Starting phenix.real_space_refine on Wed Aug 5 02:50:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnx_41428/08_2026/8tnx_41428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnx_41428/08_2026/8tnx_41428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tnx_41428/08_2026/8tnx_41428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnx_41428/08_2026/8tnx_41428.map" model { file = "/net/cci-nas-00/data/ceres_data/8tnx_41428/08_2026/8tnx_41428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnx_41428/08_2026/8tnx_41428.cif" } resolution = 3.03 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= 0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5414 2.51 5 N 1352 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8272 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4130 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 6, 'ARG:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 176 Chain: "B" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4130 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 6, 'ARG:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 176 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'OXL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'OXL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.23 Number of scatterers: 8272 At special positions: 0 Unit cell: (113.162, 96.642, 95.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1464 8.00 N 1352 7.00 C 5414 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: 0.73 Conformation dependent library (CDL) restraints added in 442.0 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 68.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 94 through 102 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 110 through 134 removed outlier: 3.625A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 155 removed outlier: 3.795A pdb=" N GLY A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 213 through 239 removed outlier: 3.626A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.889A pdb=" N VAL A 244 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 removed outlier: 3.708A pdb=" N SER A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.579A pdb=" N THR A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 301 through 316 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 396 removed outlier: 4.809A pdb=" N VAL A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 408 removed outlier: 4.038A pdb=" N LEU A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 425 through 426 No H-bonds generated for 'chain 'A' and resid 425 through 426' Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.962A pdb=" N HIS A 432 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.710A pdb=" N LYS A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 469 removed outlier: 3.787A pdb=" N VAL A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.704A pdb=" N PHE A 475 " --> pdb=" O ALA A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 526 through 547 removed outlier: 3.597A pdb=" N GLY A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 660 through 678 removed outlier: 3.553A pdb=" N ILE A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 Processing helix chain 'A' and resid 711 through 724 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 94 through 102 Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 110 through 134 removed outlier: 3.625A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 155 removed outlier: 3.795A pdb=" N GLY B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 184 Processing helix chain 'B' and resid 213 through 239 removed outlier: 3.626A pdb=" N ILE B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 248 removed outlier: 3.889A pdb=" N VAL B 244 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 273 removed outlier: 3.708A pdb=" N SER B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.579A pdb=" N THR B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 378 through 396 removed outlier: 4.809A pdb=" N VAL B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 