Starting phenix.real_space_refine on Thu Mar 13 22:15:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d67_46588/03_2025/9d67_46588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d67_46588/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9d67_46588/03_2025/9d67_46588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d67_46588/03_2025/9d67_46588.map" model { file = "/net/cci-nas-00/data/ceres_data/9d67_46588/03_2025/9d67_46588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d67_46588/03_2025/9d67_46588.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.01, per 1000 atoms: 0.65 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.91 Time building geometry restraints manager: 2.90 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: 0.06 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.760 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.030 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- 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= 0.215 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (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 TRP 0.004 0.001 TRP A 256 HIS 0.001 0.000 HIS B 41 PHE 0.016 0.002 PHE C 240 TYR 0.014 0.001 TYR B 97 ARG 0.023 0.002 ARG C 166 *********************** 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 : 1.046 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: 0.6619 (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: 0.6732 (mtmm) REVERT: B 356 ARG cc_start: 0.6903 (mmt180) cc_final: 0.6558 (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: 1.2938 time to fit residues: 308.5647 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 : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.185192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.149155 restraints weight = 2974.774| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 0.67 r_work: 0.3303 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1591 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= 0.212 Angle : 0.533 5.136 12783 Z= 0.278 Chirality : 0.039 0.150 1626 Planarity : 0.004 0.027 1557 Dihedral : 6.601 103.085 1287 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.37 % Allowed : 22.06 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.23), residues: 1200 helix: 1.56 (0.16), residues: 915 sheet: 0.19 (0.60), residues: 48 loop : -0.83 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.013 0.002 PHE C 240 TYR 0.011 0.001 TYR C 97 ARG 0.002 0.000 ARG C 166 *********************** 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 211 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 2.060 Fit side-chains REVERT: A 99 PHE cc_start: 0.7913 (t80) cc_final: 0.7581 (t80) REVERT: A 117 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7603 (mttp) REVERT: A 315 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7245 (ttm110) REVERT: A 353 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7626 (mtm-85) REVERT: A 442 LEU cc_start: 0.7545 (tp) cc_final: 0.7305 (tt) REVERT: A 444 ASP cc_start: 0.8014 (t0) cc_final: 0.7785 (t0) REVERT: B 68 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7411 (tp) REVERT: B 205 MET cc_start: 0.8365 (ptt) cc_final: 0.8145 (ptm) REVERT: B 258 MET cc_start: 0.8450 (tpp) cc_final: 0.8042 (tpt) REVERT: B 277 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6475 (mp0) REVERT: B 304 ILE cc_start: 0.7770 (tt) cc_final: 0.7461 (mt) REVERT: B 315 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7301 (ttm170) REVERT: C 68 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7410 (tp) REVERT: C 138 THR cc_start: 0.6967 (t) cc_final: 0.6579 (m) REVERT: C 205 MET cc_start: 0.8359 (ptt) cc_final: 0.8073 (ptm) REVERT: C 228 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7705 (mmtm) REVERT: C 315 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7367 (ttm110) REVERT: C 442 LEU cc_start: 0.7593 (tp) cc_final: 0.7377 (tt) REVERT: C 444 ASP cc_start: 0.8203 (t0) cc_final: 0.7862 (t70) outliers start: 24 outliers final: 4 residues processed: 199 average time/residue: 1.1506 time to fit residues: 248.4337 Evaluate side-chains 172 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 229 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 84 