Starting phenix.real_space_refine on Tue Jun 17 08:33:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ta4_41128/06_2025/8ta4_41128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ta4_41128/06_2025/8ta4_41128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ta4_41128/06_2025/8ta4_41128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ta4_41128/06_2025/8ta4_41128.map" model { file = "/net/cci-nas-00/data/ceres_data/8ta4_41128/06_2025/8ta4_41128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ta4_41128/06_2025/8ta4_41128.cif" } resolution = 2.75 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= -0.001 sd= 0.195 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 56 5.16 5 Cl 2 4.86 5 C 6376 2.51 5 N 1634 2.21 5 O 1666 1.98 5 H 10041 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19775 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 9886 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 28, 'TRANS': 596} Chain breaks: 4 Chain: "B" Number of atoms: 9887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 9887 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 28, 'TRANS': 596} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.75, per 1000 atoms: 0.49 Number of scatterers: 19775 At special positions: 0 Unit cell: (118.25, 77.572, 117.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 56 16.00 O 1666 8.00 N 1634 7.00 C 6376 6.00 H 10041 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 67.3% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 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: 6.61 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 10023 1.13 - 1.30: 1618 1.30 - 1.48: 3888 1.48 - 1.65: 4378 1.65 - 1.82: 94 Bond restraints: 20001 Sorted by residual: bond pdb=" N HIS A 804 " pdb=" H HIS A 804 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR A 450 " pdb=" H THR A 450 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ARG B 610 " pdb=" H ARG B 610 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N PHE A 261 " pdb=" H PHE A 261 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD1 PHE B 383 " pdb=" HD1 PHE B 383 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 19996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 30184 2.51 - 5.02: 4754 5.02 - 7.52: 1194 7.52 - 10.03: 65 10.03 - 12.54: 19 Bond angle restraints: 36216 Sorted by residual: angle pdb=" CA ASP A 402 " pdb=" CB ASP A 402 " pdb=" CG ASP A 402 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" CA ASP B 791 " pdb=" CB ASP B 791 " pdb=" CG ASP B 791 " ideal model delta sigma weight residual 112.60 118.16 -5.56 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA ASP B 313 " pdb=" CB ASP B 313 " pdb=" CG ASP B 313 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" CA ASP B 402 " pdb=" CB ASP B 402 " pdb=" CG ASP B 402 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.04e+01 angle pdb=" CA PHE B 401 " pdb=" CB PHE B 401 " pdb=" CG PHE B 401 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 ... (remaining 36211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 8512 17.73 - 35.47: 454 35.47 - 53.20: 160 53.20 - 70.93: 231 70.93 - 88.66: 18 Dihedral angle restraints: 9375 sinusoidal: 5044 harmonic: 4331 Sorted by residual: dihedral pdb=" CA GLY B 161 " pdb=" C GLY B 161 " pdb=" N SER B 162 " pdb=" CA SER B 162 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU B 176 " pdb=" C LEU B 176 " pdb=" N LYS B 177 " pdb=" CA LYS B 177 " ideal model delta harmonic sigma weight residual 180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASP A 317 " pdb=" C ASP A 317 " pdb=" N LEU A 318 " pdb=" CA LEU A 318 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 9372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1000 0.078 - 0.155: 446 0.155 - 0.233: 122 0.233 - 0.310: 13 0.310 - 0.388: 5 Chirality restraints: 1586 Sorted by residual: chirality pdb=" CA PRO A 380 " pdb=" N PRO A 380 " pdb=" C PRO A 380 " pdb=" CB PRO A 380 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA PRO B 380 " pdb=" N PRO B 380 " pdb=" C PRO B 380 " pdb=" CB PRO B 380 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA