Starting phenix.real_space_refine on Wed Feb 4 06:29:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d67_46588/02_2026/9d67_46588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d67_46588/02_2026/9d67_46588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d67_46588/02_2026/9d67_46588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d67_46588/02_2026/9d67_46588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d67_46588/02_2026/9d67_46588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d67_46588/02_2026/9d67_46588.map" } resolution = 2.87 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= 0.003 sd= 0.151 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 Hg 3 10.96 5 S 60 5.16 5 Na 9 4.78 5 C 6087 2.51 5 N 1479 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9297 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "B" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "C" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {None: 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 49.179 82.768 22.871 1.00 85.37 S ATOM 2858 SG CYS A 441 48.431 81.437 25.785 1.00 81.69 S ATOM 4662 SG CYS B 269 78.219 37.296 22.873 1.00 85.37 S ATOM 5943 SG CYS B 441 77.441 38.609 25.787 1.00 81.69 S ATOM 7747 SG CYS C 269 24.317 34.880 22.863 1.00 85.37 S ATOM 9028 SG CYS C 441 25.843 34.898 25.778 1.00 81.69 S Time building chain proxies: 2.29, per 1000 atoms: 0.25 Number of scatterers: 9297 At special positions: 0 Unit cell: (105.448, 103.296, 69.94, 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) Hg 3 79.96 S 60 16.00 Na 9 11.00 O 1659 8.00 N 1479 7.00 C 6087 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: 0.71 Conformation dependent library (CDL) restraints added in 373.8 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAS A 600 " pdb=" CB DAS B 605 " pdb=" CB DAS C 600 " Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 85.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 19 through 42 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.650A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 82 removed outlier: 4.480A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.822A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 117 removed outlier: 3.651A pdb=" N GLY A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.678A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.590A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.599A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.869A pdb=" N ARG A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 363 removed outlier: 4.109A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 413 through 418 removed outlier: 3.581A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 413 through 418' Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.858A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 3.563A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.741A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 42 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.651A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 82 removed outlier: 4.480A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.822A pdb=" N LEU B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 117 removed outlier: 3.650A pdb=" N GLY B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.679A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 211 through 229 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 273 removed outlier: 3.589A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.599A pdb=" N VAL B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.869A pdb=" N ARG B 280 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.108A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 390 through 408 Processing helix chain 'B' and resid 413 through 418 removed outlier: 3.581A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 413 through 418' Processing helix chain 'B' and resid 418 through 426 removed outlier: 3.859A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.563A pdb=" N VAL B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.741A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 42 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.650A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 82 removed outlier: 4.480A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 3.821A pdb=" N LEU C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 117 removed outlier: 3.651A pdb=" N GLY C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.678A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 211 through 229 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.590A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.599A pdb=" N VAL C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 removed outlier: 3.869A pdb=" N ARG C 280 " --> pdb=" O TRP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 363 removed outlier: 4.108A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 390 through 408 Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.581A pdb=" N VAL C 417 " --> pdb=" O GLN C 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.859A pdb=" N VAL C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.563A pdb=" N VAL C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 437 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.741A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 726 hydrogen bonds defined for protein. 