Starting phenix.real_space_refine on Wed Sep 17 15:03:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d67_46588/09_2025/9d67_46588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d67_46588/09_2025/9d67_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_46588/09_2025/9d67_46588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d67_46588/09_2025/9d67_46588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d67_46588/09_2025/9d67_46588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d67_46588/09_2025/9d67_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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9297 Number of models: 1 Model: "" Number of chains: 7 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: "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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' HG': 1, ' NA': 2} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Unusual residues: {' HG': 1, ' NA': 2} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {None: 3} 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 Restraints were copied for chains: B, C Time building chain proxies: 2.38, per 1000 atoms: 0.26 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: 0.87 Conformation dependent library (CDL) restraints added in 368.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.31 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: 1.56 Time building geometry restraints manager: 1.10 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: 1.080 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.670 Find NCS groups from input model: 0.210 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- 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 aren 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 : 0.367 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: 0.5733 time to fit residues: 135.8580 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 : 0.244 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.182529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.145252 restraints weight = 3024.151| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 0.70 r_work: 0.3277 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1630 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 : 6.598 102.567 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 aren 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 : 0.356 Fit side-chains REVERT: A 99 PHE cc_start: 0.7933 (t80) cc_final: 0.7571 (t80) REVERT: A 117 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7615 (mttp) REVERT: A 138 THR cc_start: 0.7079 (OUTLIER) cc_final: 0.6667 (m) REVERT: A 205 MET cc_start: 0.8189 (ptt) cc_final: 0.7935 (ptm) REVERT: A 315 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7239 (ttm110) REVERT: A 353 ARG cc_start: 0.7900 (mtm180) cc_final: 0.7641 (mtm-85) REVERT: A 442 LEU cc_start: 0.7564 (tp) cc_final: 0.7302 (tt) REVERT: A 444 ASP cc_start: 0.8022 (t0) cc_final: 0.7791 (t0) REVERT: B 39 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7632 (ttp80) REVERT: B 68 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7351 (tp) REVERT: B 205 MET cc_start: 0.8325 (ptt) cc_final: 0.8113 (ptm) REVERT: B 258 MET cc_start: 0.8476 (tpp) cc_final: 0.7959 (tpt) REVERT: B 277 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6500 (mp0) REVERT: B 304 ILE cc_start: 0.7790 (tt) cc_final: 0.7495 (mt) REVERT: B 315 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7250 (ttm170) REVERT: C 68 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7384 (tp) REVERT: C 138 THR cc_start: 0.6970 (t) cc_final: 0.6564 (m) REVERT: C 163 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.7949 (ptpt) REVERT: C 205 MET cc_start: 0.8343 (ptt) cc_final: 0.8012 (ptm) REVERT: C 315 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7313 (ttm110) REVERT: C 442 LEU cc_start: 0.7627 (tp) cc_final: 0.7395 (tt) REVERT: C 444 ASP cc_start: 0.8184 (t0) cc_final: 0.7851 (t70) outliers start: 29 outliers final: 4 residues processed: 200 average time/residue: 0.5606 time to fit residues: 120.0818 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 : 0.364 ------------------------------------------------------------------------------- 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: 0.0030 chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 