408 removed outlier: 4.038A pdb=" N LEU B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 425 through 426 No H-bonds generated for 'chain 'B' and resid 425 through 426' Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.962A pdb=" N HIS B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.710A pdb=" N LYS B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 removed outlier: 3.787A pdb=" N VAL B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.704A pdb=" N PHE B 475 " --> pdb=" O ALA B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 500 through 508 Processing helix chain 'B' and resid 508 through 525 Processing helix chain 'B' and resid 526 through 547 removed outlier: 3.596A pdb=" N GLY B 534 " --> pdb=" O GLY B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'B' and resid 660 through 678 removed outlier: 3.553A pdb=" N ILE B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 711 through 724 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 563 through 565 removed outlier: 4.633A pdb=" N ILE A 580 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEU A 556 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 13.480A pdb=" N ILE A 578 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE A 583 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N PHE A 709 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 683 " --> pdb=" O PHE A 709 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'B' and resid 563 through 565 removed outlier: 4.633A pdb=" N ILE B 580 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N LEU B 556 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 13.480A pdb=" N ILE B 578 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE B 583 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N PHE B 709 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 683 " --> pdb=" O PHE B 709 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1554 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: 1.23 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1287 1.32 - 1.44: 2271 1.44 - 1.57: 4824 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 8442 Sorted by residual: bond pdb=" CA SER A 254 " pdb=" CB SER A 254 " ideal model delta sigma weight residual 1.536 1.441 0.095 1.46e-02 4.69e+03 4.27e+01 bond pdb=" CA SER B 254 " pdb=" CB SER B 254 " ideal model delta sigma weight residual 1.536 1.441 0.095 1.46e-02 4.69e+03 4.27e+01 bond pdb=" CA SER B 126 " pdb=" CB SER B 126 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.58e-02 4.01e+03 2.50e+01 bond pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.58e-02 4.01e+03 2.50e+01 bond pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.17e-02 7.31e+03 1.37e+01 ... (remaining 8437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11063 2.24 - 4.48: 413 4.48 - 6.72: 48 6.72 - 8.96: 6 8.96 - 11.20: 8 Bond angle restraints: 11538 Sorted by residual: angle pdb=" N ALA B 441 " pdb=" CA ALA B 441 " pdb=" C ALA B 441 " ideal model delta sigma weight residual 114.39 103.19 11.20 1.45e+00 4.76e-01 5.97e+01 angle pdb=" N ALA A 441 " pdb=" CA ALA A 441 " pdb=" C ALA A 441 " ideal model delta sigma weight residual 114.39 103.19 11.20 1.45e+00 4.76e-01 5.97e+01 angle pdb=" N THR A 443 " pdb=" CA THR A 443 " pdb=" C THR A 443 " ideal model delta sigma weight residual 113.28 103.96 9.32 1.22e+00 6.72e-01 5.83e+01 angle pdb=" N THR B 443 " pdb=" CA THR B 443 " pdb=" C THR B 443 " ideal model delta sigma weight residual 113.28 103.96 9.32 1.22e+00 6.72e-01 5.83e+01 angle pdb=" N LEU A 440 " pdb=" CA LEU A 440 " pdb=" C LEU A 440 " ideal model delta sigma weight residual 113.40 102.81 10.59 1.47e+00 4.63e-01 5.19e+01 ... (remaining 11533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 4238 16.32 - 32.64: 460 32.64 - 48.96: 144 48.96 - 65.28: 36 65.28 - 81.61: 12 Dihedral angle restraints: 4890 sinusoidal: 1552 harmonic: 3338 Sorted by residual: dihedral pdb=" CD ARG A 58 " pdb=" NE ARG A 58 " pdb=" CZ ARG A 58 " pdb=" NH1 ARG A 58 " ideal model delta sinusoidal sigma weight residual 0.00 71.