work: 0.3545 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.7911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9960 Z= 0.149 Angle : 0.518 5.064 13530 Z= 0.279 Chirality : 0.038 0.141 1586 Planarity : 0.005 0.043 1676 Dihedral : 4.375 26.427 1342 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.55 % Allowed : 12.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.24), residues: 1230 helix: 2.22 (0.18), residues: 786 sheet: -1.32 (0.90), residues: 28 loop : -1.89 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.010 0.001 TYR B 492 PHE 0.011 0.001 PHE B 270 TRP 0.010 0.001 TRP A 444 HIS 0.004 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9960) covalent geometry : angle 0.51798 (13530) hydrogen bonds : bond 0.05687 ( 601) hydrogen bonds : angle 4.02540 ( 1764) *********************** 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 120 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.464 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: 0.7090 (t60) cc_final: 0.6480 (t60) REVERT: A 395 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: A 404 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7362 (mtm180) REVERT: A 575 GLN cc_start: 0.4409 (mm110) cc_final: 0.3910 (mp10) REVERT: A 816 ASP cc_start: 0.7052 (t0) cc_final: 0.6779 (p0) REVERT: B 101 MET cc_start: 0.8301 (mmm) cc_final: 0.8080 (tpt) REVERT: B 221 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6539 (ttpp) REVERT: B 238 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 425 ASN cc_start: 0.7755 (p0) cc_final: 0.7420 (t0) REVERT: B 460 MET cc_start: 0.8164 (mmm) cc_final: 0.7937 (mmt) REVERT: B 483 ASP cc_start: 0.7996 (t0) cc_final: 0.7175 (p0) REVERT: B 535 MET cc_start: 0.8643 (tpp) cc_final: 0.8252 (mmp) REVERT: B 584 MET cc_start: -0.0707 (mmt) cc_final: -0.1207 (mmt) outliers start: 16 outliers final: 14 residues processed: 117 average time/residue: 1.1558 time to fit residues: 146.1858 Evaluate side-chains 117 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 395 GLU 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 840 GLU 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 349 MET 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 102 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.198014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.138928 restraints weight = 31705.984| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.25 r_work: 0.3548 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.8066 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= 0.138 Angle : 0.510 5.534 13530 Z= 0.274 Chirality : 0.038 0.138 1586 Planarity : 0.005 0.044 1676 Dihedral : 4.296 26.835 1342 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.55 % Allowed : 13.86 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.24), residues: 1230 helix: 2.31 (0.18), residues: 786 sheet: -1.26 (0.91), residues: 28 loop : -1.89 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.008 0.001 TYR B 275 PHE 0.012 0.001 PHE B 270 TRP 0.015 0.001 TRP A 570 HIS 0.003 0.001 HIS A 807 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9960) covalent geometry : angle 0.50990 (13530) hydrogen bonds : bond 0.05423 ( 601) hydrogen bonds : angle 3.97925 ( 1764) ********************** 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: 16 poor density : 98 time to evaluate : 0.529 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: 0.7102 (t60) cc_final: 0.6472 (t60) REVERT: A 395 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: A 404 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7315 (mtm110) REVERT: A 816 ASP cc_start: 0.6984 (t0) cc_final: 0.6756 (p0) REVERT: A 840 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6043 (mt-10) REVERT: B 101 MET cc_start: 0.8252 (mmm) cc_final: 0.8046 (tpt) REVERT: B 221 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6512 (ttpp) REVERT: B 425 ASN cc_start: 0.7676 (p0) cc_final: 0.7319 (t0) REVERT: B 460 MET cc_start: 0.8148 (mmm) cc_final: 0.7947 (mmt) REVERT: B 483 ASP cc_start: 0.7984 (t0) cc_final: 0.7196 (p0) REVERT: B 584 MET cc_start: -0.0779 (mmt) cc_final: -0.1254 (mmt) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.9922 time to fit residues: 120.7312 Evaluate side-chains 113 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 395 GLU 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 840 GLU 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 349 MET 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 93 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 52 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.199905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140215 restraints weight = 31610.609| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.28 r_work: 0.3566 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.8151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9960 Z= 0.107 Angle : 0.478 4.889 13530 Z= 0.255 Chirality : 0.037 0.137 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.149 27.174 1342 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.55 % Allowed : 13.76 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.24), residues: 1230 helix: 2.51 (0.18), residues: 786 sheet: -1.43 (0.90), residues: 28 loop : -1.75 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.007 0.001 TYR B 275 PHE 0.010 0.001 PHE B 270 TRP 0.011 0.001 TRP A 444 HIS 0.003 0.001 HIS B 573 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9960) covalent geometry : angle 0.47798 (13530) hydrogen bonds : bond 0.04662 ( 601) hydrogen bonds : angle 3.89576 ( 1764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6437.65 seconds wall clock time: 109 minutes 33.22 seconds (6573.22 seconds total)