Starting phenix.real_space_refine on Wed Sep 17 14:02:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y92_39067/09_2025/8y92_39067.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y92_39067/09_2025/8y92_39067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y92_39067/09_2025/8y92_39067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y92_39067/09_2025/8y92_39067.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y92_39067/09_2025/8y92_39067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y92_39067/09_2025/8y92_39067.map" } resolution = 3.29 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= 0.000 sd= 0.046 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 40 5.16 5 Cl 2 4.86 5 Na 1 4.78 5 C 6086 2.51 5 N 1414 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9078 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' CL': 1, 'A1LX4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.21, per 1000 atoms: 0.24 Number of scatterers: 9078 At special positions: 0 Unit cell: (80.3, 116.8, 89.06, 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 40 16.00 Na 1 11.00 O 1535 8.00 N 1414 7.00 C 6086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 233.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.683A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.707A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 135 through 166 removed outlier: 3.766A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.835A pdb=" N ASP A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.642A pdb=" N TYR A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.627A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 283 removed outlier: 3.575A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.074A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.911A pdb=" N ARG A 301 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS A 303 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 320 removed outlier: 3.863A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 331 removed outlier: 4.233A pdb=" N ILE A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.652A pdb=" N VAL A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.672A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.705A pdb=" N LYS A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.527A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.544A pdb=" N PHE A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 580 removed outlier: 4.166A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Proline residue: A 570 - end of helix removed outlier: 3.625A pdb=" N THR A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 598 through 602 removed outlier: 3.898A pdb=" N ALA A 602 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.960A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 74 removed outlier: 3.674A pdb=" N PHE B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.696A pdb=" N VAL B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.667A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.613A pdb=" N MET B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.529A pdb=" N TRP B 128 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 129 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE B 130 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 134 through 166 removed outlier: 3.924A pdb=" N ILE B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 154 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.788A pdb=" N TYR B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.543A pdb=" N SER B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 253 Processing helix chain 'B' and resid 255 through 283 removed outlier: 3.645A pdb=" N SER B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Proline residue: B 270 - end of helix removed outlier: 4.049A pdb=" N THR B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.578A pdb=" N ARG B 301 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 303 " --> pdb=" O TYR B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 320 removed outlier: 4.152A pdb=" N TRP B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 332 removed outlier: 4.284A pdb=" N ILE B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 372 removed outlier: 3.508A pdb=" N ASP B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.687A pdb=" N VAL B 379 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 389 through 398 Processing helix chain 'B' and resid 400 through 435 removed outlier: 3.606A pdb=" N TRP B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 441 removed outlier: 3.794A pdb=" N LYS B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 458 Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 465 through 496 Processing helix chain 'B' and resid 497 through 509 Processing helix chain 'B' and resid 514 through 523 Processing helix chain 'B' and resid 523 through 539 Processing helix chain 'B' and resid 553 through 580 Proline residue: B 570 - end of helix removed outlier: 3.506A