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CD ARG B 58 " pdb=" NE ARG B 58 " pdb=" CZ ARG B 58 " pdb=" NH1 ARG B 58 " ideal model delta sinusoidal sigma weight residual 0.00 71.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" N LEU A 468 " pdb=" CA LEU A 468 " pdb=" CB LEU A 468 " pdb=" CG LEU A 468 " ideal model delta sinusoidal sigma weight residual -60.00 -119.18 59.18 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 965 0.044 - 0.088: 269 0.088 - 0.132: 139 0.132 - 0.176: 48 0.176 - 0.220: 21 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CA LEU B 491 " pdb=" N LEU B 491 " pdb=" C LEU B 491 " pdb=" CB LEU B 491 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU A 491 " pdb=" N LEU A 491 " pdb=" C LEU A 491 " pdb=" CB LEU A 491 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LEU A 444 " pdb=" N LEU A 444 " pdb=" C LEU A 444 " pdb=" CB LEU A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1439 not shown) Planarity restraints: 1420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 58 " -1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG B 58 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG B 58 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 58 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 58 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 58 " 1.042 9.50e-02 1.11e+02 4.67e-01 1.32e+02 pdb=" NE ARG A 58 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 58 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 58 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 58 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 159 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C HIS B 159 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS B 159 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 160 " -0.019 2.00e-02 2.50e+03 ... (remaining 1417 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2277 2.80 - 3.33: 8170 3.33 - 3.85: 13985 3.85 - 4.38: 15915 4.38 - 4.90: 27421 Nonbonded interactions: 67768 Sorted by model distance: nonbonded pdb=" O MET B 220 " pdb=" OG1 THR B 224 " model vdw 2.278 3.040 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 224 " model vdw 2.278 3.040 nonbonded pdb=" O LEU A 122 " pdb=" OG SER A 126 " model vdw 2.296 3.040 nonbonded pdb=" O LEU B 122 " pdb=" OG SER B 126 " model vdw 2.296 3.040 nonbonded pdb=" O SER B 126 " pdb=" OG SER B 130 " model vdw 2.329 3.040 ... (remaining 67763 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.100 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.007 0.095 8442 Z= 0.466 Angle : 0.901 11.203 11538 Z= 0.645 Chirality : 0.058 0.220 1442 Planarity : 0.018 0.467 1420 Dihedral : 16.340 81.606 2734 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.83 % Favored : 96.82 % Rotamer: Outliers : 4.12 % Allowed : 25.62 % Favored : 70.25 % 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 are not related in a simple way. whole: 0.06 (0.24), residues: 1132 helix: 0.35 (0.19), residues: 754 sheet: 1.76 (0.72), residues: 50 loop : -0.73 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 178 TYR 0.015 0.001 TYR B 588 PHE 0.013 0.001 PHE B 434 TRP 0.005 0.001 TRP B 376 HIS 0.003 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.47 ( 8442) covalent geometry : angle 0.90106 / 0.64 (11538) hydrogen bonds : bond 0.18141 / 12.10 ( 538) hydrogen bonds : angle 6.65252 / 5.00 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.295 Fit side-chains REVERT: A 238 PHE cc_start: 0.7371 (t80) cc_final: 0.7099 (t80) REVERT: A 239 PHE cc_start: 0.6150 (m-80) cc_final: 0.5927 (m-10) REVERT: A 270 LYS cc_start: 0.7068 (mtmt) cc_final: 0.6532 (ttpp) REVERT: A 489 VAL cc_start: 0.8078 (t) cc_final: 0.7871 (t) REVERT: A 490 ASN cc_start: 0.7544 (m110) cc_final: 0.7319 (m-40) REVERT: A 716 MET cc_start: 0.7895 (mmm) cc_final: 0.7635 (mmm) REVERT: B 238 PHE cc_start: 0.7370 (t80) cc_final: 0.7101 (t80) REVERT: B 239 PHE cc_start: 0.6147 (m-80) cc_final: 0.5928 (m-10) REVERT: B 270 LYS cc_start: 0.7064 (mtmt) cc_final: 0.6530 (ttpp) REVERT: B 489 VAL cc_start: 