ASP B 402 " pdb=" N ASP B 402 " pdb=" C ASP B 402 " pdb=" CB ASP B 402 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 1583 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 404 " 0.196 9.50e-02 1.11e+02 1.53e-01 4.32e+02 pdb=" NE ARG B 404 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 404 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 404 " -0.073 2.00e-02 2.50e+03 pdb=" NH2 ARG B 404 " 0.033 2.00e-02 2.50e+03 pdb="HH11 ARG B 404 " -0.177 2.00e-02 2.50e+03 pdb="HH12 ARG B 404 " 0.293 2.00e-02 2.50e+03 pdb="HH21 ARG B 404 " 0.056 2.00e-02 2.50e+03 pdb="HH22 ARG B 404 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 25 " 0.275 9.50e-02 1.11e+02 1.21e-01 1.46e+02 pdb=" NE ARG B 25 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG B 25 " 0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG B 25 " 0.093 2.00e-02 2.50e+03 pdb=" NH2 ARG B 25 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 25 " -0.178 2.00e-02 2.50e+03 pdb="HH12 ARG B 25 " 0.068 2.00e-02 2.50e+03 pdb="HH21 ARG B 25 " -0.072 2.00e-02 2.50e+03 pdb="HH22 ARG B 25 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.142 2.00e-02 2.50e+03 5.11e-02 1.05e+02 pdb=" CG TRP A 106 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.050 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 TRP A 106 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP A 106 " 0.025 2.00e-02 2.50e+03 pdb=" HE3 TRP A 106 " 0.073 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 106 " -0.029 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 106 " -0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP A 106 " -0.069 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 914 2.18 - 2.79: 34141 2.79 - 3.39: 55064 3.39 - 4.00: 75504 4.00 - 4.60: 106702 Nonbonded interactions: 272325 Sorted by model distance: nonbonded pdb=" OE2 GLU B 264 " pdb=" HG SER B 516 " model vdw 1.580 2.450 nonbonded pdb=" OE2 GLU A 264 " pdb=" HG SER A 516 " model vdw 1.581 2.450 nonbonded pdb=" OE1 GLU B 320 " pdb=" HH TYR B 499 " model vdw 1.600 2.450 nonbonded pdb=" OE1 GLU A 238 " pdb=" HH TYR B 576 " model vdw 1.605 2.450 nonbonded pdb=" HG1 THR A 831 " pdb=" OE1 GLU A 834 " model vdw 1.607 2.450 ... (remaining 272320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 512 or (resid 513 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 514 through 841 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.330 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 42.260 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 167 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.8589 (mt0) cc_final: 0.8195 (mp10) REVERT: A 153 GLN cc_start: 0.8742 (tt0) cc_final: 0.8507 (tt0) REVERT: A 295 TRP cc_start: 0.6854 (t-100) cc_final: 0.6048 (t60) REVERT: A 344 LYS cc_start: 0.8514 (tptp) cc_final: 0.8221 (tppt) REVERT: A 492 TYR cc_start: 0.8097 (m-80) cc_final: 0.7825 (m-80) REVERT: A 567 GLU cc_start: 0.7756 (tt0) cc_final: 0.7391 (mt-10) REVERT: A 579 ARG cc_start: 0.8450 (mtt180) cc_final: 0.8114 (mtt90) REVERT: A 610 ARG cc_start: 0.7619 (ptm160) cc_final: 0.7404 (ptt-90) REVERT: B 22 MET cc_start: 0.8123 (mtt) cc_final: 0.7713 (mtt) REVERT: B 89 GLU cc_start: 0.8018 (mp0) cc_final: 0.7762 (mp0) REVERT: B 200 MET cc_start: 0.8823 (mmm) cc_final: 0.8602 (mmm) REVERT: B 221 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7614 (mttm) REVERT: B 239 MET cc_start: 0.7890 (ptm) cc_final: 0.7648 (ttp) REVERT: B 270 PHE cc_start: 0.8326 (t80) cc_final: 0.7857 (t80) REVERT: B 441 MET cc_start: 0.8689 (mmm) cc_final: 0.8462 (mmm) REVERT: B 445 MET cc_start: 0.8801 (mtt) cc_final: 0.8535 (mtt) REVERT: B 599 ASP cc_start: 0.7812 (m-30) cc_final: 0.7516 (m-30) REVERT: B 620 SER cc_start: 0.8822 (t) cc_final: 0.8410 (p) REVERT: B 621 MET cc_start: 0.8515 (mmt) cc_final: 0.8161 (mmt) REVERT: B 778 GLN cc_start: 0.4738 (OUTLIER) cc_final: 0.4486 (pp30) REVERT: B 800 ARG cc_start: 0.8873 (mtp180) cc_final: 0.8226 (mtm180) REVERT: B 803 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8687 (tp) outliers start: 14 outliers final: 3 residues processed: 162 average time/residue: 2.9305 time to fit residues: 507.7471 Evaluate side-chains 123 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 778 GLN 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: 0.