2133 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: 1.18 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1788 1.33 - 1.45: 1951 1.45 - 1.57: 5567 1.57 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 9417 Sorted by residual: bond pdb=" N VAL C 417 " pdb=" CA VAL C 417 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.80e+00 bond pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.34e+00 bond pdb=" N VAL B 417 " pdb=" CA VAL B 417 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.28e+00 bond pdb=" N LEU C 328 " pdb=" CA LEU C 328 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.35e-02 5.49e+03 5.57e+00 bond pdb=" N ARG A 445 " pdb=" CA ARG A 445 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.45e+00 ... (remaining 9412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 12180 1.26 - 2.52: 459 2.52 - 3.78: 112 3.78 - 5.04: 29 5.04 - 6.29: 3 Bond angle restraints: 12783 Sorted by residual: angle pdb=" CA PRO A 412 " pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 121.23 117.53 3.70 1.07e+00 8.73e-01 1.19e+01 angle pdb=" CA PRO C 412 " pdb=" C PRO C 412 " pdb=" O PRO C 412 " ideal model delta sigma weight residual 121.23 117.53 3.70 1.07e+00 8.73e-01 1.19e+01 angle pdb=" CA PRO B 412 " pdb=" C PRO B 412 " pdb=" O PRO B 412 " ideal model delta sigma weight residual 121.23 117.56 3.67 1.07e+00 8.73e-01 1.18e+01 angle pdb=" CA VAL A 417 " pdb=" C VAL A 417 " pdb=" O VAL A 417 " ideal model delta sigma weight residual 120.85 117.88 2.97 1.06e+00 8.90e-01 7.87e+00 angle pdb=" CA VAL C 417 " pdb=" C VAL C 417 " pdb=" O VAL C 417 " ideal model delta sigma weight residual 120.85 117.88 2.97 1.06e+00 8.90e-01 7.86e+00 ... (remaining 12778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.63: 5238 25.63 - 51.26: 330 51.26 - 76.90: 42 76.90 - 102.53: 3 102.53 - 128.16: 3 Dihedral angle restraints: 5616 sinusoidal: 2127 harmonic: 3489 Sorted by residual: dihedral pdb=" CA DAS B 605 " pdb=" CB DAS B 605 " pdb=" CG DAS B 605 " pdb=" OD1 DAS B 605 " ideal model delta sinusoidal sigma weight residual -30.00 -158.16 128.16 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" CA DAS A 600 " pdb=" CB DAS A 600 " pdb=" CG DAS A 600 " pdb=" OD1 DAS A 600 " ideal model delta sinusoidal sigma weight residual -30.00 -158.16 128.16 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" CA DAS C 600 " pdb=" CB DAS C 600 " pdb=" CG DAS C 600 " pdb=" OD1 DAS C 600 " ideal model delta sinusoidal sigma weight residual -30.00 -158.14 128.14 1 2.00e+01 2.50e-03 3.88e+01 ... (remaining 5613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1191 0.040 - 0.080: 354 0.080 - 0.120: 69 0.120 - 0.160: 9 0.160 - 0.200: 3 Chirality restraints: 1626 Sorted by residual: chirality pdb=" CA MET B 367 " pdb=" N MET B 367 " pdb=" C MET B 367 " pdb=" CB MET B 367 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA MET A 367 " pdb=" N MET A 367 " pdb=" C MET A 367 " pdb=" CB MET A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA MET C 367 " pdb=" N MET C 367 " pdb=" C MET C 367 " pdb=" CB MET C 367 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 1623 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 166 " -0.250 9.50e-02 1.11e+02 1.13e-01 9.43e+00 pdb=" NE ARG A 166 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 166 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 166 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 166 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 166 " 0.250 9.50e-02 1.11e+02 1.13e-01 9.42e+00 pdb=" NE ARG C 166 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG C 166 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG C 166 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C 166 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 166 " 0.250 9.50e-02 1.11e+02 1.13e-01 9.35e+00 pdb=" NE ARG B 166 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 166 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 166 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 166 " 0.002 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 221 2.69 - 3.25: 10163 3.25 - 3.80: 15569 3.80 - 4.35: 20822 4.35 - 4.90: 34232 Nonbonded interactions: 81007 Sorted by model distance: nonbonded pdb=" O THR A 364 " pdb="NA NA A 602 " model vdw 2.143 2.470 nonbonded pdb=" O THR B 364 " pdb="NA NA B 603 " model vdw 2.143 2.470 nonbonded pdb=" O THR C 364 " pdb="NA NA C 602 " model vdw 2.143 2.470 nonbonded pdb=" O ALA A 408 " pdb="NA NA A 602 " model vdw 2.161 2.470 nonbonded pdb=" O ALA B 408 " pdb="NA NA B 603 " model vdw 2.161 2.470 ... (remaining 81002 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' and (resid 17 through 470 or resid 601 through 603)) selection = (chain 'B' and (resid 17 through 470 or resid 602 through 604)) selection = (chain 'C' and (resid 17 through 470 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.750 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 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 0.038 9417 Z= 0.173 Angle : 0.605 6.295 12783 Z= 0.326 Chirality : 0.040 0.200 1626 Planarity : 0.007 0.113 1557 Dihedral : 16.101 128.161 3366 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 