pdb=" N THR B 580 " --> pdb=" O LYS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 593 removed outlier: 3.729A pdb=" N TYR B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 3.524A pdb=" N VAL B 601 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 602 " --> pdb=" O HIS B 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 598 through 602' Processing helix chain 'B' and resid 610 through 616 removed outlier: 4.170A pdb=" N TRP B 614 " --> pdb=" O GLN B 610 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1728 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: 1.29 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1342 1.32 - 1.44: 2934 1.44 - 1.56: 5028 1.56 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9366 Sorted by residual: bond pdb=" CA VAL A 74 " pdb=" C VAL A 74 " ideal model delta sigma weight residual 1.523 1.416 0.107 1.27e-02 6.20e+03 7.13e+01 bond pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 1.524 1.433 0.091 1.35e-02 5.49e+03 4.57e+01 bond pdb=" N ASP A 75 " pdb=" CA ASP A 75 " ideal model delta sigma weight residual 1.456 1.371 0.084 1.44e-02 4.82e+03 3.44e+01 bond pdb=" CA ALA A 77 " pdb=" C ALA A 77 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N ALA A 73 " pdb=" CA ALA A 73 " ideal model delta sigma weight residual 1.459 1.420 0.039 1.17e-02 7.31e+03 1.12e+01 ... (remaining 9361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 12752 4.80 - 9.60: 23 9.60 - 14.40: 0 14.40 - 19.20: 0 19.20 - 24.00: 1 Bond angle restraints: 12776 Sorted by residual: angle pdb=" N ASP A 75 " pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 109.18 85.18 24.00 1.42e+00 4.96e-01 2.86e+02 angle pdb=" CA ALA A 73 " pdb=" C ALA A 73 " pdb=" N VAL A 74 " ideal model delta sigma weight residual 116.92 121.89 -4.97 1.16e+00 7.43e-01 1.83e+01 angle pdb=" N ASP A 75 " pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " ideal model delta sigma weight residual 111.22 105.08 6.14 1.58e+00 4.01e-01 1.51e+01 angle pdb=" CA ALA A 73 " pdb=" C ALA A 73 " pdb=" O ALA A 73 " ideal model delta sigma weight residual 121.00 117.29 3.71 1.05e+00 9.07e-01 1.25e+01 angle pdb=" C ASN B 198 " pdb=" N HIS B 199 " pdb=" CA HIS B 199 " ideal model delta sigma weight residual 120.79 125.70 -4.91 1.39e+00 5.18e-01 1.25e+01 ... (remaining 12771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.60: 5111 28.60 - 57.19: 117 57.19 - 85.79: 9 85.79 - 114.38: 0 114.38 - 142.98: 1 Dihedral angle restraints: 5238 sinusoidal: 1974 harmonic: 3264 Sorted by residual: dihedral pdb=" N ASP A 75 " pdb=" C ASP A 75 " pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " ideal model delta harmonic sigma weight residual 122.80 104.46 18.34 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" C10 A1LX4 B 701 " pdb=" C11 A1LX4 B 701 " pdb=" N12 A1LX4 B 701 " pdb=" C13 A1LX4 B 701 " ideal model delta sinusoidal sigma weight residual -79.57 63.41 -142.98 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C VAL A 74 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " pdb=" CB VAL A 74 " ideal model delta harmonic sigma weight residual -122.00 -130.95 8.95 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 5235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1342 0.070 - 0.139: 75 0.139 - 0.208: 1 0.208 - 0.278: 1 0.278 - 0.347: 1 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA LEU A 76 " pdb=" N LEU A 76 " pdb=" C LEU A 76 " pdb=" CB LEU A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ALA A 77 " pdb=" N ALA A 77 " pdb=" C ALA A 77 " pdb=" CB ALA A 77 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 1417 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 71 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.35e+00 pdb=" C GLY A 71 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY A 71 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 72 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 107 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 108 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 569 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO B 570 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 570 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 570 " 0.021 5.00e-02 4.00e+02 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 65 2.54 - 3.13: 7267 3.13 - 3.72: 15084 3.72 - 4.31: 20518 4.31 - 4.90: 34248 Nonbonded interactions: 77182 Sorted by model distance: nonbonded pdb=" N ASP A 75 " pdb=" O ASP A 75 " model vdw 1.954 2.496 nonbonded pdb=" OG SER B 318 " pdb="CL CL B 703 " model vdw 2.152 3.190 nonbonded pdb=" OG SER A 583 " pdb=" OE1 GLU A 586 " model vdw 2.190 3.040 nonbonded pdb=" OG SER A 318 " pdb="CL CL A 702 " model vdw 2.215 3.190 nonbonded pdb=" O LEU A 163 " pdb=" OG SER A 166 " model vdw 2.236 3.040 ... (remaining 77177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 53 through 701) selection = (chain 'B' and resid 53 through 701) } 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: 2.150 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 