113 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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 = 0.4156 r_free = 0.4156 target = 0.198149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.161062 restraints weight = 2931.561| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 0.75 r_work: 0.3650 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2015 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= 0.123 Angle : 0.487 5.139 12783 Z= 0.253 Chirality : 0.038 0.138 1626 Planarity : 0.003 0.029 1557 Dihedral : 6.229 86.787 1287 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.56 % Allowed : 21.46 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.23), residues: 1200 helix: 1.69 (0.16), residues: 918 sheet: 0.11 (0.59), residues: 48 loop : -1.00 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 93 TYR 0.009 0.001 TYR A 162 PHE 0.011 0.001 PHE C 240 TRP 0.009 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9417) covalent geometry : angle 0.48729 (12783) hydrogen bonds : bond 0.03941 ( 726) hydrogen bonds : angle 4.44052 ( 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 213 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.324 Fit side-chains REVERT: A 99 PHE cc_start: 0.7915 (t80) cc_final: 0.7496 (t80) REVERT: A 117 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7614 (mttp) REVERT: A 205 MET cc_start: 0.8168 (ptt) cc_final: 0.7913 (ptm) REVERT: A 277 GLU cc_start: 0.6534 (tm-30) cc_final: 0.5928 (pm20) REVERT: A 303 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7615 (tp) REVERT: A 315 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7236 (ttm110) REVERT: A 353 ARG cc_start: 0.7892 (mtm180) cc_final: 0.7659 (mtm-85) REVERT: A 356 ARG cc_start: 0.6911 (mmt180) cc_final: 0.6660 (mmt180) REVERT: A 444 ASP cc_start: 0.8021 (t0) cc_final: 0.7755 (t70) REVERT: B 68 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7295 (tp) REVERT: B 138 THR cc_start: 0.6898 (OUTLIER) cc_final: 0.6536 (m) REVERT: B 205 MET cc_start: 0.8182 (ptt) cc_final: 0.7946 (ptm) REVERT: B 228 LYS cc_start: 0.8315 (mmtt) cc_final: 0.7605 (mmtm) REVERT: B 258 MET cc_start: 0.8537 (tpp) cc_final: 0.8187 (tpt) REVERT: B 277 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6453 (pm20) REVERT: B 304 ILE cc_start: 0.7754 (tt) cc_final: 0.7544 (mt) REVERT: B 315 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7329 (ttm170) REVERT: B 445 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6970 (mtt90) REVERT: C 68 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7281 (tp) REVERT: C 138 THR cc_start: 0.6910 (OUTLIER) cc_final: 0.6509 (m) REVERT: C 167 GLU cc_start: 0.7427 (pp20) cc_final: 0.7051 (pp20) REVERT: C 205 MET cc_start: 0.8128 (ptt) cc_final: 0.7774 (ptm) REVERT: C 207 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8272 (m) REVERT: C 228 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7489 (mtmt) REVERT: C 304 ILE cc_start: 0.7928 (tt) cc_final: 0.7604 (mt) REVERT: C 315 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7372 (ttm110) REVERT: C 353 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7535 (mtp180) REVERT: C 356 ARG cc_start: 0.6698 (mmt180) cc_final: 0.6223 (ptp-170) REVERT: C 419 MET cc_start: 0.8747 (mmm) cc_final: 0.8526 (tpp) REVERT: C 442 LEU cc_start: 0.7396 (tp) cc_final: 0.7177 (tt) REVERT: C 444 ASP cc_start: 0.8105 (t0) cc_final: 0.7808 (t70) outliers start: 36 outliers final: 12 residues processed: 197 average time/residue: 0.5844 time to fit residues: 122.6767 Evaluate side-chains 184 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE 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 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 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 207 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 0.0040 chunk 2 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.197349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.159648 restraints weight = 2739.537| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 0.76 r_work: 0.3629 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9417 Z= 0.126 Angle : 0.491 5.155 12783 Z= 0.253 Chirality : 0.038 0.135 1626 Planarity : 0.003 0.031 1557 Dihedral : 5.906 74.728 1287 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 aren not related in