22.55 % Favored : 77.45 % 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: 0.93 (0.24), residues: 1200 helix: 1.15 (0.17), residues: 924 sheet: -0.46 (0.66), residues: 54 loop : -1.11 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG C 166 TYR 0.014 0.001 TYR B 97 PHE 0.016 0.002 PHE C 240 TRP 0.004 0.001 TRP A 256 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9417) covalent geometry : angle 0.60451 (12783) hydrogen bonds : bond 0.13956 ( 726) hydrogen bonds : angle 6.27246 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.7113 (t80) cc_final: 0.6592 (t80) REVERT: A 103 LEU cc_start: 0.7427 (mm) cc_final: 0.7209 (mm) REVERT: A 117 LYS cc_start: 0.7594 (mtmm) cc_final: 0.6834 (mttp) REVERT: A 142 MET cc_start: 0.8083 (tpp) cc_final: 0.7764 (mmp) REVERT: A 205 MET cc_start: 0.7813 (ptt) cc_final: 0.7247 (pmm) REVERT: A 207 SER cc_start: 0.7809 (p) cc_final: 0.7498 (m) REVERT: A 255 MET cc_start: 0.8217 (tpp) cc_final: 0.7881 (mmm) REVERT: A 258 MET cc_start: 0.7963 (tpp) cc_final: 0.7721 (ttt) REVERT: A 315 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.6987 (ttm110) REVERT: A 352 LYS cc_start: 0.6843 (mttp) cc_final: 0.6613 (mtmm) REVERT: B 205 MET cc_start: 0.8009 (ptt) cc_final: 0.7295 (pmm) REVERT: B 255 MET cc_start: 0.8249 (tpp) cc_final: 0.7857 (mmm) REVERT: B 258 MET cc_start: 0.8131 (tpp) cc_final: 0.7918 (ttt) REVERT: B 277 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6502 (mp0) REVERT: B 315 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.6999 (ttm170) REVERT: B 352 LYS cc_start: 0.6964 (mttp) cc_final: 0.6729 (mtmm) REVERT: B 356 ARG cc_start: 0.6903 (mmt180) cc_final: 0.6559 (mmt180) REVERT: B 399 ILE cc_start: 0.8138 (mm) cc_final: 0.7898 (mt) REVERT: C 60 MET cc_start: 0.8451 (mmm) cc_final: 0.8251 (mmm) REVERT: C 99 PHE cc_start: 0.7593 (t80) cc_final: 0.7392 (t80) REVERT: C 138 THR cc_start: 0.6518 (t) cc_final: 0.6176 (m) REVERT: C 205 MET cc_start: 0.7997 (ptt) cc_final: 0.7545 (ptm) REVERT: C 241 ASN cc_start: 0.8351 (t0) cc_final: 0.8062 (m-40) REVERT: C 315 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7067 (ttm110) REVERT: C 318 MET cc_start: 0.6261 (tpt) cc_final: 0.6035 (tpp) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.4965 time to fit residues: 117.7045 Evaluate side-chains 169 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 347 ASN B 322 GLN B 347 ASN C 322 GLN C 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.183267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.146071 restraints weight = 3013.546| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 0.69 r_work: 0.3282 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9417 Z= 0.159 Angle : 0.552 5.529 12783 Z= 0.286 Chirality : 0.040 0.154 1626 Planarity : 0.004 0.028 1557 Dihedral : 6.598 102.566 1287 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.87 % Allowed : 21.76 % Favored : 75.37 % 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 are not related in a simple way. whole: 1.44 (0.23), residues: 1200 helix: 1.48 (0.16), residues: 915 sheet: 0.26 (0.59), residues: 48 loop : -0.85 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 93 TYR 0.012 0.001 TYR C 97 PHE 0.015 0.002 PHE B 240 TRP 0.009 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9417) covalent geometry : angle 0.55162 (12783) hydrogen bonds : bond 0.04469 ( 726) hydrogen bonds : angle 4.68203 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.325 Fit side-chains REVERT: A 99 PHE cc_start: 0.7940 (t80) cc_final: 0.7583 (t80) REVERT: A 117 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7623 (mttp) REVERT: A 138 THR cc_start: 0.7089 (OUTLIER) cc_final: 0.6677 (m) REVERT: A 205 MET cc_start: 0.8190 (ptt) cc_final: 0.7939 (ptm) REVERT: A 315 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7245 (ttm110) REVERT: A 353 ARG cc_start: 0.7911 (mtm180) cc_final: 0.7651 (mtm-85) REVERT: A 442 LEU cc_start: 0.7574 (tp) cc_final: 0.7311 (tt) REVERT: A 444 ASP cc_start: 0.8027 (t0) cc_final: 0.7796 (t0) REVERT: B 39 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7640 (ttp80) REVERT: B 68 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7357 (tp) REVERT: B 205 MET cc_start: 0.8329 (ptt) cc_final: 0.8118 (ptm) REVERT: B 258 MET cc_start: 0.8477 (tpp) cc_final: 0.7961 (tpt) REVERT: B 277 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6504 (mp0) REVERT: B 304 ILE cc_start: 0.7802 (tt) cc_final: 0.7508 (mt) REVERT: B 315 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7265 (ttm170) REVERT: C 68 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7388 (tp) REVERT: C 138 THR cc_start: 0.6981 (t) cc_final: 0.6576 (m) REVERT: C 163 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.7964 (ptpt) REVERT: C 205 MET cc_start: 0.8345 (ptt) cc_final: 0.8017 (ptm) REVERT: C 315 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7324 (ttm110) REVERT: C 442 LEU cc_start: 0.7637 (tp) cc_final: 0.7405 (tt) REVERT: C 444 ASP cc_start: 0.8191 (t0) cc_final: 0.7859 (t70) outliers start: 29 outliers final: 4 residues processed: 200 average time/residue: 0.5554 time to fit residues: 118.8111 Evaluate side-chains 169 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 229 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 0.0010 chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.192192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.157654 restraints weight = 2940.667| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 0.63 r_work: 0.3403 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9417 Z= 0.137 Angle : 0.507 5.147 12783 Z= 0.262 Chirality : 0.039 0.139 1626 Planarity : 0.003 0.030 1557 Dihedral : 6.329 87.747 1287 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.06 % Allowed : 21.17 % Favored : 74.78 % 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: 1.43 (0.23), residues: 1200 helix: 1.50 (0.16), residues: 933 sheet: 0.16 (0.60), residues: 48 loop : -1.14 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 445 TYR 0.010 0.001 TYR A 162 PHE 0.014 0.001 PHE B 240 TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9417) covalent geometry : angle 0.50675 (12783) hydrogen bonds : bond 0.04147 ( 726) hydrogen bonds : angle 4.49457 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.414 Fit side-chains REVERT: A 99 PHE cc_start: 0.7966 (t80) cc_final: 0.7591 (t80) REVERT: A 117 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7576 (mttp) REVERT: A 255 MET cc_start: 0.8615 (mmm) cc_final: 0.8408 (mmm) REVERT: A 277 GLU cc_start: 0.6641 (tm-30) cc_final: 0.6103 (pm20) REVERT: A 315 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7301 (ttm110) REVERT: A 320 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7999 (mtp) REVERT: A 353 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7696 (mtm-85) REVERT: A 444 ASP cc_start: 0.8026 (t0) cc_final: 0.7750 (t0) REVERT: B 68 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7385 (tp) REVERT: B 138 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6632 (m) REVERT: B 205 MET cc_start: 0.8256 (ptt) cc_final: 0.8035 (ptm) REVERT: B 228 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7676 (mmtm) REVERT: B 258 MET cc_start: 0.8482 (tpp) cc_final: 0.8132 (tpt) REVERT: B 277 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6463 (pm20) REVERT: B 315 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7314 (ttm170) REVERT: B 445 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7819 (mtt90) REVERT: C 68 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7366 (tp) REVERT: C 138 THR cc_start: 0.6974 (OUTLIER) cc_final: 0.6546 (m) REVERT: C 163 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.7975 (ptpt) REVERT: C 167 GLU cc_start: 0.7492 (pp20) cc_final: 0.7146 (pp20) REVERT: C 205 MET cc_start: 0.8217 (ptt) cc_final: 0.7879 (ptm) REVERT: C 228 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7604 (mtmt) REVERT: C 304 ILE cc_start: 0.7960 (tt) cc_final: 0.7650 (mt) REVERT: C 315 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7306 (ttm110) REVERT: C 357 PHE cc_start: 0.7937 (t80) cc_final: 0.7695 (t80) REVERT: C 419 MET cc_start: 0.8873 (mmm) cc_final: 0.8553 (tpp) REVERT: C 442 LEU cc_start: 0.7436 (tp) cc_final: 0.7217 (tt) REVERT: C 444 ASP cc_start: 0.8097 (t0) cc_final: 0.7809 (t70) outliers start: 41 outliers final: 12 residues processed: 195 average time/residue: 0.5968 time to fit residues: 124.0651 Evaluate side-chains 182 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.195537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.160198 restraints weight = 2516.572| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 0.66 r_work: 0.3600 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9417 Z= 0.162 Angle : 0.534 5.353 12783 Z= 0.275 Chirality : 0.040 0.140 1626 Planarity : 0.004 0.033 1557 Dihedral : 6.134 77.328 1287 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.26 % Allowed : 22.35 % Favored : 74.38 % 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: 1.30 (0.23), residues: 1200 helix: 1.41 (0.16), residues: 930 sheet: 0.13 (0.62), residues: 48 loop : -1.17 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.011 0.001 TYR B 162 PHE 0.017 0.002 PHE C 240 TRP 0.012 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9417) covalent geometry : angle 0.53391 (12783) hydrogen bonds : bond 0.04347 ( 726) hydrogen bonds : angle 4.51432 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.360 Fit side-chains REVERT: A 99 PHE cc_start: 0.8006 (t80) cc_final: 0.7574 (t80) REVERT: A 117 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7671 (mttp) REVERT: A 138 THR cc_start: 0.7017 (OUTLIER) cc_final: 0.6601 (m) REVERT: A 277 GLU cc_start: 0.6466 (tm-30) cc_final: 0.6250 (mp0) REVERT: A 303 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7478 (tp) REVERT: A 315 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7364 (ttm110) REVERT: A 320 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.8007 (mtp) REVERT: A 353 ARG cc_start: 0.7931 (mtm180) cc_final: 0.7689 (mtm-85) REVERT: A 444 ASP cc_start: 0.8087 (t0) cc_final: 0.7886 (t0) REVERT: B 68 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7285 (tp) REVERT: B 138 THR cc_start: 0.6972 (OUTLIER) cc_final: 0.6645 (m) REVERT: B 228 LYS cc_start: 0.8387 (mmtt) cc_final: 0.7698 (mmtm) REVERT: B 258 MET cc_start: 0.8431 (tpp) cc_final: 0.8098 (tpt) REVERT: B 277 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6521 (pm20) REVERT: B 303 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7618 (mt) REVERT: B 315 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7348 (ttm170) REVERT: B 399 