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 796 GLN B 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100355 restraints weight = 32683.904| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.04 r_work: 0.3031 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1987 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= 0.174 Angle : 0.666 6.403 13530 Z= 0.374 Chirality : 0.041 0.151 1586 Planarity : 0.006 0.052 1676 Dihedral : 6.027 72.175 1352 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.26 % Allowed : 7.07 % Favored : 91.67 % 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: 0.31 (0.22), residues: 1230 helix: 1.07 (0.17), residues: 782 sheet: -1.78 (0.93), residues: 20 loop : -1.27 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 444 HIS 0.006 0.002 HIS A 513 PHE 0.016 0.001 PHE A 358 TYR 0.016 0.002 TYR A 23 ARG 0.005 0.000 ARG B 572 Details of bonding type rmsd hydrogen bonds : bond 0.08220 ( 601) hydrogen bonds : angle 4.75348 ( 1764) covalent geometry : bond 0.00345 ( 9960) covalent geometry : angle 0.66644 (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 139 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7399 (mt0) cc_final: 0.7120 (mt0) REVERT: A 18 GLU cc_start: 0.7456 (tt0) cc_final: 0.7088 (tt0) REVERT: A 577 ARG cc_start: 0.7176 (mtp85) cc_final: 0.6824 (mmp80) REVERT: A 579 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7283 (mtt180) REVERT: A 823 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7410 (mp) REVERT: B 22 MET cc_start: 0.8081 (mtt) cc_final: 0.7876 (mtt) REVERT: B 89 GLU cc_start: 0.7307 (mp0) cc_final: 0.6968 (mp0) REVERT: B 221 LYS cc_start: 0.6979 (ttmm) cc_final: 0.6691 (mttm) REVERT: B 441 MET cc_start: 0.8395 (mmm) cc_final: 0.8195 (mmm) REVERT: B 620 SER cc_start: 0.8454 (t) cc_final: 0.7678 (p) REVERT: B 621 MET cc_start: 0.8578 (mmt) cc_final: 0.8334 (mmt) REVERT: B 823 ILE cc_start: 0.8550 (mt) cc_final: 0.8260 (tp) outliers start: 13 outliers final: 4 residues processed: 133 average time/residue: 2.7438 time to fit residues: 392.9281 Evaluate side-chains 121 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 611 MET 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: 2.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098447 restraints weight = 32668.205| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.02 r_work: 0.2987 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9960 Z= 0.195 Angle : 0.586 4.594 13530 Z= 0.323 Chirality : 0.041 0.152 1586 Planarity : 0.005 0.054 1676 Dihedral : 5.167 37.898 1347 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.45 % Allowed : 8.53 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1230 helix: 1.41 (0.18), residues: 780 sheet: -1.43 (0.71), residues: 38 loop : -1.65 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 444 HIS 0.006 0.002 HIS A 513 PHE 0.014 0.002 PHE A 463 TYR 0.014 0.002 TYR A 492 ARG 0.011 0.001 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.07414 ( 601) hydrogen bonds : angle 4.29703 ( 1764) covalent geometry : bond 0.00475 ( 9960) covalent geometry : angle 0.58576 (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 141 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7365 (mt0) cc_final: 0.7036 (mt0) REVERT: A 18 GLU cc_start: 0.7735 (tt0) cc_final: 0.7306 (tt0) REVERT: A 314 PHE cc_start: 0.7780 (m-80) cc_final: 0.7570 (m-80) REVERT: A 460 MET cc_start: 0.8189 (mmt) cc_final: 0.7961 (mmt) REVERT: A 579 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7444 (mtt180) REVERT: A 616 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: A 834 GLU cc_start: 0.8020 (mp0) cc_final: 0.7502 (mp0) REVERT: B 22 MET cc_start: 0.8057 (mtt) cc_final: 0.7746 (mtt) REVERT: B 221 LYS cc_start: 0.7210 (ttmm) cc_final: 0.6912 (ttmm) REVERT: B 460 MET cc_start: 0.7765 (mmt) cc_final: 0.7439 (mmt) REVERT: B 619 GLU cc_start: 0.7639 (mp0) cc_final: 0.7279 (mp0) REVERT: B 620 SER