a simple way. whole: 1.60 (0.23), residues: 1200 helix: 1.62 (0.16), residues: 933 sheet: 0.07 (0.62), residues: 48 loop : -1.07 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 39 TYR 0.010 0.001 TYR B 162 PHE 0.013 0.001 PHE C 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 0.00287 ( 9417) covalent geometry : angle 0.49062 (12783) hydrogen bonds : bond 0.03882 ( 726) hydrogen bonds : angle 4.37384 ( 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 201 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.361 Fit side-chains REVERT: A 99 PHE cc_start: 0.7879 (t80) cc_final: 0.7445 (t80) REVERT: A 117 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7563 (mttp) REVERT: A 138 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6536 (m) REVERT: A 277 GLU cc_start: 0.6344 (tm-30) cc_final: 0.6108 (mp0) REVERT: A 303 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7570 (tp) REVERT: A 315 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7221 (ttm110) REVERT: A 353 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7635 (mtm-85) REVERT: A 356 ARG cc_start: 0.6968 (mmt180) cc_final: 0.6649 (mmt180) REVERT: A 444 ASP cc_start: 0.7980 (t0) cc_final: 0.7719 (t0) REVERT: B 68 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7326 (tp) REVERT: B 99 PHE cc_start: 0.7972 (t80) cc_final: 0.7679 (t80) REVERT: B 138 THR cc_start: 0.6845 (OUTLIER) cc_final: 0.6501 (m) REVERT: B 205 MET cc_start: 0.8175 (ptt) cc_final: 0.7939 (ptm) REVERT: B 228 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7502 (mmtm) REVERT: B 258 MET cc_start: 0.8444 (tpp) cc_final: 0.8163 (tpt) REVERT: B 277 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6414 (pm20) REVERT: B 315 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7266 (ttm170) REVERT: B 399 ILE cc_start: 0.8645 (mt) cc_final: 0.8444 (mm) REVERT: B 445 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.6846 (mtt90) REVERT: C 40 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6992 (mt-10) REVERT: C 68 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7207 (tp) REVERT: C 138 THR cc_start: 0.6937 (OUTLIER) cc_final: 0.6526 (m) REVERT: C 205 MET cc_start: 0.8172 (ptt) cc_final: 0.7828 (ptm) REVERT: C 207 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8265 (m) REVERT: C 228 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7481 (mmtm) REVERT: C 304 ILE cc_start: 0.7728 (tt) cc_final: 0.7417 (mt) REVERT: C 315 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7365 (ttm110) REVERT: C 419 MET cc_start: 0.8860 (mmm) cc_final: 0.8463 (tpp) REVERT: C 444 ASP cc_start: 0.8009 (t0) cc_final: 0.7754 (t70) outliers start: 33 outliers final: 12 residues processed: 188 average time/residue: 0.5736 time to fit residues: 115.3795 Evaluate side-chains 185 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 235 ILE 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 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 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 207 SER 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: 0.9980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 116 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.195860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.160257 restraints weight = 2390.432| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 0.66 r_work: 0.3636 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2332 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= 0.137 Angle : 0.506 5.211 12783 Z= 0.260 Chirality : 0.039 0.135 1626 Planarity : 0.003 0.033 1557 Dihedral : 4.962 62.800 1287 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.37 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 aren not related in a simple way. whole: 1.53 (0.23), residues: 1200 helix: 1.58 (0.16), residues: 933 sheet: -0.02 (0.62), residues: 48 loop : -1.08 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 445 TYR 0.012 0.001 TYR A 162 PHE 0.015 0.002 PHE B 240 TRP 0.011 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9417) covalent geometry : angle 0.50624 (12783) hydrogen bonds : bond 0.04006 ( 726) hydrogen bonds : angle 4.38163 ( 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 210 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.366 Fit side-chains REVERT: A 99 PHE cc_start: 0.7944 (t80) cc_final: 0.7474 (t80) REVERT: A 117 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7629 (mttp) REVERT: A 138 THR cc_start: 0.6885 (OUTLIER) cc_final: 0.6559 (m) REVERT: A 277 GLU cc_start: 0.6376 (tm-30) cc_final: 0.6111 (mp0) REVERT: A 303 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7450 (tp) REVERT: A 315 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7341 (ttm110) REVERT: A 353 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7668 (mtm-85) REVERT: A 356 ARG cc_start: 0.7010 (mmt180) cc_final: 0.6701 (mmt180) REVERT: A 444 ASP cc_start: 0.7954 (t0) cc_final: 0.7690 (t0) REVERT: B 68 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7269 (tp) REVERT: B 99 PHE cc_start: 0.8008 (t80) cc_final: 0.7719 (t80) REVERT: B 138 THR cc_start: 0.6802 (OUTLIER) cc_final: 0.6501 (m) REVERT: B 167 GLU cc_start: 0.7790 (pp20) cc_final: 0.7359 (pp20) REVERT: B 228 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7589 (mmtm) REVERT: B 258 MET cc_start: 0.8446 (tpp) cc_final: 0.8112 (tpt) REVERT: B 272 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6837 (mp0) REVERT: B 277 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6485 (pm20) REVERT: B 315 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7290 (ttm170) REVERT: B 445 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6847 (mtt90) REVERT: C 68 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7218 (tp) REVERT: C 117 LYS cc_start: 0.8311 (mtmm) cc_final: 0.6614 (tmtt) REVERT: C 138 THR cc_start: 0.6805 (OUTLIER) cc_final: 0.6375 (m) REVERT: C 163 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.7916 (ptpt) REVERT: C 205 MET cc_start: 0.8165 (ptt) cc_final: 0.7832 (ptm) REVERT: C 207 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8288 (m) REVERT: C 228 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7508 (mtmt) REVERT: C 277 GLU cc_start: 0.6409 (tm-30) cc_final: 0.6160 (pm20) REVERT: C 304 ILE cc_start: 0.7767 (tt) cc_final: 0.7509 (mt) REVERT: C 315 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7380 (ttm110) REVERT: C 419 MET cc_start: 0.8859 (mmm) cc_final: 0.8567 (tpp) REVERT: C 442 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7042 (tt) REVERT: C 444 ASP cc_start: 0.8050 (t0) cc_final: 0.7815 (t70) outliers start: 34 outliers final: 11 residues processed: 198 average time/residue: 0.5723 time to fit residues: 120.9723 Evaluate side-chains 183 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 207 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 115 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.196224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.160746 restraints weight = 2301.194| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 0.66 r_work: 0.3641 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9417 Z= 0.131 Angle : 0.496 5.288 12783 Z= 0.255 Chirality : 0.038 0.134 1626 Planarity : 0.003 0.034 1557 Dihedral : 4.120 38.510 1287 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.35 % Allowed : 22.06 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.23), residues: 1200 helix: 1.54 (0.16), residues: 936 sheet: -0.18 (0.63), residues: 48 loop : -1.07 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 445 TYR 0.010 0.001 TYR C 162 PHE 0.014 0.002 PHE C 240 TRP 0.012 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9417) covalent geometry : angle 0.49559 (12783) hydrogen bonds : bond 0.03894 ( 726) hydrogen bonds : angle 4.34010 ( 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 207 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 0.409 Fit side-chains REVERT: A 99 PHE cc_start: 0.7912 (t80) cc_final: 0.7443 (t80) REVERT: A 117 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7603 (mttp) REVERT: A 167 GLU cc_start: 0.7518 (pp20) cc_final: 0.7050 (pp20) REVERT: A 277 GLU cc_start: 0.6378 (tm-30) cc_final: 0.6140 (mp0) REVERT: A 303 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7441 (tp) REVERT: A 315 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7297 (ttm110) REVERT: A 353 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7656 (mtm-85) REVERT: A 356 ARG cc_start: 0.6986 (mmt180) cc_final: 0.6674 (mmt180) REVERT: A 444 ASP cc_start: 0.7863 (t0) cc_final: 0.7600 (t70) REVERT: B 68 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7271 (tp) REVERT: B 99 PHE cc_start: 0.7960 (t80) cc_final: 