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 : 0.003 0.107 9366 Z= 0.217 Angle : 0.636 24.001 12776 Z= 0.389 Chirality : 0.037 0.347 1420 Planarity : 0.004 0.042 1556 Dihedral : 11.667 142.975 3162 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.73 % Allowed : 7.77 % Favored : 87.50 % Cbeta Deviations : 0.10 % 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 (0.23), residues: 1126 helix: -0.36 (0.17), residues: 766 sheet: None (None), residues: 0 loop : -1.50 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.006 0.001 TYR B 572 PHE 0.012 0.001 PHE B 362 TRP 0.010 0.001 TRP B 308 HIS 0.001 0.000 HIS B 199 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9366) covalent geometry : angle 0.63574 (12776) hydrogen bonds : bond 0.15166 ( 587) hydrogen bonds : angle 5.40212 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 126 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7614 (p) REVERT: A 306 THR cc_start: 0.7747 (p) cc_final: 0.7434 (t) REVERT: A 455 LEU cc_start: 0.7424 (mt) cc_final: 0.7219 (mt) REVERT: B 507 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: B 586 GLU cc_start: 0.7668 (mp0) cc_final: 0.7034 (mp0) outliers start: 45 outliers final: 9 residues processed: 298 average time/residue: 0.0878 time to fit residues: 37.8294 Evaluate side-chains 179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 531 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.199119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.175391 restraints weight = 12962.677| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.31 r_work: 0.4046 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9366 Z= 0.140 Angle : 0.557 7.670 12776 Z= 0.283 Chirality : 0.039 0.137 1420 Planarity : 0.004 0.047 1556 Dihedral : 7.399 109.611 1265 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.78 % Allowed : 14.81 % Favored : 81.41 % 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: 0.45 (0.25), residues: 1126 helix: 0.87 (0.18), residues: 774 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 216 TYR 0.013 0.001 TYR A 111 PHE 0.017 0.001 PHE B 316 TRP 0.010 0.001 TRP A 128 HIS 0.005 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9366) covalent geometry : angle 0.55695 (12776) hydrogen bonds : bond 0.04249 ( 587) hydrogen bonds : angle 4.53298 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.246 Fit side-chains REVERT: A 306 THR cc_start: 0.7942 (p) cc_final: 0.7569 (t) REVERT: A 425 GLU cc_start: 0.7326 (tt0) cc_final: 0.7057 (tt0) REVERT: B 202 TYR cc_start: 0.5382 (OUTLIER) cc_final: 0.3443 (t80) REVERT: B 364 ILE cc_start: 0.8492 (mp) cc_final: 0.8257 (mp) REVERT: B 507 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: B 601 VAL cc_start: 0.8603 (t) cc_final: 0.8282 (m) outliers start: 36 outliers final: 23 residues processed: 196 average time/residue: 0.0667 time to fit residues: 20.4862 Evaluate side-chains 163 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 531 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 14 optimal weight: 0.0040 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 48 optimal weight: 0.2980 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.189856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.164490 restraints weight = 13004.604| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.36 r_work: 0.3919 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9366 Z= 0.147 Angle : 0.557 7.713 12776 Z= 0.286 Chirality : 0.040 0.133 1420 Planarity : 0.004 0.036 1556 Dihedral : 6.484 88.195 1256 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.25 % Allowed : 14.39 % Favored : 80.36 % 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: 0.76 (0.25), residues: 1126 helix: 1.07 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -0.73 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.018 0.002 TYR A 111 PHE 0.023 0.002 PHE B 275 TRP 0.014 0.001 TRP A 128 HIS 0.003 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9366) covalent geometry : angle 0.55654 (12776) hydrogen bonds : bond 0.04817 ( 587) hydrogen bonds : angle 4.58718 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.338 Fit side-chains REVERT: A 473 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.5939 (t0) REVERT: A 487 MET cc_start: 0.8617 (tpp) cc_final: 0.8177 (tpp) REVERT: A 566 MET cc_start: 0.5646 (mtt) cc_final: 0.5212 (mtt) REVERT: B 202 TYR cc_start: 0.5440 (OUTLIER) cc_final: 0.3423 (t80) REVERT: B 425 GLU cc_start: 0.7488 (tt0) cc_final: 0.7264 (tt0) REVERT: B 486 LEU cc_start: 0.7759 (tp) cc_final: 0.7406 (tp) REVERT: B 507 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: B 566 MET cc_start: 0.5601 (mtt) cc_final: 0.5339 (mtt) REVERT: B 601 VAL cc_start: 0.8606 (t) cc_final: 0.8293 (m) outliers start: 50 outliers final: 33 residues processed: 188 average time/residue: 0.0721 time to fit residues: 21.0629 Evaluate side-chains 179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 531 