cc_start: 0.8519 (t) cc_final: 0.7688 (p) REVERT: B 621 MET cc_start: 0.8658 (mmt) cc_final: 0.8414 (mmt) REVERT: B 823 ILE cc_start: 0.8516 (mt) cc_final: 0.8253 (tp) REVERT: B 833 LYS cc_start: 0.7571 (ttmm) cc_final: 0.7358 (ttmm) outliers start: 15 outliers final: 4 residues processed: 133 average time/residue: 2.6449 time to fit residues: 378.9569 Evaluate side-chains 122 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain B residue 313 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 0.0170 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 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: 7.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.100032 restraints weight = 33042.548| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.01 r_work: 0.3007 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9960 Z= 0.161 Angle : 0.534 4.692 13530 Z= 0.291 Chirality : 0.039 0.153 1586 Planarity : 0.005 0.043 1676 Dihedral : 4.895 40.883 1344 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.45 % Allowed : 8.91 % Favored : 89.63 % 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: 0.81 (0.23), residues: 1230 helix: 1.68 (0.18), residues: 780 sheet: -0.95 (0.82), residues: 28 loop : -1.60 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 444 HIS 0.004 0.001 HIS B 573 PHE 0.012 0.001 PHE B 279 TYR 0.008 0.001 TYR B 492 ARG 0.003 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.06655 ( 601) hydrogen bonds : angle 4.18533 ( 1764) covalent geometry : bond 0.00375 ( 9960) covalent geometry : angle 0.53449 (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 140 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7182 (mt0) cc_final: 0.6781 (mt0) REVERT: A 18 GLU cc_start: 0.7739 (tt0) cc_final: 0.7273 (tt0) REVERT: A 314 PHE cc_start: 0.7614 (m-80) cc_final: 0.7409 (m-80) REVERT: A 360 MET cc_start: 0.7438 (tpp) cc_final: 0.7028 (tpt) REVERT: A 579 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7524 (mtt180) REVERT: A 834 GLU cc_start: 0.7826 (mp0) cc_final: 0.7306 (mp0) REVERT: B 22 MET cc_start: 0.7985 (mtt) cc_final: 0.7652 (mtt) REVERT: B 153 GLN cc_start: 0.8140 (tp40) cc_final: 0.7932 (tp-100) REVERT: B 221 LYS cc_start: 0.6982 (ttmm) cc_final: 0.6683 (ttmm) REVERT: B 460 MET cc_start: 0.7610 (mmt) cc_final: 0.7288 (mmt) REVERT: B 619 GLU cc_start: 0.7628 (mp0) cc_final: 0.7195 (mp0) REVERT: B 620 SER cc_start: 0.8268 (t) cc_final: 0.7495 (p) REVERT: B 621 MET cc_start: 0.8583 (mmt) cc_final: 0.8354 (mmt) REVERT: B 823 ILE cc_start: 0.8420 (mt) cc_final: 0.8158 (tp) REVERT: B 833 LYS cc_start: 0.7412 (ttmm) cc_final: 0.7195 (ttmm) outliers start: 15 outliers final: 6 residues processed: 135 average time/residue: 2.6110 time to fit residues: 379.0714 Evaluate side-chains 128 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101959 restraints weight = 33031.056| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.03 r_work: 0.3055 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9960 Z= 0.122 Angle : 0.492 4.684 13530 Z= 0.265 Chirality : 0.037 0.150 1586 Planarity : 0.004 0.048 1676 Dihedral : 4.644 42.017 1344 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.16 % Allowed : 9.30 % Favored : 89.53 % 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: 1.14 (0.24), residues: 1230 helix: 2.02 (0.18), residues: 778 sheet: -0.94 (0.78), residues: 28 loop : -1.63 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 444 HIS 0.004 0.001 HIS A 817 PHE 0.009 0.001 PHE B 279 TYR 0.007 0.001 TYR A 492 ARG 0.005 0.000 ARG A 610 Details of bonding type rmsd hydrogen bonds : bond 0.05589 ( 601) hydrogen bonds : angle 4.04171 ( 1764) covalent geometry : bond 0.00270 ( 9960) covalent geometry : angle 0.49206 (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 137 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7165 (mt0) cc_final: 0.6747 (mt0) REVERT: A 18 GLU cc_start: 0.7761 (tt0) cc_final: 0.7242 (tt0) REVERT: A 314 PHE cc_start: 0.7633 (m-80) cc_final: 0.6760 (m-80) REVERT: A 360 MET cc_start: 0.7305 (tpp) cc_final: 0.7028 (tpt) REVERT: A 579 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7503 (mtt180) REVERT: A 611 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7309 (pmt) REVERT: A 616 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7439 (tt0) REVERT: A 834 GLU cc_start: 0.7831 (mp0) cc_final: 0.7327 (mp0) REVERT: B 22 MET cc_start: 0.7915 (mtt) cc_final: 0.7605 (mtt) REVERT: B 221 LYS cc_start: 0.6876 (ttmm) cc_final: 0.6568 (ttmm) REVERT: B 460 MET cc_start: 0.7633 (mmt) cc_final: 0.7329 (mmt) REVERT: B 611 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7725 (pmt) REVERT: B 619 GLU cc_start: 0.7566 (mp0) cc_final: 0.7133 (mp0) REVERT: B 620 SER cc_start: 0.8278 (t) cc_final: 0.7557 (p) REVERT: B 621 MET cc_start: 0.8585 (mmt) cc_final: 0.8375 (mmt) REVERT: B 823 ILE cc_start: 0.8368 (mt) cc_final: 0.8160 (tp) REVERT: B 833 LYS cc_start: 0.7415 (ttmm) cc_final: 0.7198 (ttmm) outliers start: 12 outliers final: 5 residues processed: 132 average time/residue: 2.5060 time to fit residues: 356.7444 Evaluate side-chains 128 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100648 restraints weight = 32888.295| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.02 r_work: 0.3036 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9960 Z= 0.149 Angle : 0.508 4.820 13530 Z= 0.273 Chirality : 0.038 0.150 1586 Planarity : 0.005 0.045 1676 Dihedral : 4.627 44.526 1344 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.36 % Allowed : 9.69 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1230 helix: 2.03 (0.18), residues: 778 sheet: -1.06 (0.77), residues: 28 loop : -1.66 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 444 HIS 0.003 0.001 HIS B 486 PHE 0.014 0.001 PHE B 279 TYR 0.008 0.001 TYR B 492 ARG 0.004 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.06130 ( 601) hydrogen bonds : angle 4.01682 ( 1764) covalent geometry : bond 0.00355 ( 9960) covalent geometry : angle 0.50752 (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 137 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7184 (mt0) cc_final: 0.6748 (mt0) REVERT: A 18 GLU cc_start: 0.7780 (tt0) cc_final: 0.7259 (tt0) REVERT: A 314 PHE cc_start: 0.7643 (m-80) cc_final: 0.6803 (m-80) REVERT: A 360 MET cc_start: 0.7301 (tpp) cc_final: 0.7050 (tpt) REVERT: A 579 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7499 (mtt180) REVERT: A 616 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: A 834 GLU cc_start: 0.7831 (mp0) cc_final: 0.7268 (mp0) REVERT: B 22 MET cc_start: 0.7900 (mtt) cc_final: 0.7586 (mtt) REVERT: B 221 LYS cc_start: 0.6994 (ttmm) cc_final: 0.6741 (ttmm) REVERT: B 460 MET cc_start: 0.7639 (mmt) cc_final: 0.7394 (mmt) REVERT: B 619 GLU cc_start: 0.7563 (mp0) cc_final: 0.7106 (mp0) REVERT: B 620 SER cc_start: 0.8280 (t) cc_final: 0.7571 (p) REVERT: B 823 ILE cc_start: 0.8252 (mt) cc_final: 0.8039 (tp) REVERT: B 833 LYS cc_start: 0.7413 (ttmm) cc_final: 0.7193 (ttmm) outliers start: 14 outliers final: 8 residues processed: 133 average time/residue: 2.6611 time to fit residues: 380.3017 Evaluate side-chains 132 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.099126 restraints weight = 32956.428| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.02 r_work: 0.3030 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3092 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= 0.156 Angle : 0.510 4.781 13530 Z= 0.276 Chirality : 0.038 0.149 1586 Planarity : 0.005 0.043 1676 Dihedral : 4.630 48.041 1344 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.74 % Allowed : 9.40 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1230 helix: 2.00 (0.18), residues: 778 sheet: -1.12 (0.78), residues: 28 loop : -1.69 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 444 HIS 0.005 0.001 HIS B 486 PHE 0.013 0.001 PHE B 279 TYR 0.007 0.001 TYR B 275 ARG 0.004 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.06245 ( 601) hydrogen bonds : angle 4.02036 ( 1764) covalent geometry : bond 0.00374 ( 9960) covalent geometry : angle 0.50989 (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 137 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7220 (mt0) cc_final: 0.6807 (mt0) REVERT: A 18 GLU cc_start: 0.7779 (tt0) cc_final: 0.7271 (tt0) REVERT: A 223 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4736 (pp) REVERT: A 314 PHE cc_start: 0.7672 (m-80) cc_final: 0.6846 (m-80) REVERT: A 360 MET cc_start: 0.7298 (tpp) cc_final: 0.7064 (tpt) REVERT: A 579 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7364 (mtt180) REVERT: A 611 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7389 (pmt) REVERT: A 616 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: A 834 GLU cc_start: 0.7875 (mp0) cc_final: 0.7310 (mp0) REVERT: B 16 GLN cc_start: 0.8087 (pt0) cc_final: 0.7696 (tt0) REVERT: B 22 MET cc_start: 0.7911 (mtt) cc_final: 0.7579 (mtt) REVERT: B 221 LYS cc_start: 0.7012 (ttmm) cc_final: 0.6753 (ttmm) REVERT: B 460 MET cc_start: 0.7676 (mmt) cc_final: 0.7452 (mmt) REVERT: B 619 GLU cc_start: 0.7537 (mp0) cc_final: 0.7069 (mp0) REVERT: B 620 SER cc_start: 0.8296 (t) cc_final: 0.7594 (p) REVERT: B 823 ILE cc_start: 0.8252 (mt) cc_final: 0.8034 (tp) REVERT: B 833 LYS cc_start: 0.7425 (ttmm) cc_final: 0.7206 (ttmm) outliers start: 18 outliers final: 9 residues processed: 128 average time/residue: 2.6747 time to fit residues: 369.2236 Evaluate side-chains 130 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 614 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: 3.9990 chunk 108 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.138562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100802 restraints weight = 33043.424| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.02 r_work: 0.3048 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3174 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= 0.125 Angle : 0.484 4.766 13530 Z= 0.260 Chirality : 0.037 0.151 1586 Planarity : 0.004 0.042 1676 Dihedral : 4.522 49.894 1344 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.26 % Allowed : 9.88 % Favored : 88.86 % 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: 2.20 (0.18), residues: 776 sheet: -1.10 (0.79), residues: 28 loop : -1.65 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 444 HIS 0.004 0.001 HIS B 486 PHE 0.011 0.001 PHE B 279 TYR 0.007 0.001 TYR B 110 ARG 0.004 0.000 ARG A 471 Details of bonding type rmsd hydrogen bonds : bond 0.05549 ( 601) hydrogen bonds : angle 3.95422 ( 1764) covalent geometry : bond 0.00287 ( 9960) covalent geometry : angle 0.48399 (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 138 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7227 (mt0) cc_final: 0.6772 (mt0) REVERT: A 18 GLU cc_start: 0.7775 (tt0) cc_final: 0.7264 (tt0) REVERT: A 314 PHE cc_start: 0.7651 (m-80) cc_final: 0.6818 (m-80) REVERT: A 360 MET cc_start: 0.7253 (tpp) cc_final: 0.7049 (tpt) REVERT: A 616 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: A 834 GLU cc_start: 0.7872 (mp0) cc_final: 0.7317 (mp0) REVERT: B 16 GLN cc_start: 0.8070 (pt0) cc_final: 0.7712 (tt0) REVERT: B 22 MET cc_start: 0.7903 (mtt) cc_final: 0.7577 (mtt) REVERT: B 153 GLN cc_start: 0.8176 (tp40) cc_final: 0.7951 (tp40) REVERT: B 221 LYS cc_start: 0.6958 (ttmm) cc_final: 0.6694 (ttmm) REVERT: B 619 GLU cc_start: 0.7539 (mp0) cc_final: 0.7083 (mp0) REVERT: B 620 SER cc_start: 0.8284 (t) cc_final: 0.7587 (p) REVERT: B 823 ILE cc_start: 0.8228 (mt) cc_final: 0.8028 (tp) outliers start: 13 outliers final: 6 residues processed: 134 average time/residue: 2.7229 time to fit residues: 391.6366 Evaluate side-chains 128 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 98 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 43 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103956 restraints weight = 32817.212| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.03 r_work: 0.3102 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3373 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= 0.100 Angle : 0.464 4.722 13530 Z= 0.246 Chirality : 0.036 0.147 1586 Planarity : 0.004 0.044 1676 Dihedral : 4.228 50.855 1342 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.07 % Allowed : 10.27 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1230 helix: 2.46 (0.19), residues: 778 sheet: -1.01 (0.79), residues: 28 loop : -1.53 