0.7651 (t80) REVERT: B 138 THR cc_start: 0.6979 (OUTLIER) cc_final: 0.6728 (m) REVERT: B 167 GLU cc_start: 0.7747 (pp20) cc_final: 0.7475 (pp20) REVERT: B 228 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7552 (mmtm) REVERT: B 258 MET cc_start: 0.8434 (tpp) cc_final: 0.8136 (tpt) REVERT: B 277 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6441 (pm20) REVERT: B 315 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7300 (ttm170) REVERT: B 445 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6817 (mtt90) REVERT: C 68 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7199 (tp) REVERT: C 117 LYS cc_start: 0.8282 (mtmm) cc_final: 0.6551 (tmtt) REVERT: C 138 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6349 (m) REVERT: C 163 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.7845 (ptpt) REVERT: C 205 MET cc_start: 0.8162 (ptt) cc_final: 0.7828 (ptm) REVERT: C 207 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8261 (m) REVERT: C 228 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7480 (mtmt) REVERT: C 231 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: C 277 GLU cc_start: 0.6409 (tm-30) cc_final: 0.6130 (pm20) REVERT: C 304 ILE cc_start: 0.7754 (tt) cc_final: 0.7495 (mt) REVERT: C 315 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7399 (ttm110) REVERT: C 357 PHE cc_start: 0.7865 (t80) cc_final: 0.7647 (t80) REVERT: C 419 MET cc_start: 0.8873 (mmm) cc_final: 0.8593 (tpp) REVERT: C 442 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6950 (tt) REVERT: C 444 ASP cc_start: 0.7990 (t0) cc_final: 0.7699 (t70) outliers start: 44 outliers final: 13 residues processed: 192 average time/residue: 0.5552 time to fit residues: 114.0944 Evaluate side-chains 183 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 436 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 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 207 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 75 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.194697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.164419 restraints weight = 2179.639| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 0.49 r_work: 0.3453 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2587 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= 0.114 Angle : 0.482 5.218 12783 Z= 0.247 Chirality : 0.038 0.145 1626 Planarity : 0.003 0.033 1557 Dihedral : 3.705 31.714 1287 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.97 % Allowed : 23.54 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.23), residues: 1200 helix: 1.76 (0.16), residues: 924 sheet: -0.29 (0.63), residues: 48 loop : -0.94 (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 0.010 0.001 PHE C 240 TRP 0.014 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9417) covalent geometry : angle 0.48225 (12783) hydrogen bonds : bond 0.03661 ( 726) hydrogen bonds : angle 4.29016 ( 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 196 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.347 Fit side-chains REVERT: A 99 PHE cc_start: 0.7941 (t80) cc_final: 0.7540 (t80) REVERT: A 117 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7630 (mttp) REVERT: A 167 GLU cc_start: 0.7420 (pp20) cc_final: 0.7029 (pp20) REVERT: A 272 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6866 (mp0) REVERT: A 277 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6352 (mp0) REVERT: A 303 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 315 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7360 (ttm110) REVERT: A 356 ARG cc_start: 0.7164 (mmt180) cc_final: 0.6935 (mmt180) REVERT: A 444 ASP cc_start: 0.7783 (t0) cc_final: 0.7493 (t70) REVERT: B 68 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7411 (tp) REVERT: B 99 PHE cc_start: 0.8003 (t80) cc_final: 0.7717 (t80) REVERT: B 114 VAL cc_start: 0.8040 (t) cc_final: 0.7823 (m) REVERT: B 138 THR cc_start: 0.6909 (OUTLIER) cc_final: 0.6673 (m) REVERT: B 167 GLU cc_start: 0.7594 (pp20) cc_final: 0.7242 (pp20) REVERT: B 228 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7673 (mmtm) REVERT: B 258 MET cc_start: 0.8361 (tpp) cc_final: 0.8084 (tpt) REVERT: B 277 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6423 (pm20) REVERT: B 303 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7541 (mt) REVERT: B 315 