0.8076 (t) cc_final: 0.7868 (t) REVERT: B 490 ASN cc_start: 0.7539 (m110) cc_final: 0.7315 (m-40) REVERT: B 716 MET cc_start: 0.7895 (mmm) cc_final: 0.7634 (mmm) outliers start: 33 outliers final: 13 residues processed: 176 average time/residue: 0.0690 time to fit residues: 17.7651 Evaluate side-chains 124 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.2462 > 50:) chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS A 432 HIS A 490 ASN A 547 GLN A 685 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS B 432 HIS B 490 ASN B 547 GLN B 685 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.197399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134666 restraints weight = 8147.785| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.36 r_work: 0.3502 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8442 Z= 0.150 Angle : 0.565 7.729 11538 Z= 0.294 Chirality : 0.041 0.127 1442 Planarity : 0.004 0.043 1420 Dihedral : 5.939 55.148 1225 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.88 % Allowed : 19.88 % Favored : 75.25 % 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 are not related in a simple way. whole: 1.12 (0.25), residues: 1132 helix: 1.14 (0.19), residues: 768 sheet: 1.63 (0.73), residues: 50 loop : -0.21 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 672 TYR 0.018 0.001 TYR B 151 PHE 0.015 0.001 PHE A 434 TRP 0.007 0.001 TRP B 290 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8442) covalent geometry : angle 0.56537 / 0.29 (11538) hydrogen bonds : bond 0.04575 / 3.13 ( 538) hydrogen bonds : angle 4.26510 / 3.09 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.298 Fit side-chains REVERT: A 136 GLU cc_start: 0.7328 (mp0) cc_final: 0.6958 (mp0) REVERT: A 145 PHE cc_start: 0.8090 (t80) cc_final: 0.7820 (t80) REVERT: A 239 PHE cc_start: 0.6161 (m-80) cc_final: 0.5603 (m-10) REVERT: A 270 LYS cc_start: 0.6178 (mtmt) cc_final: 0.5643 (ttpt) REVERT: A 301 ASN cc_start: 0.7568 (t0) cc_final: 0.7347 (t0) REVERT: A 490 ASN cc_start: 0.7353 (m-40) cc_final: 0.7087 (m-40) REVERT: A 672 ARG cc_start: 0.7164 (ttp80) cc_final: 0.6484 (ttm170) REVERT: A 716 MET cc_start: 0.7608 (mmm) cc_final: 0.7159 (mmm) REVERT: B 136 GLU cc_start: 0.7349 (mp0) cc_final: 0.6982 (mp0) REVERT: B 145 PHE cc_start: 0.8099 (t80) cc_final: 0.7829 (t80) REVERT: B 239 PHE cc_start: 0.6157 (m-80) cc_final: 0.5603 (m-10) REVERT: B 270 LYS cc_start: 0.6200 (mtmt) cc_final: 0.5663 (ttpt) REVERT: B 301 ASN cc_start: 0.7576 (t0) cc_final: 0.7356 (t0) REVERT: B 490 ASN cc_start: 0.7355 (m-40) cc_final: 0.7089 (m-40) REVERT: B 672 ARG cc_start: 0.7132 (ttp80) cc_final: 0.6454 (ttm170) REVERT: B 716 MET cc_start: 0.7589 (mmm) cc_final: 0.7148 (mmm) outliers start: 39 outliers final: 26 residues processed: 159 average time/residue: 0.0747 time to fit residues: 16.9918 Evaluate side-chains 152 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 721 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125835 restraints weight = 8200.164| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.38 r_work: 0.3383 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8442 Z= 0.202 Angle : 0.611 8.881 11538 Z= 0.310 Chirality : 0.044 0.172 1442 Planarity : 0.004 0.037 1420 Dihedral : 5.619 51.280 1218 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.00 % Allowed : 20.38 % Favored : 75.62 % 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 are not related in a simple way. whole: 1.07 (0.25), residues: 1132 helix: 1.11 (0.19), residues: 772 sheet: 1.36 (0.73), residues: 50 loop : -0.22 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 671 TYR 0.014 0.002 TYR B 232 PHE 0.018 0.002 PHE A 658 TRP 0.008 0.001 TRP A 376 HIS 0.004 0.001 HIS B 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.20 ( 8442) covalent geometry : angle 0.61102 / 0.31 (11538) hydrogen bonds : bond 0.05032 / 3.47 ( 538) hydrogen bonds : angle 4.01131 / 2.88 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.237 Fit side-chains REVERT: A 136 GLU cc_start: 0.7352 (mp0) cc_final: 0.7072 (mp0) REVERT: A 270 LYS cc_start: 0.6115 (mtmt) cc_final: 0.5477 (ttpp) REVERT: A 301 ASN cc_start: 0.7400 (t0) cc_final: 0.7148 (t0) REVERT: A 716 MET cc_start: 0.7657 (mmm) cc_final: 0.7218 (mmm) REVERT: B 136 GLU cc_start: 0.7345 (mp0) cc_final: 0.7064 (mp0) REVERT: B 270 LYS cc_start: 0.6119 (mtmt) cc_final: 0.5485 (ttpp) REVERT: B 301 ASN cc_start: 0.7410 (t0) cc_final: 0.7161 (t0) REVERT: B 716 MET cc_start: 0.7633 (mmm) cc_final: 0.7206 (mmm) outliers start: 32 outliers final: 23 residues processed: 158 average time/residue: 0.0742 time to fit residues: 16.8945 Evaluate side-chains 157 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.190223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126682 restraints weight = 8326.874| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.39 r_work: 0.3392 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8442 Z= 0.158 Angle : 0.542 8.226 11538 Z= 0.272 Chirality : 0.041 0.132 1442 Planarity : 0.003 0.033 1420 Dihedral : 5.360 50.031 1216 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.25 % Allowed : 21.50 % Favored : 75.25 % 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 are not related in a simple way. whole: 1.26 (0.25), residues: 1132 helix: 1.30 (0.19), residues: 768 sheet: 1.33 (0.73), residues: 50 loop : -0.26 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 672 TYR 0.014 0.001 TYR A 151 PHE 0.015 0.001 PHE B 434 TRP 0.008 0.001 TRP A 98 HIS 0.002 0.001 HIS B 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 8442) covalent geometry : angle 0.54160 / 0.27 (11538) hydrogen bonds : bond 0.04271 / 2.96 ( 538) hydrogen bonds : angle 3.83682 / 2.75 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.312 Fit side-chains REVERT: A 136 GLU cc_start: 0.7264 (mp0) cc_final: 0.6996 (mp0) REVERT: A 270 LYS cc_start: 0.6095 (mtmt) cc_final: 0.5374 (ttpp) REVERT: A 301 ASN cc_start: 0.7420 (t0) cc_final: 0.7096 (t0) REVERT: A 418 MET cc_start: 0.6742 (tpp) cc_final: 0.6479 (tpp) REVERT: A 672 ARG cc_start: 0.7114 (ttp80) cc_final: 0.6430 (ttm170) REVERT: A 716 MET cc_start: 0.7724 (mmm) cc_final: 0.7336 (mmm) REVERT: B 136 GLU cc_start: 0.7253 (mp0) cc_final: 0.6984 (mp0) REVERT: B 270 LYS cc_start: 0.6093 (mtmt) cc_final: 0.5374 (ttpp) REVERT: B 301 ASN cc_start: 0.7426 (t0) cc_final: 0.7103 (t0) REVERT: B 418 MET cc_start: 0.6734 (tpp) cc_final: 0.6472 (tpp) REVERT: B 672 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6432 (ttm170) REVERT: B 716 MET cc_start: 0.7687 (mmm) cc_final: 0.7312 (mmm) outliers start: 26 outliers final: 21 residues processed: 150 average time/residue: 0.0823 time to fit residues: 17.6522 Evaluate side-chains 150 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.191049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127481 restraints weight = 8266.368| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.39 r_work: 0.3403 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8442 Z= 0.134 Angle : 0.519 8.600 11538 Z= 0.260 Chirality : 0.040 0.129 1442 Planarity : 0.003 0.031 1420 Dihedral : 5.161 50.255 1216 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.88 % Allowed : 20.75 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1132 helix: 1.48 (0.19), residues: 768 sheet: 1.42 (0.74), residues: 50 loop : -0.23 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 672 TYR 0.018 0.001 TYR A 151 PHE 0.015 0.001 PHE B 434 TRP 0.008 0.001 TRP A 98 HIS 0.001 0.000 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 8442) covalent geometry : angle 0.51921 / 0.26 (11538) hydrogen bonds : bond 0.03941 / 2.72 ( 538) hydrogen bonds : angle 3.72249 / 2.66 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.299 Fit side-chains REVERT: A 136 GLU cc_start: 0.7129 (mp0) cc_final: 0.6793 (mp0) REVERT: A 270 LYS cc_start: 0.6156 (mtmt) cc_final: 0.5353 (ttpp) REVERT: A 296 ASN cc_start: 0.7165 (m110) cc_final: 0.6604 (m110) REVERT: A 368 PHE cc_start: 0.8186 (m-80) cc_final: 0.7962 (m-80) REVERT: A 672 ARG cc_start: 0.7132 (ttp80) cc_final: 0.6442 (ttm170) REVERT: A 716 MET cc_start: 0.7693 (mmm) cc_final: 0.7310 (mmm) REVERT: B 136 GLU cc_start: 