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 444 HIS 0.004 0.001 HIS A 817 PHE 0.007 0.001 PHE A 279 TYR 0.007 0.001 TYR B 492 ARG 0.005 0.000 ARG B 586 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 601) hydrogen bonds : angle 3.83570 ( 1764) covalent geometry : bond 0.00211 ( 9960) covalent geometry : angle 0.46393 (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 131 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7228 (mt0) cc_final: 0.6784 (mt0) REVERT: A 18 GLU cc_start: 0.7765 (tt0) cc_final: 0.7224 (tt0) REVERT: A 314 PHE cc_start: 0.7632 (m-80) cc_final: 0.6862 (m-80) REVERT: A 616 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: A 834 GLU cc_start: 0.7865 (mp0) cc_final: 0.7328 (mp0) REVERT: B 16 GLN cc_start: 0.8032 (pt0) cc_final: 0.7693 (tt0) REVERT: B 22 MET cc_start: 0.7875 (mtt) cc_final: 0.7589 (mtt) REVERT: B 153 GLN cc_start: 0.8165 (tp40) cc_final: 0.7935 (tp40) REVERT: B 221 LYS cc_start: 0.6849 (ttmm) cc_final: 0.6586 (ttmm) REVERT: B 619 GLU cc_start: 0.7574 (mp0) cc_final: 0.7124 (mp0) REVERT: B 620 SER cc_start: 0.8281 (t) cc_final: 0.7595 (p) outliers start: 11 outliers final: 6 residues processed: 128 average time/residue: 2.5253 time to fit residues: 348.6519 Evaluate side-chains 122 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102566 restraints weight = 32698.529| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.01 r_work: 0.3062 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9960 Z= 0.123 Angle : 0.478 4.716 13530 Z= 0.254 Chirality : 0.037 0.156 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.274 52.588 1342 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.78 % Allowed : 11.24 % Favored : 87.98 % 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: 1.58 (0.24), residues: 1230 helix: 2.39 (0.19), residues: 780 sheet: -1.01 (0.79), residues: 28 loop : -1.50 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 444 HIS 0.003 0.001 HIS A 817 PHE 0.011 0.001 PHE B 279 TYR 0.008 0.001 TYR B 275 ARG 0.003 0.000 ARG B 586 Details of bonding type rmsd hydrogen bonds : bond 0.05261 ( 601) hydrogen bonds : angle 3.84374 ( 1764) covalent geometry : bond 0.00285 ( 9960) covalent geometry : angle 0.47766 (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 124 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 16 GLN cc_start: 0.7277 (mt0) cc_final: 0.6826 (mt0) REVERT: A 18 GLU cc_start: 0.7796 (tt0) cc_final: 0.7270 (tt0) REVERT: A 314 PHE cc_start: 0.7695 (m-80) cc_final: 0.6905 (m-80) REVERT: A 616 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: A 834 GLU cc_start: 0.7914 (mp0) cc_final: 0.7395 (mp0) REVERT: B 16 GLN cc_start: 0.8081 (pt0) cc_final: 0.7740 (tt0) REVERT: B 22 MET cc_start: 0.7924 (mtt) cc_final: 0.7621 (mtt) REVERT: B 619 GLU cc_start: 0.7628 (mp0) cc_final: 0.7183 (mp0) REVERT: B 620 SER cc_start: 0.8312 (t) cc_final: 0.7628 (p) outliers start: 8 outliers final: 5 residues processed: 122 average time/residue: 2.6233 time to fit residues: 345.0456 Evaluate side-chains 119 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100076 restraints weight = 32993.122| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.02 r_work: 0.3048 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3322 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= 0.144 Angle : 0.497 4.788 13530 Z= 0.266 Chirality : 0.038 0.154 1586 Planarity : 0.004 0.043 1676 Dihedral : 4.376 55.416 1342 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.97 % Allowed : 10.95 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1230 helix: 2.25 (0.18), residues: 780 sheet: -1.03 (0.80), residues: 28 loop : -1.52 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 444 HIS 0.003 0.001 HIS A 817 PHE 0.012 0.001 PHE B 279 TYR 0.007 0.001 TYR B 275 ARG 0.007 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.05809 ( 601) hydrogen bonds : angle 3.89345 ( 1764) covalent geometry : bond 0.00344 ( 9960) covalent geometry : angle 0.49654 (13530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13221.34 seconds wall clock time: 223 minutes 48.81 seconds (13428.81 seconds total)