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7333 (ttm170) REVERT: C 68 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7314 (tp) REVERT: C 114 VAL cc_start: 0.8233 (t) cc_final: 0.7965 (m) REVERT: C 138 THR cc_start: 0.6859 (OUTLIER) cc_final: 0.6536 (m) REVERT: C 205 MET cc_start: 0.8176 (ptt) cc_final: 0.7879 (ptm) REVERT: C 207 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8141 (m) REVERT: C 228 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7578 (mtmt) REVERT: C 315 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7418 (ttm110) REVERT: C 357 PHE cc_start: 0.7890 (t80) cc_final: 0.7686 (t80) REVERT: C 419 MET cc_start: 0.8868 (mmm) cc_final: 0.8577 (tpp) REVERT: C 442 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6817 (pt) REVERT: C 444 ASP cc_start: 0.7918 (t0) cc_final: 0.7641 (t70) outliers start: 30 outliers final: 11 residues processed: 185 average time/residue: 0.5631 time to fit residues: 111.3249 Evaluate side-chains 178 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 C residue 21 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 207 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 111 optimal weight: 0.0770 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.188473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.157075 restraints weight = 2289.563| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 0.51 r_work: 0.3431 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2573 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= 0.150 Angle : 0.532 6.828 12783 Z= 0.271 Chirality : 0.040 0.149 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.893 34.082 1287 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.46 % Allowed : 22.95 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.23), residues: 1200 helix: 1.52 (0.16), residues: 936 sheet: -0.23 (0.64), residues: 48 loop : -1.12 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 445 TYR 0.010 0.001 TYR B 162 PHE 0.016 0.002 PHE C 240 TRP 0.016 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9417) covalent geometry : angle 0.53248 (12783) hydrogen bonds : bond 0.04082 ( 726) hydrogen bonds : angle 4.39212 ( 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 192 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.295 Fit side-chains REVERT: A 99 PHE cc_start: 0.8084 (t80) cc_final: 0.7660 (t80) REVERT: A 117 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7629 (mttp) REVERT: A 167 GLU cc_start: 0.7418 (pp20) cc_final: 0.7037 (pp20) REVERT: A 272 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6858 (mp0) REVERT: A 277 GLU cc_start: 0.6675 (tm-30) cc_final: 0.6447 (mp0) REVERT: A 303 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7612 (tp) REVERT: A 315 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7386 (ttm110) REVERT: A 444 ASP cc_start: 0.7905 (t0) cc_final: 0.7652 (t70) REVERT: B 68 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7372 (tp) REVERT: B 99 PHE cc_start: 0.8041 (t80) cc_final: 0.7784 (t80) REVERT: B 138 THR cc_start: 0.6913 (OUTLIER) cc_final: 0.6698 (m) REVERT: B 167 GLU cc_start: 0.7579 (pp20) cc_final: 0.7307 (pp20) REVERT: B 228 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7717 (mmtm) REVERT: B 258 MET cc_start: 0.8385 (tpp) cc_final: 0.8131 (tpt) REVERT: B 277 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6545 (pm20) REVERT: B 315 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7336 (ttm170) REVERT: C 68 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7350 (tp) REVERT: C 117 LYS cc_start: 0.8304 (mtmm) cc_final: 0.6618 (tmtt) REVERT: C 138 THR cc_start: 0.6996 (OUTLIER) cc_final: 0.6630 (m) REVERT: C 163 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.7999 (ptpt) REVERT: C 205 MET cc_start: 0.8241 (ptt) cc_final: 0.7940 (ptm) REVERT: C 207 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8280 (m) REVERT: C 228 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7676 (mmtm) REVERT: C 231 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: C 304 ILE cc_start: 0.7892 (tt) cc_final: 0.7595 (mt) REVERT: C 315 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7452 (ttm110) REVERT: C 419 MET cc_start: 0.8953 (mmm) cc_final: 0.8675 (tpp) REVERT: C 442 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6975 (tt) REVERT: C 444 ASP cc_start: 