0.7115 (mp0) cc_final: 0.6781 (mp0) REVERT: B 270 LYS cc_start: 0.6160 (mtmt) cc_final: 0.5358 (ttpp) REVERT: B 296 ASN cc_start: 0.7170 (m110) cc_final: 0.6610 (m110) REVERT: B 368 PHE cc_start: 0.8191 (m-80) cc_final: 0.7967 (m-80) REVERT: B 672 ARG cc_start: 0.7095 (ttp80) cc_final: 0.6422 (ttm170) REVERT: B 716 MET cc_start: 0.7654 (mmm) cc_final: 0.7285 (mmm) outliers start: 31 outliers final: 25 residues processed: 153 average time/residue: 0.0736 time to fit residues: 16.1621 Evaluate side-chains 147 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 101 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 GLN B 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.192047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128860 restraints weight = 8140.748| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.37 r_work: 0.3423 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8442 Z= 0.111 Angle : 0.499 8.335 11538 Z= 0.248 Chirality : 0.039 0.124 1442 Planarity : 0.003 0.031 1420 Dihedral : 5.046 51.361 1216 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.25 % Allowed : 21.62 % Favored : 75.12 % 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 are not related in a simple way. whole: 1.70 (0.25), residues: 1132 helix: 1.64 (0.19), residues: 768 sheet: 1.51 (0.74), residues: 50 loop : -0.13 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 672 TYR 0.016 0.001 TYR A 151 PHE 0.014 0.001 PHE A 434 TRP 0.008 0.001 TRP A 98 HIS 0.001 0.000 HIS B 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 8442) covalent geometry : angle 0.49943 / 0.25 (11538) hydrogen bonds : bond 0.03615 / 2.50 ( 538) hydrogen bonds : angle 3.66455 / 2.62 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.313 Fit side-chains REVERT: A 136 GLU cc_start: 0.7028 (mp0) cc_final: 0.6368 (mt-10) REVERT: A 270 LYS cc_start: 0.6174 (mtmt) cc_final: 0.5310 (ttpp) REVERT: A 275 LEU cc_start: 0.7546 (mt) cc_final: 0.7335 (mp) REVERT: A 296 ASN cc_start: 0.7104 (m110) cc_final: 0.6615 (m110) REVERT: A 368 PHE cc_start: 0.8119 (m-80) cc_final: 0.7846 (m-80) REVERT: A 716 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7327 (mmm) REVERT: B 136 GLU cc_start: 0.7023 (mp0) cc_final: 0.6361 (mt-10) REVERT: B 270 LYS cc_start: 0.6166 (mtmt) cc_final: 0.5304 (ttpp) REVERT: B 275 LEU cc_start: 0.7544 (mt) cc_final: 0.7335 (mp) REVERT: B 296 ASN cc_start: 0.7113 (m110) cc_final: 0.6626 (m110) REVERT: B 368 PHE cc_start: 0.8122 (m-80) cc_final: 0.7852 (m-80) REVERT: B 672 ARG cc_start: 0.7172 (ttp80) cc_final: 0.6407 (ttm110) REVERT: B 716 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7304 (mmm) outliers start: 26 outliers final: 22 residues processed: 146 average time/residue: 0.0813 time to fit residues: 16.9353 Evaluate side-chains 150 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 36 optimal weight: 0.0070 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.189063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125453 restraints weight = 8226.284| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.37 r_work: 0.3377 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8442 Z= 0.159 Angle : 0.542 8.991 11538 Z= 0.271 Chirality : 0.041 0.137 1442 Planarity : 0.003 0.031 1420 Dihedral : 5.108 51.436 1216 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.88 % Allowed : 21.38 % Favored : 74.75 % 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 are not related in a simple way. whole: 1.54 (0.25), residues: 1132 helix: 1.56 (0.19), residues: 768 sheet: 1.37 (0.74), residues: 50 loop : -0.28 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 672 TYR 0.015 0.001 TYR A 151 PHE 0.017 0.002 PHE B 434 TRP 0.006 0.001 TRP A 98 HIS 0.001 0.000 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 8442) covalent geometry : angle 0.54187 / 0.27 (11538) hydrogen bonds : bond 0.04256 / 2.95 ( 538) hydrogen bonds : angle 3.69211 / 2.64 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.297 Fit side-chains REVERT: A 136 GLU cc_start: 0.7072 (mp0) cc_final: 0.6423 (mt-10) REVERT: A 270 LYS cc_start: 