ILE cc_start: 0.8735 (mt) cc_final: 0.8535 (mm) REVERT: B 445 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7843 (mtt90) REVERT: C 68 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7292 (tp) REVERT: C 117 LYS cc_start: 0.8295 (mtmm) cc_final: 0.6619 (tmtt) REVERT: C 138 THR cc_start: 0.6964 (OUTLIER) cc_final: 0.6545 (m) REVERT: C 163 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.7977 (ptpt) REVERT: C 205 MET cc_start: 0.8222 (ptt) cc_final: 0.7947 (ptm) REVERT: C 228 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7595 (mtmt) REVERT: C 235 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7951 (tt) REVERT: C 304 ILE cc_start: 0.7806 (tt) cc_final: 0.7521 (mt) REVERT: C 315 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7346 (ttm110) REVERT: C 419 MET cc_start: 0.8919 (mmm) cc_final: 0.8612 (tpp) REVERT: C 442 LEU cc_start: 0.7444 (tp) cc_final: 0.7217 (tt) REVERT: C 444 ASP cc_start: 0.8114 (t0) cc_final: 0.7909 (t70) outliers start: 33 outliers final: 13 residues processed: 188 average time/residue: 0.5842 time to fit residues: 117.3172 Evaluate side-chains 180 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 100 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 101 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.197436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.162004 restraints weight = 2336.839| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 0.66 r_work: 0.3659 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9417 Z= 0.117 Angle : 0.478 5.302 12783 Z= 0.247 Chirality : 0.038 0.134 1626 Planarity : 0.004 0.034 1557 Dihedral : 4.849 62.479 1287 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.36 % Allowed : 22.75 % Favored : 73.89 % 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: 1.59 (0.23), residues: 1200 helix: 1.62 (0.16), residues: 933 sheet: -0.05 (0.62), residues: 48 loop : -1.08 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 39 TYR 0.011 0.001 TYR A 162 PHE 0.010 0.001 PHE C 240 TRP 0.010 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9417) covalent geometry : angle 0.47802 (12783) hydrogen bonds : bond 0.03733 ( 726) hydrogen bonds : angle 4.31704 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.361 Fit side-chains REVERT: A 99 PHE cc_start: 0.7890 (t80) cc_final: 0.7441 (t80) REVERT: A 117 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7610 (mttp) REVERT: A 167 GLU cc_start: 0.7463 (pp20) cc_final: 0.7142 (pp20) REVERT: A 277 GLU cc_start: 0.6421 (tm-30) cc_final: 0.6188 (mp0) REVERT: A 303 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7634 (tp) REVERT: A 315 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7314 (ttm110) REVERT: A 320 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7972 (mtp) REVERT: A 353 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7655 (mtm-85) REVERT: A 444 ASP cc_start: 0.7900 (t0) cc_final: 0.7611 (t70) REVERT: B 48 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7487 (mp0) REVERT: B 68 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7278 (tp) REVERT: B 99 PHE cc_start: 0.7972 (t80) cc_final: 0.7660 (t80) REVERT: B 138 THR cc_start: 0.6843 (OUTLIER) cc_final: 0.6487 (m) REVERT: B 167 GLU cc_start: 0.7746 (pp20) cc_final: 0.7317 (pp20) REVERT: B 228 LYS cc_start: 0.8291 (mmtt) cc_final: 0.7578 (mmtm) REVERT: B 258 MET cc_start: 0.8441 (tpp) cc_final: 0.8117 (tpt) REVERT: B 272 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6777 (mp0) REVERT: B 277 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6449 (pm20) REVERT: B 315 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7314 (ttm170) REVERT: B 445 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6870 (mtt90) REVERT: C 40 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7151 (mt-10) REVERT: C 68 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7202 (tp) REVERT: C 138 THR cc_start: 0.6993 (OUTLIER) cc_final: 0.6559 (m) REVERT: C 152 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7898 (mt-10) REVERT: C 163 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.7894 (ptpt) REVERT: C 205 MET cc_start: 0.8152 (ptt) cc_final: 0.7881 (ptm) REVERT: C 228 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7496 (mmtm) REVERT: C 277 GLU cc_start: 0.6491 (tm-30) cc_final: 0.6245 (pm20) REVERT: C 304 ILE cc_start: 0.7765 (tt) cc_final: 0.7504 (mt) REVERT: C 315 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7386 (ttm110) REVERT: C 419 MET cc_start: 0.8849 (mmm) cc_final: 0.8591 (tpp) REVERT: C 442 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6964 (tt) REVERT: C 444 ASP cc_start: 0.7982 (t0) cc_final: 0.7705 (t70) outliers start: 34 outliers final: 10 residues processed: 194 average time/residue: 0.5792 time to fit residues: 120.0595 Evaluate side-chains 182 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.195803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.160305 restraints weight = 2309.988| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 0.65 r_work: 0.3636 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9417 Z= 0.135 Angle : 0.505 6.005 12783 Z= 0.259 Chirality : 0.039 0.133 1626 Planarity : 0.004 0.033 1557 Dihedral : 4.089 37.367 1287 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.76 % Allowed : 22.55 