0.7975 (t0) cc_final: 0.7747 (t70) outliers start: 35 outliers final: 14 residues processed: 178 average time/residue: 0.5612 time to fit residues: 106.9849 Evaluate side-chains 176 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 258 MET 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 229 MET 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 207 SER 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 396 THR Chi-restraints excluded: chain C residue 437 ILE 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: 0.5980 chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 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 = 0.4073 r_free = 0.4073 target = 0.191743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.160447 restraints weight = 2346.917| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 0.52 r_work: 0.3421 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2632 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= 0.133 Angle : 0.515 7.401 12783 Z= 0.261 Chirality : 0.039 0.145 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.815 31.769 1287 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.87 % Allowed : 23.64 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.23), residues: 1200 helix: 1.68 (0.16), residues: 924 sheet: -0.29 (0.64), residues: 48 loop : -1.02 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 39 TYR 0.011 0.001 TYR B 162 PHE 0.014 0.002 PHE C 240 TRP 0.018 0.001 TRP A 256 HIS 0.001 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9417) covalent geometry : angle 0.51522 (12783) hydrogen bonds : bond 0.03916 ( 726) hydrogen bonds : angle 4.35782 ( 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 190 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.312 Fit side-chains REVERT: A 99 PHE cc_start: 0.8025 (t80) cc_final: 0.7637 (t80) REVERT: A 117 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7617 (mttp) REVERT: A 167 GLU cc_start: 0.7389 (pp20) cc_final: 0.6959 (pp20) REVERT: A 277 GLU cc_start: 0.6650 (tm-30) cc_final: 0.6406 (mp0) REVERT: A 303 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7597 (tp) REVERT: A 315 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7373 (ttm110) REVERT: A 444 ASP cc_start: 0.7866 (t0) cc_final: 0.7595 (t70) REVERT: B 68 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7393 (tp) REVERT: B 99 PHE cc_start: 0.7991 (t80) cc_final: 0.7728 (t80) REVERT: B 167 GLU cc_start: 0.7553 (pp20) cc_final: 0.7281 (pp20) REVERT: B 228 LYS cc_start: 0.8327 (mmtt) cc_final: 0.7704 (mmtm) REVERT: B 258 MET cc_start: 0.8382 (tpp) cc_final: 0.8128 (tpt) REVERT: B 315 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7338 (ttm170) REVERT: B 440 ASP cc_start: 0.7729 (t70) cc_final: 0.7431 (t0) REVERT: C 68 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7325 (tp) REVERT: C 114 VAL cc_start: 0.8264 (t) cc_final: 0.8058 (m) REVERT: C 117 LYS cc_start: 0.8291 (mtmm) cc_final: 0.6613 (tmtt) REVERT: C 205 MET cc_start: 0.8233 (ptt) cc_final: 0.7926 (ptm) REVERT: C 207 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.8192 (m) REVERT: C 228 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7603 (mmtm) REVERT: C 231 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: C 277 GLU cc_start: 0.6560 (tm-30) cc_final: 0.6322 (pm20) REVERT: C 304 ILE cc_start: 0.7869 (tt) cc_final: 0.7580 (mt) REVERT: C 315 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7430 (ttm110) REVERT: C 357 PHE cc_start: 0.7968 (t80) cc_final: 0.7745 (t80) REVERT: C 419 MET cc_start: 0.8977 (mmm) cc_final: 0.8777 (mmm) REVERT: C 442 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6885 (tt) REVERT: C 444 ASP cc_start: 0.7957 (t0) cc_final: 0.7711 (t70) outliers start: 29 outliers final: 15 residues processed: 181 average time/residue: 0.5601 time to fit residues: 108.2759 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 258 MET 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 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 437 ILE 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 207 SER 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: 0.6980 chunk 109 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 112 optimal weight: 0.0370 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.191995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.160606 