0.6225 (mtmt) cc_final: 0.5456 (ttpp) REVERT: A 296 ASN cc_start: 0.7189 (m110) cc_final: 0.6667 (m110) REVERT: A 368 PHE cc_start: 0.8140 (m-80) cc_final: 0.7841 (m-80) REVERT: A 672 ARG cc_start: 0.7174 (ttp80) cc_final: 0.6449 (ttm170) REVERT: A 716 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7325 (mmm) REVERT: B 136 GLU cc_start: 0.7058 (mp0) cc_final: 0.6410 (mt-10) REVERT: B 270 LYS cc_start: 0.6237 (mtmt) cc_final: 0.5467 (ttpp) REVERT: B 296 ASN cc_start: 0.7192 (m110) cc_final: 0.6672 (m110) REVERT: B 368 PHE cc_start: 0.8146 (m-80) cc_final: 0.7842 (m-80) REVERT: B 672 ARG cc_start: 0.7157 (ttp80) cc_final: 0.6431 (ttm170) REVERT: B 716 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7300 (mmm) outliers start: 31 outliers final: 28 residues processed: 153 average time/residue: 0.0748 time to fit residues: 16.5302 Evaluate side-chains 158 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 0.0270 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.190672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.127516 restraints weight = 8206.616| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.38 r_work: 0.3402 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8442 Z= 0.123 Angle : 0.504 8.548 11538 Z= 0.251 Chirality : 0.039 0.128 1442 Planarity : 0.003 0.032 1420 Dihedral : 5.026 51.823 1216 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.50 % Allowed : 22.00 % Favored : 74.50 % 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 are not related in a simple way. whole: 1.67 (0.25), residues: 1132 helix: 1.68 (0.19), residues: 768 sheet: 1.37 (0.73), residues: 50 loop : -0.27 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 672 TYR 0.016 0.001 TYR A 151 PHE 0.014 0.001 PHE B 434 TRP 0.008 0.001 TRP B 98 HIS 0.001 0.000 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 8442) covalent geometry : angle 0.50387 / 0.25 (11538) hydrogen bonds : bond 0.03747 / 2.59 ( 538) hydrogen bonds : angle 3.61902 / 2.59 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.249 Fit side-chains REVERT: A 270 LYS cc_start: 0.6231 (mtmt) cc_final: 0.5479 (ttpp) REVERT: A 296 ASN cc_start: 0.7143 (m110) cc_final: 0.6568 (m110) REVERT: A 368 PHE cc_start: 0.8121 (m-80) cc_final: 0.7852 (m-80) REVERT: A 672 ARG cc_start: 0.7170 (ttp80) cc_final: 0.6434 (ttm170) REVERT: A 716 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7273 (mmm) REVERT: B 270 LYS cc_start: 0.6242 (mtmt) cc_final: 0.5486 (ttpp) REVERT: B 296 ASN cc_start: 0.7143 (m110) cc_final: 0.6566 (m110) REVERT: B 368 PHE cc_start: 0.8123 (m-80) cc_final: 0.7853 (m-80) REVERT: B 672 ARG cc_start: 0.7164 (ttp80) cc_final: 0.6440 (ttm170) REVERT: B 716 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7252 (mmm) outliers start: 28 outliers final: 24 residues processed: 147 average time/residue: 0.0819 time to fit residues: 17.2091 Evaluate side-chains 151 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.190809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127834 restraints weight = 8202.114| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.36 r_work: 0.3405 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8442 Z= 0.120 Angle : 0.504 8.611 11538 Z= 0.250 Chirality : 0.039 0.129 1442 Planarity : 0.003 0.032 1420 Dihedral : 4.980 52.067 1216 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.50 % Allowed : 22.75 % Favored : 73.75 % 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 are not related in a simple way. whole: 1.75 (0.25), residues: 1132 helix: 1.74 (0.19), residues: 768 sheet: 1.37 (0.73), residues: 50 loop : -0.25 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 672 TYR 0.015 0.001 TYR A 151 PHE 0.015 0.001 PHE A 434 TRP 0.008 0.001 TRP B 98 HIS 0.001 0.000 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8442) covalent geometry : angle 0.50369 / 0.25 (11538) hydrogen bonds : bond 0.03659 / 2.53 ( 538) hydrogen bonds : angle 3.56728 / 2.55 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.283 Fit side-chains REVERT: A 270 LYS cc_start: 0.6183 (mtmt) cc_final: 0.5405 (ttpp) REVERT: A 275 LEU cc_start: 0.7595 (mt) cc_final: 0.7391 (mp) REVERT: A 296 ASN cc_start: 0.7025 (m110) cc_final: 0.6573 (m110) REVERT: A 597 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7907 (m) REVERT: A 672 ARG cc_start: 0.7140 (ttp80) cc_final: 0.6440 (ttm170) REVERT: A 716 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7284 (mmm) REVERT: B 270 LYS cc_start: 0.6193 (mtmt) cc_final: 0.5415 (ttpp) REVERT: B 296 ASN cc_start: 0.7028 (m110) cc_final: 0.6579 (m110) REVERT: B 597 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7887 (m) REVERT: B 672 ARG cc_start: 0.7178 (ttp80) cc_final: 0.6452 (ttm170) REVERT: B 716 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7269 (mmm) outliers start: 28 outliers final: 24 residues processed: 146 average time/residue: 0.0860 time to fit residues: 17.9562 Evaluate side-chains 149 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.190269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132362 restraints weight = 8318.094| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.52 r_work: 0.3424 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8442 Z= 0.211 Angle : 0.584 9.462 11538 Z= 0.291 Chirality : 0.042 0.143 1442 Planarity : 0.003 0.031 1420 Dihedral : 5.192 51.745 1216 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.75 % Allowed : 22.62 % Favored : 73.62 % 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 are not related in a simple way. whole: 1.41 (0.25), residues: 1132 helix: 1.52 (0.19), residues: 768 sheet: 1.13 (0.73), residues: 50 loop : -0.48 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 671 TYR 0.018 0.002 TYR B 151 PHE 0.018 0.002 PHE B 434 TRP 0.005 0.001 TRP B 505 HIS 0.002 0.000 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.21 ( 8442) covalent geometry : angle 0.58442 / 0.29 (11538) hydrogen bonds : bond 0.04667 / 3.24 ( 538) hydrogen bonds : angle 3.70640 / 2.66 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.275 Fit side-chains REVERT: A 270 LYS cc_start: 0.6560 (mtmt) cc_final: 0.5905 (ttpp) REVERT: A 296 ASN cc_start: 0.7331 (m110) cc_final: 0.6795 (m110) REVERT: A 672 ARG cc_start: 0.7443 (ttp80) cc_final: 0.6719 (ttm170) REVERT: A 716 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7595 (mmm) REVERT: B 270 LYS cc_start: 0.6499 (mtmt) cc_final: 0.5833 (ttpp) REVERT: B 296 ASN cc_start: 0.7341 (m110) cc_final: 0.6757 (m110) REVERT: B 672 ARG cc_start: 0.7448 (ttp80) cc_final: 0.6726 (ttm170) REVERT: B 716 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7595 (mmm) outliers start: 30 outliers final: 26 residues processed: 150 average time/residue: 0.0822 time to fit residues: 17.6346 Evaluate side-chains 158 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 424 CYS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 716 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 80 optimal weight: 0.0370 chunk 87 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.191561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127734 restraints weight = 8275.511| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.44 r_work: 0.3397 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8442 Z= 0.119 Angle : 0.514 8.543 11538 Z= 0.254 Chirality : 0.039 0.129 1442 Planarity : 0.003 0.032 1420 Dihedral : 5.086 52.176 1216 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.75 % Allowed : 23.00 % Favored : 74.25 % 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 are not related in a simple way. whole: 1.64 (0.25), residues: 1132 helix: 1.68 (0.19), residues: 768 sheet: 1.25 (0.73), residues: 50 loop : -0.34 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 672 TYR 0.017 0.001 TYR B 151 PHE 0.014 0.001 PHE A 434 TRP 0.008 0.001 TRP A 98 HIS 0.001 0.000 HIS A 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8442) covalent geometry : angle 0.51392 / 0.25 (11538) hydrogen bonds : bond 0.03769 / 2.60 ( 538) hydrogen bonds : angle 3.62363 / 2.59 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2486.66 seconds wall clock time: 43 minutes 8.59 seconds (2588.59 seconds total)