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.189409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.155401 restraints weight = 2612.793| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 0.60 r_work: 0.3398 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2026 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= 0.173 Angle : 0.487 5.147 12783 Z= 0.253 Chirality : 0.038 0.138 1626 Planarity : 0.003 0.029 1557 Dihedral : 6.206 87.152 1287 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.76 % Allowed : 21.56 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1200 helix: 1.71 (0.16), residues: 924 sheet: 0.09 (0.59), residues: 48 loop : -0.94 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.011 0.001 PHE C 240 TYR 0.009 0.001 TYR A 162 ARG 0.001 0.000 ARG A 93 *********************** 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 227 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.991 Fit side-chains REVERT: A 99 PHE cc_start: 0.7924 (t80) cc_final: 0.7580 (t80) REVERT: A 117 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7665 (mttp) REVERT: A 138 THR cc_start: 0.7070 (OUTLIER) cc_final: 0.6703 (m) REVERT: A 277 GLU cc_start: 0.6468 (tm-30) cc_final: 0.5924 (pm20) REVERT: A 303 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7685 (tp) REVERT: A 315 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7319 (ttm110) REVERT: A 353 ARG cc_start: 0.7939 (mtm180) cc_final: 0.7726 (mtm-85) REVERT: A 356 ARG cc_start: 0.7022 (mmt180) cc_final: 0.6762 (mmt180) REVERT: A 444 ASP cc_start: 0.7961 (t0) cc_final: 0.7699 (t0) REVERT: B 48 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7722 (mp0) REVERT: B 68 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7369 (tp) REVERT: B 138 THR cc_start: 0.6971 (OUTLIER) cc_final: 0.6633 (m) REVERT: B 167 GLU cc_start: 0.7787 (pp20) cc_final: 0.7492 (pp20) REVERT: B 228 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7506 (mmtm) REVERT: B 258 MET cc_start: 0.8462 (tpp) cc_final: 0.8116 (tpt) REVERT: B 303 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7592 (tt) REVERT: B 304 ILE cc_start: 0.7809 (tt) cc_final: 0.7582 (mt) REVERT: B 315 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7391 (ttm170) REVERT: B 445 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6979 (mtt90) REVERT: C 68 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7376 (tp) REVERT: C 138 THR cc_start: 0.7112 (OUTLIER) cc_final: 0.6707 (m) REVERT: C 163 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.7978 (ptpt) REVERT: C 205 MET cc_start: 0.8147 (ptt) cc_final: 0.7881 (ptm) REVERT: C 228 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7491 (mtmt) REVERT: C 304 ILE cc_start: 0.7972 (tt) cc_final: 0.7665 (mt) REVERT: C 315 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7491 (ttm110) REVERT: C 356 ARG cc_start: 0.6746 (mmt180) cc_final: 0.6315 (ptp-170) REVERT: C 442 LEU cc_start: 0.7331 (tp) cc_final: 0.7129 (tt) REVERT: C 444 ASP cc_start: 0.8043 (t0) cc_final: 0.7749 (t70) outliers start: 38 outliers final: 10 residues processed: 215 average time/residue: 1.4065 time to fit residues: 323.4279 Evaluate side-chains 185 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 303 LEU Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.197857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.160178 restraints weight = 2789.845| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 0.77 r_work: 0.3654 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9417 Z= 0.180 Angle : 0.491 5.149 12783 Z= 0.254 Chirality : 0.038 0.134 1626 Planarity : 0.003 0.030 1557 Dihedral : 6.000 78.052 1287 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.46 % Allowed : 22.65 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.23), residues: 1200 helix: 1.66 (0.16), residues: 933 sheet: 0.07 (0.62), residues: 48 loop : -1.05 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.012 0.001 PHE B 240 TYR 0.009 0.001 TYR B 162 ARG 0.002 0.000 ARG C 445 *********************** 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 204 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.022 Fit side-chains REVERT: A 99 PHE cc_start: 0.7858 (t80) cc_final: 0.7390 (t80) REVERT: A 117 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7546 (mttp) REVERT: A 138 THR cc_start: 0.6861 (OUTLIER) cc_final: 0.6496 (m) REVERT: A 277 GLU cc_start: 0.6280 (tm-30) cc_final: 0.6064 (mp0) REVERT: A 303 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7545 (tp) REVERT: A 315 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7179 (ttm110) REVERT: A 353 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7641 (mtm-85) REVERT: A 356 ARG cc_start: 0.6966 (mmt180) cc_final: 0.6641 (mmt180) REVERT: A 444 ASP cc_start: 0.7943 (t0) cc_final: 0.7684 (t0) REVERT: B 68 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7308 (tp) REVERT: B 99 PHE cc_start: 0.7975 (t80) cc_final: 0.7678 (t80) REVERT: B 138 THR cc_start: 0.6813 (OUTLIER) cc_final: 0.6478 (m) REVERT: B 228 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7427 (mmtm) REVERT: B 258 MET cc_start: 0.8479 (tpp) cc_final: 0.8157 (tpt) REVERT: B 272 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: B 303 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7472 (tt) REVERT: B 304 ILE cc_start: 0.7646 (tt) cc_final: 0.7441 (mt) REVERT: B 315 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7264 (ttm170) REVERT: B 399 ILE cc_start: 0.8632 (mt) cc_final: 0.8426 (mm) REVERT: B 445 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6875 (mtt90) REVERT: C 68 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7204 (tp) REVERT: C 86 VAL cc_start: 0.5923 (OUTLIER) cc_final: 0.5719 (p) REVERT: C 138 THR cc_start: 0.6910 (OUTLIER) cc_final: 0.6487 (m) REVERT: C 163 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.7817 (ptpt) REVERT: C 205 MET cc_start: 0.8118 (ptt) cc_final: 0.7770 (ptm) REVERT: C 228 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7347 (mtmt) REVERT: C 235 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7915 (tt) REVERT: C 304 ILE cc_start: 0.7716 (tt) cc_final: 0.7398 (mt) REVERT: C 315 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7357 (ttm110) REVERT: C 444 ASP cc_start: 0.8036 (t0) cc_final: 0.7718 (t70) outliers start: 35 outliers final: 10 residues processed: 189 average time/residue: 1.2920 time to fit residues: 262.6188 Evaluate side-chains 184 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 119 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 104 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 41 optimal weight: 0.0070 chunk 113 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.198636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.163721 restraints weight = 2624.186| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 0.68 r_work: 0.3655 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9417 Z= 0.187 Angle : 0.489 5.661 12783 Z= 0.252 Chirality : 0.038 0.134 1626 Planarity : 0.003 0.032 1557 Dihedral : 5.286 70.805 1287 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.66 % Allowed : 23.64 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.23), residues: 1200 helix: 1.67 (0.16), residues: 933 sheet: 0.01 (0.63), residues: 48 loop : -1.05 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.013 0.001 PHE B 240 TYR 0.010 0.001 TYR A 162 ARG 0.001 0.000 ARG A 39 *********************** 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: 37 poor density : 173 time to evaluate : 1.174 Fit side-chains REVERT: A 99 PHE cc_start: 0.7936 (t80) cc_final: 0.7487 (t80) REVERT: A 117 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7615 (mttp) REVERT: A 138 THR cc_start: 0.6922 (OUTLIER) cc_final: 0.6539 (m) REVERT: A 277 GLU cc_start: 0.6404 (tm-30) cc_final: 0.6157 (mp0) REVERT: A 303 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7631 (tp) REVERT: A 315 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7255 (ttm110) REVERT: A 353 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7676 (mtm-85) REVERT: A 356 ARG cc_start: 0.6992 (mmt180) cc_final: 0.6682 (mmt180) REVERT: A 444 ASP cc_start: 0.7938 (t0) cc_final: 0.7658 (t70) REVERT: B 48 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7700 (mp0) REVERT: B 68 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7364 (tp) REVERT: B 99 PHE cc_start: 0.8013 (t80) cc_final: 0.7728 (t80) REVERT: B 138 THR cc_start: 0.6824 (OUTLIER) cc_final: 0.6555 (m) REVERT: B 167 GLU cc_start: 0.7793 (pp20) cc_final: 