restraints weight = 2472.915| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 0.53 r_work: 0.3552 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9417 Z= 0.119 Angle : 0.511 8.744 12783 Z= 0.258 Chirality : 0.038 0.142 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.712 29.797 1287 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.18 % Allowed : 24.63 % 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 aren not related in a simple way. whole: 1.77 (0.23), residues: 1200 helix: 1.79 (0.16), residues: 924 sheet: -0.32 (0.64), residues: 48 loop : -0.97 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.011 0.001 TYR B 162 PHE 0.011 0.001 PHE C 306 TRP 0.018 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9417) covalent geometry : angle 0.51133 (12783) hydrogen bonds : bond 0.03716 ( 726) hydrogen bonds : angle 4.28762 ( 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 178 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.372 Fit side-chains REVERT: A 99 PHE cc_start: 0.7988 (t80) cc_final: 0.7636 (t80) REVERT: A 117 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7664 (mttp) REVERT: A 167 GLU cc_start: 0.7332 (pp20) cc_final: 0.6924 (pp20) REVERT: A 277 GLU cc_start: 0.6620 (tm-30) cc_final: 0.6412 (mp0) REVERT: A 303 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7619 (tp) REVERT: A 315 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7384 (ttm110) REVERT: A 444 ASP cc_start: 0.7807 (t0) cc_final: 0.7486 (t70) REVERT: B 68 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7449 (tp) REVERT: B 99 PHE cc_start: 0.7995 (t80) cc_final: 0.7623 (t80) REVERT: B 167 GLU cc_start: 0.7494 (pp20) cc_final: 0.7232 (pp20) REVERT: B 228 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7657 (mmtm) REVERT: B 258 MET cc_start: 0.8406 (tpp) cc_final: 0.8107 (tpt) REVERT: B 315 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7366 (ttm170) REVERT: B 419 MET cc_start: 0.8832 (tpt) cc_final: 0.8554 (tpt) REVERT: B 440 ASP cc_start: 0.7695 (t70) cc_final: 0.7381 (t70) REVERT: C 22 LEU cc_start: 0.8257 (mp) cc_final: 0.7911 (mt) REVERT: C 68 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7377 (tp) REVERT: C 114 VAL cc_start: 0.8259 (t) cc_final: 0.8043 (m) REVERT: C 205 MET cc_start: 0.8233 (ptt) cc_final: 0.7935 (ptm) REVERT: C 207 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.8227 (m) REVERT: C 228 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7587 (mmtm) REVERT: C 231 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: C 277 GLU cc_start: 0.6442 (tm-30) cc_final: 0.6241 (pm20) REVERT: C 315 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7415 (ttm110) REVERT: C 357 PHE cc_start: 0.7980 (t80) cc_final: 0.7765 (t80) REVERT: C 419 MET cc_start: 0.8928 (mmm) cc_final: 0.8579 (tpp) REVERT: C 442 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6847 (pt) REVERT: C 444 ASP cc_start: 0.7928 (t0) cc_final: 0.7680 (t70) outliers start: 22 outliers final: 12 residues processed: 169 average time/residue: 0.5340 time to fit residues: 96.8253 Evaluate side-chains 172 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 258 MET 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 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 207 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.184886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.152016 restraints weight = 2378.599| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 0.56 r_work: 0.3403 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9417 Z= 0.154 Angle : 0.554 9.549 12783 Z= 0.279 Chirality : 0.040 0.147 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.867 30.617 1287 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.37 % Allowed : 24.73 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.23), residues: 1200 helix: 1.68 (0.16), residues: 921 sheet: -0.26 (0.65), residues: 48 loop : -1.10 (0.40), residues: 231 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 0.016 0.002 PHE C 240 TRP 0.020 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9417) covalent geometry : angle 0.55432 (12783) hydrogen bonds : bond 0.04155 ( 726) hydrogen bonds : angle 4.40236 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3381.42 seconds wall clock time: 58 minutes 22.12 seconds (3502.12 seconds total)