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.23), residues: 1200 helix: 1.55 (0.16), residues: 939 sheet: -0.12 (0.63), residues: 48 loop : -0.99 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 445 TYR 0.011 0.001 TYR B 162 PHE 0.014 0.002 PHE C 240 TRP 0.013 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9417) covalent geometry : angle 0.50534 (12783) hydrogen bonds : bond 0.03959 ( 726) hydrogen bonds : angle 4.34751 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.331 Fit side-chains REVERT: A 99 PHE cc_start: 0.7950 (t80) cc_final: 0.7486 (t80) REVERT: A 117 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7594 (mttp) REVERT: A 167 GLU cc_start: 0.7489 (pp20) cc_final: 0.7050 (pp20) REVERT: A 277 GLU cc_start: 0.6398 (tm-30) cc_final: 0.6181 (mp0) REVERT: A 303 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7658 (tp) REVERT: A 315 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7356 (ttm110) REVERT: A 353 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7682 (mtm-85) REVERT: A 444 ASP cc_start: 0.7893 (t0) cc_final: 0.7637 (t70) REVERT: B 68 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7358 (tp) REVERT: B 99 PHE cc_start: 0.7999 (t80) cc_final: 0.7723 (t80) REVERT: B 138 THR cc_start: 0.6812 (OUTLIER) cc_final: 0.6534 (m) REVERT: B 167 GLU cc_start: 0.7773 (pp20) cc_final: 0.7505 (pp20) REVERT: B 228 LYS cc_start: 0.8361 (mmtt) cc_final: 0.7622 (mmtm) REVERT: B 258 MET cc_start: 0.8433 (tpp) cc_final: 0.8129 (tpt) REVERT: B 272 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6791 (mp0) REVERT: B 277 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6516 (pm20) REVERT: B 315 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7321 (ttm170) REVERT: C 68 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7229 (tp) REVERT: C 117 LYS cc_start: 0.8304 (mtmm) cc_final: 0.6603 (tmtt) REVERT: C 138 THR cc_start: 0.6884 (OUTLIER) cc_final: 0.6459 (m) REVERT: C 163 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.7890 (ptpt) REVERT: C 205 MET cc_start: 0.8150 (ptt) cc_final: 0.7906 (ptm) REVERT: C 228 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7473 (mtmt) REVERT: C 231 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: C 277 GLU cc_start: 0.6510 (tm-30) cc_final: 0.6252 (pm20) REVERT: C 304 ILE cc_start: 0.7810 (tt) cc_final: 0.7553 (mt) REVERT: C 315 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7395 (ttm110) REVERT: C 357 PHE cc_start: 0.7861 (t80) cc_final: 0.7640 (t80) REVERT: C 419 MET cc_start: 0.8915 (mmm) cc_final: 0.8663 (tpp) REVERT: C 442 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6971 (tt) REVERT: C 444 ASP cc_start: 0.7997 (t0) cc_final: 0.7725 (t70) outliers start: 38 outliers final: 10 residues processed: 197 average time/residue: 0.5642 time to fit residues: 118.8322 Evaluate side-chains 175 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 75 optimal weight: 0.0870 chunk 13 optimal weight: 0.0570 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.197624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.163224 restraints weight = 2419.756| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 0.65 r_work: 0.3657 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9417 Z= 0.124 Angle : 0.496 5.208 12783 Z= 0.253 Chirality : 0.038 0.138 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.813 34.137 1287 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.36 % Allowed : 23.44 % Favored : 73.19 % 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: 1.57 (0.23), residues: 1200 helix: 1.59 (0.16), residues: 939 sheet: -0.25 (0.64), residues: 48 loop : -0.97 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.010 0.001 TYR B 162 PHE 0.012 0.001 PHE C 240 TRP 0.014 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9417) covalent geometry : angle 0.49556 (12783) hydrogen bonds : bond 0.03807 ( 726) hydrogen bonds : angle 4.30068 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.359 Fit side-chains REVERT: A 99 PHE cc_start: 0.7902 (t80) cc_final: 0.7421 (t80) REVERT: A 117 LYS cc_start: 0.8206 (mtmm) cc_final: 0.7600 (mttp) REVERT: A 167 GLU cc_start: 0.7437 (pp20) cc_final: 0.7026 (pp20) REVERT: A 272 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: A 303 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7658 (tp) REVERT: A 315 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7328 (ttm110) REVERT: A 444 ASP cc_start: 0.7840 (t0) cc_final: 0.7556 (t70) REVERT: B 68 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7306 (tp) REVERT: B 99 PHE cc_start: 0.7977 (t80) cc_final: 0.7686 (t80) REVERT: B 138 THR cc_start: 0.6932 (OUTLIER) cc_final: 0.6674 (m) REVERT: B 167 GLU cc_start: 0.7611 (pp20) cc_final: 0.7218 (pp20) REVERT: B 228 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7603 (mmtm) REVERT: B 258 MET cc_start: 0.8420 (tpp) cc_final: 0.8130 (tpt) REVERT: B 277 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6501 (pm20) REVERT: B 315 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7340 (ttm170) REVERT: B 440 ASP cc_start: 0.7501 (t70) cc_final: 0.7221 (t0) REVERT: C 68 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7222 (tp) REVERT: C 114 VAL cc_start: 0.8198 (t) cc_final: 0.7943 (m) REVERT: C 117 LYS cc_start: 0.8294 (mtmm) cc_final: 0.6589 (tmtt) REVERT: C 205 MET cc_start: 0.8165 (ptt) cc_final: 0.7863 (ptm) REVERT: C 228 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7478 (mmtm) REVERT: C 231 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: C 304 ILE cc_start: 0.7800 (tt) cc_final: 0.7491 (mt) REVERT: C 315 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7423 (ttm110) REVERT: C 419 MET cc_start: 0.8875 (mmm) cc_final: 0.8642 (tpp) REVERT: C 442 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6775 (pt) REVERT: C 444 ASP cc_start: 0.7962 (t0) cc_final: 0.7694 (t70) outliers start: 34 outliers final: 10 residues processed: 188 average time/residue: 0.5603 time to fit residues: 112.8943 Evaluate side-chains 173 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.190774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.159263 restraints weight = 2283.621| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 0.50 r_work: 0.3415 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9417 Z= 0.175 Angle : 0.562 6.007 12783 Z= 0.287 Chirality : 0.041 0.156 1626 Planarity : 0.004 0.035 1557 Dihedral : 4.049 35.671 1287 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.76 % Allowed : 22.95 % Favored : 73.29 % 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: 1.29 (0.23), residues: 1200 helix: 1.40 (0.16), residues: 936 sheet: -0.19 (0.65), residues: 48 loop : -1.14 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 445 TYR 0.011 0.001 TYR B 162 PHE 0.018 0.002 PHE C 240 TRP 0.017 0.002 TRP A 256 HIS 0.002 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9417) covalent geometry : angle 0.56204 (12783) hydrogen bonds : bond 0.04366 ( 726) hydrogen bonds : angle 4.48098 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.8069 (t80) cc_final: 0.7641 (t80) REVERT: A 117 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7661 (mttp) REVERT: A 167 GLU cc_start: 0.7452 (pp20) cc_final: 0.7046 (pp20) REVERT: A 272 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: A 303 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7744 (tp) REVERT: A 315 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7444 (ttm110) REVERT: A 444 ASP cc_start: 0.7972 (t0) cc_final: 0.7750 (t0) REVERT: B 68 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7402 (tp) REVERT: B 138 THR cc_start: 0.7058 (OUTLIER) cc_final: 0.6823 (m) REVERT: B 167 GLU cc_start: 0.7683 (pp20) cc_final: 0.7463 (pp20) REVERT: B 228 LYS cc_start: 0.8431 (mmtt) cc_final: 0.7818 (mmtm) REVERT: B 258 MET cc_start: 0.8384 (tpp) cc_final: 0.8100 (tpt) REVERT: B 315 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7366 (ttm170) REVERT: B 445 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7785 (mtt90) REVERT: C 68 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7374 (tp) REVERT: C 117 LYS cc_start: 0.8255 (mtmm) cc_final: 0.6568 (tmtt) REVERT: C 163 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8003 (ptpt) REVERT: C 205 MET cc_start: 0.8202 (ptt) cc_final: 0.7946 (ptm) REVERT: C 228 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7679 (mmtm) REVERT: C 231 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: C 304 ILE cc_start: 0.7892 (tt) cc_final: 0.7652 (mt) REVERT: C 315 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7472 (ttm110) REVERT: C 419 MET cc_start: 0.8944 (mmm) cc_final: 0.8730 (tpp) REVERT: C 442 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7043 (tt) REVERT: C 444 ASP cc_start: 0.7980 (t0) cc_final: 0.7765 (t70) outliers start: 38 outliers final: 12 residues processed: 183 average time/residue: 0.6147 time to fit residues: 119.8423 Evaluate side-chains 176 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.182934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.149068 restraints weight = 2392.724| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 0.58 r_work: 0.3465 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9417 Z= 0.134 Angle : 0.522 6.870 12783 Z= 0.266 Chirality : 0.039 0.150 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.864 33.532 1287 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.87 % Allowed : 24.13 % Favored : 73.00 % 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: 1.51 (0.23), residues: 1200 helix: 1.61 (0.16), residues: 921 sheet: -0.35 (0.65), residues: 48 loop : -1.06 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 353 TYR 0.011 0.001 TYR B 162 PHE 0.013 0.002 PHE B 240 TRP 0.018 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9417) covalent geometry : angle 0.52189 (12783) hydrogen bonds : bond 0.03961 ( 726) hydrogen bonds : angle 4.38282 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.8037 (t80) cc_final: 0.7651 (t80) REVERT: A 117 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7669 (mttp) REVERT: A 167 GLU cc_start: 0.7350 (pp20) cc_final: 0.6947 (pp20) REVERT: A 272 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: A 303 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 315 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7419 (ttm110) REVERT: A 444 ASP cc_start: 0.7863 (t0) cc_final: 0.7561 (t70) REVERT: B 68 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7426 (tp) REVERT: B 99 PHE cc_start: 0.8017 (t80) cc_final: 0.7758 (t80) REVERT: B 138 THR cc_start: 0.6965 (OUTLIER) cc_final: 0.6723 (m) REVERT: B 167 GLU cc_start: 0.7525 (pp20) cc_final: 0.7260 (pp20) REVERT: B 