PHE Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.190162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.165023 restraints weight = 13087.904| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.34 r_work: 0.3930 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9366 Z= 0.124 Angle : 0.525 6.382 12776 Z= 0.269 Chirality : 0.039 0.164 1420 Planarity : 0.004 0.038 1556 Dihedral : 6.117 82.294 1254 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.25 % Allowed : 15.13 % Favored : 79.62 % 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: 1.02 (0.26), residues: 1126 helix: 1.22 (0.19), residues: 796 sheet: None (None), residues: 0 loop : -0.54 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.017 0.001 TYR A 111 PHE 0.016 0.001 PHE A 359 TRP 0.008 0.001 TRP B 80 HIS 0.003 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9366) covalent geometry : angle 0.52454 (12776) hydrogen bonds : bond 0.04440 ( 587) hydrogen bonds : angle 4.51988 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.342 Fit side-chains REVERT: A 133 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: A 225 SER cc_start: 0.8210 (m) cc_final: 0.7714 (t) REVERT: A 481 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8319 (tp) REVERT: A 566 MET cc_start: 0.5623 (mtt) cc_final: 0.5351 (mtt) REVERT: A 584 LEU cc_start: 0.7570 (mm) cc_final: 0.6834 (pt) REVERT: B 202 TYR cc_start: 0.5382 (OUTLIER) cc_final: 0.3420 (t80) REVERT: B 507 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7137 (tp40) outliers start: 50 outliers final: 32 residues processed: 181 average time/residue: 0.0668 time to fit residues: 19.2156 Evaluate side-chains 177 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 531 PHE Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 0.0030 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.189327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.164078 restraints weight = 13092.980| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.33 r_work: 0.3922 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9366 Z= 0.122 Angle : 0.520 8.616 12776 Z= 0.265 Chirality : 0.038 0.127 1420 Planarity : 0.004 0.036 1556 Dihedral : 6.007 81.084 1254 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.83 % Allowed : 16.91 % Favored : 78.26 % 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: 1.17 (0.26), residues: 1126 helix: 1.32 (0.19), residues: 796 sheet: None (None), residues: 0 loop : -0.44 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.016 0.001 TYR B 111 PHE 0.022 0.001 PHE A 275 TRP 0.007 0.001 TRP A 128 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9366) covalent geometry : angle 0.51977 (12776) hydrogen bonds : bond 0.04405 ( 587) hydrogen bonds : angle 4.50753 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.338 Fit side-chains REVERT: A 133 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: A 225 SER cc_start: 0.8202 (m) cc_final: 0.7709 (t) REVERT: A 481 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8324 (tp) REVERT: A 566 MET cc_start: 0.5668 (mtt) cc_final: 0.5399 (mtt) REVERT: A 584 LEU cc_start: 0.7617 (mm) cc_final: 0.6834 (pt) REVERT: A 588 LEU cc_start: 0.8067 (mt) cc_final: 0.7817 (mt) REVERT: B 122 GLU cc_start: 0.8120 (mp0) cc_final: 0.7885 (mp0) REVERT: B 133 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: B 202 TYR cc_start: 0.5399 (OUTLIER) cc_final: 0.3605 (t80) REVERT: B 507 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7449 (tm-30) outliers start: 46 outliers final: 36 residues processed: 184 average time/residue: 0.0640 time to fit residues: 18.8506 Evaluate side-chains 180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 531 PHE Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.192691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.166930 restraints weight = 12995.504| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.36 r_work: 0.3954 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9366 Z= 0.130 Angle : 0.527 7.022 12776 Z= 0.269 Chirality : 0.039 0.135 1420 Planarity : 0.004 0.034 1556 Dihedral : 6.013 84.991 1254 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.94 % Allowed : 17.86 % Favored : 77.21 % 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 (0.26), residues: 1126 helix: 1.32 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.029 0.001 TYR B 111 PHE 0.015 0.001 PHE B 362 TRP 0.008 0.001 TRP B 559 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9366) covalent geometry : angle 0.52682 (12776) hydrogen bonds : bond 0.04518 ( 587) hydrogen bonds : angle 4.55052 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.384 Fit side-chains REVERT: A 133 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: A 225 SER cc_start: 0.8155 (m) cc_final: 0.7671 (t) REVERT: A 292 ASN cc_start: 0.7901 (m-40) cc_final: 0.7419 (m-40) REVERT: A 473 ASP cc_start: 0.6560 (OUTLIER) cc_final: 0.5778 (t0) REVERT: A 481 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8299 (tp) REVERT: B 122 GLU cc_start: 0.8145 (mp0) cc_final: 0.7906 (mp0) REVERT: B 133 