228 LYS cc_start: 0.8387 (mmtt) cc_final: 0.7804 (mmtm) REVERT: B 258 MET cc_start: 0.8385 (tpp) cc_final: 0.8106 (tpt) REVERT: B 315 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7395 (ttm170) REVERT: B 440 ASP cc_start: 0.7542 (t70) cc_final: 0.7248 (t0) REVERT: B 445 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7450 (mmt180) REVERT: C 22 LEU cc_start: 0.8271 (mp) cc_final: 0.7917 (mt) REVERT: C 68 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7393 (tp) REVERT: C 205 MET cc_start: 0.8125 (ptt) cc_final: 0.7867 (ptm) REVERT: C 228 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7617 (mtmt) REVERT: C 231 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: C 277 GLU cc_start: 0.6621 (tm-30) cc_final: 0.6399 (pm20) REVERT: C 304 ILE cc_start: 0.7889 (tt) cc_final: 0.7637 (mt) REVERT: C 315 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7496 (ttm110) REVERT: C 419 MET cc_start: 0.8907 (mmm) cc_final: 0.8693 (tpp) REVERT: C 442 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6935 (tt) REVERT: C 444 ASP cc_start: 0.7981 (t0) cc_final: 0.7744 (t70) outliers start: 29 outliers final: 14 residues processed: 175 average time/residue: 0.5914 time to fit residues: 110.5904 Evaluate side-chains 170 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.182502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.148237 restraints weight = 2443.063| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 0.59 r_work: 0.3481 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9417 Z= 0.145 Angle : 0.546 8.397 12783 Z= 0.278 Chirality : 0.040 0.149 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.902 33.197 1287 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.57 % Allowed : 24.83 % Favored : 72.60 % 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: 1.50 (0.23), residues: 1200 helix: 1.59 (0.16), residues: 921 sheet: -0.31 (0.65), residues: 48 loop : -1.06 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 353 TYR 0.011 0.001 TYR B 162 PHE 0.015 0.002 PHE B 240 TRP 0.020 0.002 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9417) covalent geometry : angle 0.54593 (12783) hydrogen bonds : bond 0.04076 ( 726) hydrogen bonds : angle 4.41252 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.338 Fit side-chains REVERT: A 99 PHE cc_start: 0.8035 (t80) cc_final: 0.7637 (t80) REVERT: A 117 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7693 (mttp) REVERT: A 167 GLU cc_start: 0.7348 (pp20) cc_final: 0.6952 (pp20) REVERT: A 272 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: A 303 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7769 (tp) REVERT: A 315 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7414 (ttm110) REVERT: A 444 ASP cc_start: 0.7902 (t0) cc_final: 0.7632 (t70) REVERT: B 68 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7387 (tp) REVERT: B 99 PHE cc_start: 0.8019 (t80) cc_final: 0.7752 (t80) REVERT: B 167 GLU cc_start: 0.7498 (pp20) cc_final: 0.7249 (pp20) REVERT: B 228 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7774 (mmtm) REVERT: B 258 MET cc_start: 0.8369 (tpp) cc_final: 0.8118 (tpt) REVERT: B 315 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7396 (ttm170) REVERT: B 445 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7807 (mtt90) REVERT: C 22 LEU cc_start: 0.8286 (mp) cc_final: 0.7941 (mt) REVERT: C 68 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7401 (tp) REVERT: C 205 MET cc_start: 0.8117 (ptt) cc_final: 0.7855 (ptm) REVERT: C 228 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7607 (mtmt) REVERT: C 231 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: C 304 ILE cc_start: 0.7898 (tt) cc_final: 0.7641 (mt) REVERT: C 315 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7500 (ttm110) REVERT: C 419 MET cc_start: 0.8874 (mmm) cc_final: 0.8649 (tpp) REVERT: C 442 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6934 (tt) REVERT: C 444 ASP cc_start: 0.7950 (t0) cc_final: 0.7715 (t70) outliers start: 26 outliers final: 14 residues processed: 167 average time/residue: 0.5751 time to fit residues: 102.7936 Evaluate side-chains 170 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 86 optimal weight: 0.0270 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.185267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.151010 restraints weight = 2444.481| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 0.59 r_work: 0.3414 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9417 Z= 0.130 Angle : 0.531 9.572 12783 Z= 0.270 Chirality : 0.039 0.146 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.806 31.613 1287 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.47 % Allowed : 24.83 % Favored : 72.70 % 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 (0.23), residues: 1200 helix: 1.71 (0.16), residues: 924 sheet: -0.36 (0.65), residues: 48 loop : -0.98 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 353 TYR 0.011 0.001 TYR B 162 PHE 0.012 0.001 PHE C 240 TRP 0.023 0.002 TRP A 256 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9417) covalent geometry : angle 0.53129 (12783) hydrogen bonds : bond 0.03860 ( 726) hydrogen bonds : angle 4.34136 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3402.89 seconds wall clock time: 58 minutes 46.01 seconds (3526.01 seconds total)