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: B 202 TYR cc_start: 0.5418 (OUTLIER) cc_final: 0.3768 (t80) REVERT: B 280 HIS cc_start: 0.5879 (t70) cc_final: 0.5496 (m-70) REVERT: B 473 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.5796 (t0) REVERT: B 507 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: B 584 LEU cc_start: 0.7332 (mm) cc_final: 0.6794 (pt) outliers start: 47 outliers final: 34 residues processed: 178 average time/residue: 0.0685 time to fit residues: 19.2268 Evaluate side-chains 180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.192244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.166548 restraints weight = 13050.697| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.35 r_work: 0.3959 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9366 Z= 0.127 Angle : 0.528 7.561 12776 Z= 0.267 Chirality : 0.038 0.130 1420 Planarity : 0.004 0.032 1556 Dihedral : 5.873 83.574 1252 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.73 % Allowed : 18.49 % Favored : 76.79 % 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: 1.27 (0.26), residues: 1126 helix: 1.40 (0.19), residues: 786 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.018 0.001 TYR B 111 PHE 0.023 0.001 PHE A 275 TRP 0.010 0.001 TRP A 404 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9366) covalent geometry : angle 0.52799 (12776) hydrogen bonds : bond 0.04516 ( 587) hydrogen bonds : angle 4.55791 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 0.339 Fit side-chains REVERT: A 133 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: A 225 SER cc_start: 0.8119 (m) cc_final: 0.7677 (t) REVERT: A 292 ASN cc_start: 0.7947 (m-40) cc_final: 0.7470 (m-40) REVERT: A 481 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 588 LEU cc_start: 0.8069 (mt) cc_final: 0.7850 (mt) REVERT: B 122 GLU cc_start: 0.8155 (mp0) cc_final: 0.7849 (mp0) REVERT: B 133 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: B 202 TYR cc_start: 0.5376 (OUTLIER) cc_final: 0.3713 (t80) REVERT: B 507 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: B 508 MET cc_start: 0.8029 (mmm) cc_final: 0.7745 (ttm) REVERT: B 584 LEU cc_start: 0.7374 (mm) cc_final: 0.6743 (pt) outliers start: 45 outliers final: 33 residues processed: 177 average time/residue: 0.0705 time to fit residues: 19.6201 Evaluate side-chains 178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.190601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.164637 restraints weight = 13053.066| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.35 r_work: 0.3938 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9366 Z= 0.138 Angle : 0.564 11.084 12776 Z= 0.282 Chirality : 0.039 0.154 1420 Planarity : 0.004 0.037 1556 Dihedral : 5.898 84.942 1252 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.15 % Allowed : 18.38 % Favored : 76.47 % 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: 1.27 (0.26), residues: 1126 helix: 1.38 (0.19), residues: 786 sheet: None (None), residues: 0 loop : -0.29 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.019 0.001 TYR B 111 PHE 0.019 0.001 PHE A 528 TRP 0.011 0.001 TRP B 559 HIS 0.005 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9366) covalent geometry : angle 0.56416 (12776) hydrogen bonds : bond 0.04681 ( 587) hydrogen bonds : angle 4.62087 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.417 Fit side-chains REVERT: A 133 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8495 (m-80) REVERT: A 225 SER cc_start: 0.8148 (m) cc_final: 0.7669 (t) REVERT: A 292 ASN cc_start: 0.7950 (m-40) cc_final: 0.7471 (m-40) REVERT: A 473 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.5995 (t0) REVERT: A 481 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8391 (tp) REVERT: A 566 MET cc_start: 0.5880 (mtm) cc_final: 0.5579 (mtt) REVERT: B 133 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: B 202 TYR cc_start: 0.5376 (OUTLIER) cc_final: 0.3701 (t80) REVERT: B 297 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7879 (mt) REVERT: B 473 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.5922 (t0) REVERT: B 481 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8385 (tp) REVERT: B 584 LEU cc_start: 0.7384 (mm) cc_final: 0.6838 (pt) outliers start: 49 outliers final: 34 residues processed: 174 average time/residue: 0.0692 time to fit residues: 19.0496 Evaluate side-chains 179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 91 optimal weight: 0.3980 chunk 94 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.192769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.167115 restraints weight = 12995.429| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.35 r_work: 0.3955 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9366 Z= 0.123 Angle : 0.547 10.293 12776 Z= 0.274 Chirality : 0.039 0.153 1420 Planarity : 0.004 0.039 1556 Dihedral : 5.851 86.091 1252 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.20 % Allowed : 19.43 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.33 (0.26), residues: 1126 helix: 1.43 (0.19), residues: 786 sheet: None (None), residues: 0 loop : -0.30 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 56 TYR 0.020 0.001 TYR B 111 PHE 0.023 0.001 PHE A 275 TRP 0.012 0.001 TRP B 559 HIS 0.005 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9366) covalent geometry : angle 0.54724 (12776) hydrogen bonds : bond 0.04458 ( 587) hydrogen bonds : angle 4.56849 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.372 Fit side-chains REVERT: A 133 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8490 (m-80) REVERT: A 225 SER cc_start: 0.8132 (m) cc_final: 0.7641 (t) REVERT: A 292 ASN cc_start: 0.7925 (m-40) cc_final: 0.7471 (m-40) REVERT: A 481 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8369 (tp) REVERT: A 588 LEU cc_start: 0.8037 (mt) cc_final: 0.7823 (mt) REVERT: B 202 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.3607 (t80) REVERT: B 280 HIS cc_start: 0.5773 (t70) cc_final: 0.5422 (m-70) REVERT: B 292 ASN cc_start: 0.7991 (m-40) cc_final: 0.7543 (m-40) REVERT: B 362 PHE cc_start: 0.7681 (m-80) cc_final: 0.7441 (m-80) REVERT: B 481 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8355 (tp) REVERT: B 507 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: B 519 LEU cc_start: 0.8605 (mt) cc_final: 0.8284 (mt) REVERT: B 584 LEU cc_start: 0.7363 (mm) cc_final: 0.6817 (pt) outliers start: 40 outliers final: 32 residues processed: 166 average time/residue: 0.0686 time to fit residues: 18.0437 Evaluate side-chains 175 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.190513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.164460 restraints weight = 13076.342| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.36 r_work: 0.3929 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9366 Z= 0.141 Angle : 0.575 10.336 12776 Z= 0.287 Chirality : 0.039 0.147 1420 Planarity : 0.004 0.040 1556 Dihedral : 5.784 77.499 1252 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.20 % Allowed : 19.75 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.27 (0.26), residues: 1126 helix: 1.38 (0.19), residues: 786 sheet: None (None), residues: 0 loop : -0.29 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.019 0.001 TYR B 111 PHE 0.015 0.001 PHE B 362 TRP 0.015 0.001 TRP B 559 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9366) covalent geometry : angle 0.57538 (12776) hydrogen bonds : bond 0.04703 ( 587) hydrogen bonds : angle 4.63110 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 144 time to evaluate : 0.342 Fit side-chains REVERT: A 133 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8553 (m-80) REVERT: A 225 SER cc_start: 0.8107 (m) cc_final: 0.7616 (t) REVERT: A 292 ASN cc_start: 0.7923 (m-40) cc_final: 0.7475 (m-40) REVERT: A 473 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6023 (t0) REVERT: A 481 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8397 (tp) REVERT: A 566 MET cc_start: 0.5942 (mtm) cc_final: 0.5708 (mtt) REVERT: A 588 LEU cc_start: 0.8053 (mt) cc_final: 0.7849 (mt) REVERT: A 600 LEU cc_start: 0.9099 (pp) cc_final: 0.8878 (tt) REVERT: B 202 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.3699 (t80) REVERT: B 280 HIS cc_start: 0.5854 (t70) cc_final: 0.5460 (m-70) REVERT: B 292 ASN cc_start: 0.7971 (m-40) cc_final: 0.7526 (m-40) REVERT: B 473 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.5915 (t0) REVERT: B 481 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8383 (tp) REVERT: B 507 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: B 584 LEU cc_start: 0.7380 (mm) cc_final: 0.6781 (pt) outliers start: 40 outliers final: 31 residues processed: 172 average time/residue: 0.0737 time to fit residues: 19.8393 Evaluate side-chains 180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 236 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 615 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 105 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.191974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.166334 restraints weight = 12934.193| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.33 r_work: 0.3946 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9366 Z= 0.128 Angle : 0.558 10.062 12776 Z= 0.278 Chirality : 0.039 0.145 1420 Planarity : 0.004 0.042 1556 Dihedral : 5.738 75.935 1252 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.99 % Allowed : 19.85 % Favored : 76.16 % 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: 1.43 (0.26), residues: 1126 helix: 1.50 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -0.16 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 56 TYR 0.019 0.001 TYR B 111 PHE 0.030 0.001 PHE A 528 TRP 0.013 0.001 TRP B 559 HIS 0.009 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9366) covalent geometry : angle 0.55782 (12776) hydrogen bonds : bond 0.04558 ( 587) hydrogen bonds : angle 4.61085 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 1859.58 seconds wall clock time: 32 minutes 33.14 seconds (1953.14 seconds total)