0.7370 (pp20) REVERT: B 228 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7525 (mmtm) REVERT: B 258 MET cc_start: 0.8456 (tpp) cc_final: 0.8126 (tpt) REVERT: B 272 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: B 277 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6214 (pm20) REVERT: B 315 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7323 (ttm170) REVERT: B 445 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6878 (mtt90) REVERT: C 68 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7269 (tp) REVERT: C 138 THR cc_start: 0.6856 (OUTLIER) cc_final: 0.6461 (m) REVERT: C 205 MET cc_start: 0.8124 (ptt) cc_final: 0.7819 (ptm) REVERT: C 228 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7445 (mtmt) REVERT: C 235 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7943 (tt) REVERT: C 277 GLU cc_start: 0.6445 (tm-30) cc_final: 0.6205 (pm20) REVERT: C 304 ILE cc_start: 0.7776 (tt) cc_final: 0.7502 (mt) REVERT: C 315 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7368 (ttm110) REVERT: C 357 PHE cc_start: 0.7803 (t80) cc_final: 0.7569 (t80) REVERT: C 444 ASP cc_start: 0.8037 (t0) cc_final: 0.7796 (t70) outliers start: 37 outliers final: 11 residues processed: 196 average time/residue: 1.2050 time to fit residues: 252.9952 Evaluate side-chains 190 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 229 MET Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 445 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 437 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.197483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.163386 restraints weight = 2380.560| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 0.64 r_work: 0.3646 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9417 Z= 0.200 Angle : 0.500 5.145 12783 Z= 0.257 Chirality : 0.039 0.133 1626 Planarity : 0.004 0.033 1557 Dihedral : 4.369 56.590 1287 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.76 % Allowed : 23.24 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1200 helix: 1.59 (0.16), residues: 939 sheet: -0.15 (0.63), residues: 48 loop : -1.02 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 PHE 0.014 0.002 PHE B 240 TYR 0.011 0.001 TYR B 162 ARG 0.002 0.000 ARG B 353 *********************** 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 210 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.982 Fit side-chains REVERT: A 99 PHE cc_start: 0.7946 (t80) cc_final: 0.7504 (t80) REVERT: A 117 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7640 (mttp) REVERT: A 138 THR cc_start: 0.6847 (OUTLIER) cc_final: 0.6493 (m) REVERT: A 167 GLU cc_start: 0.7451 (pp20) cc_final: 0.7154 (pp20) REVERT: A 277 GLU cc_start: 0.6431 (tm-30) cc_final: 0.6215 (mp0) REVERT: A 303 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7628 (tp) REVERT: A 315 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7318 (ttm110) REVERT: A 353 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7694 (mtm-85) REVERT: A 356 ARG cc_start: 0.7013 (mmt180) cc_final: 0.6702 (mmt180) REVERT: A 444 ASP cc_start: 0.7910 (t0) cc_final: 0.7601 (t70) REVERT: B 68 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7344 (tp) REVERT: B 99 PHE cc_start: 0.7991 (t80) cc_final: 0.7705 (t80) REVERT: B 138 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6626 (m) REVERT: B 228 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7561 (mmtm) REVERT: B 258 MET cc_start: 0.8406 (tpp) cc_final: 0.8129 (tpt) REVERT: B 272 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: B 303 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7435 (mt) REVERT: B 315 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7323 (ttm170) REVERT: C 68 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7246 (tp) REVERT: C 117 LYS cc_start: 0.8327 (mtmm) cc_final: 0.6626 (tmtt) REVERT: C 138 THR cc_start: 0.6884 (OUTLIER) cc_final: 0.6549 (m) REVERT: C 167 GLU cc_start: 0.7294 (pp20) cc_final: 0.7080 (pp20) REVERT: C 205 MET cc_start: 0.8185 (ptt) cc_final: 0.7877 (ptm) REVERT: C 228 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7540 (mmtm) REVERT: C 235 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7900 (tt) REVERT: C 277 GLU cc_start: 0.6470 (tm-30) cc_final: 0.6212 (pm20) REVERT: C 304 ILE cc_start: 0.7787 (tt) cc_final: 0.7529 (mt) REVERT: C 315 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7386 (ttm110) REVERT: C 357 PHE cc_start: 0.7920 (t80) cc_final: 0.7689 (t80) REVERT: C 374 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8141 (mm-30) REVERT: C 419 MET cc_start: 0.8965 (mmm) cc_final: 0.8555 (mmm) REVERT: C 442 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7009 (tt) REVERT: C 444 ASP cc_start: 0.8010 (t0) cc_final: 0.7762 (t70) outliers start: 38 outliers final: 12 residues processed: 198 average time/residue: 1.1548 time to fit residues: 244.9394 Evaluate side-chains 186 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 272 GLU Chi-restraints excluded: chain B residue 303 LEU 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 235 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 442 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 0.9990 chunk 93 optimal weight: 0.0970 chunk 101 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4162 r_free = 0.4162 target = 0.198208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164361 restraints weight = 2387.195| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 0.63 r_work: 0.3662 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2589 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= 0.185 Angle : 0.493 5.413 12783 Z= 0.253 Chirality : 0.038 0.147 1626 Planarity : 0.003 0.033 1557 Dihedral : 3.853 35.157 1287 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.36 % Allowed : 23.34 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1200 helix: 1.72 (0.16), residues: 924 sheet: -0.24 (0.63), residues: 48 loop : -0.98 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 256 HIS 0.001 0.001 HIS B 296 PHE 0.012 0.001 PHE C 240 TYR 0.010 0.001 TYR B 162 ARG 0.002 0.000 ARG C 353 *********************** 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 208 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.7931 (t80) cc_final: 0.7479 (t80) REVERT: A 117 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7635 (mttp) REVERT: A 167 GLU cc_start: 0.7444 (pp20) cc_final: 0.7033 (pp20) REVERT: A 272 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6875 (mp0) REVERT: A 277 GLU cc_start: 0.6521 (tm-30) cc_final: 0.6279 (mp0) REVERT: A 303 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7468 (tp) REVERT: A 315 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7335 (ttm110) REVERT: A 356 ARG cc_start: 0.7047 (mmt180) cc_final: 0.6795 (mmt180) REVERT: A 444 ASP cc_start: 0.7856 (t0) cc_final: 0.7564 (t70) REVERT: B 48 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7655 (mp0) REVERT: B 68 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7373 (tp) REVERT: B 99 PHE cc_start: 0.7999 (t80) cc_final: 0.7702 (t80) REVERT: B 114 VAL cc_start: 0.8054 (t) cc_final: 0.7833 (m) REVERT: B 138 THR cc_start: 0.6929 (OUTLIER) cc_final: 0.6690 (m) REVERT: B 167 GLU cc_start: 0.7785 (pp20) cc_final: 0.7449 (pp20) REVERT: B 228 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7582 (mmtm) REVERT: B 258 MET cc_start: 0.8396 (tpp) cc_final: 0.8110 (tpt) REVERT: B 272 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: B 277 GLU cc_start: 0.6494 (tm-30) cc_final: 0.6280 (mp0) REVERT: B 315 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7316 (ttm170) REVERT: B 445 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7379 (mmt180) REVERT: C 68 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7237 (tp) REVERT: C 114 VAL cc_start: 0.8202 (t) cc_final: 0.7925 (m) REVERT: C 117 LYS cc_start: 0.8333 (mtmm) cc_final: 0.6654 (tmtt) REVERT: C 205 MET cc_start: 0.8131 (ptt) cc_final: 0.7818 (ptm) REVERT: C 228 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7513 (mtmt) REVERT: C 235 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7877 (tt) REVERT: C 277 GLU cc_start: 0.6424 (tm-30) cc_final: 0.6178 (pm20) REVERT: C 304 ILE cc_start: 0.7800 (tt) cc_final: 0.7484 (mt) REVERT: C 315 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7408 (ttm110) REVERT: C 357 PHE cc_start: 0.7912 (t80) cc_final: 0.7692 (t80) REVERT: C 419 MET cc_start: 0.8962 (mmm) cc_final: 0.8685 (mmm) REVERT: C 444 ASP cc_start: 0.7974 (t0) cc_final: 0.7698 (t70) outliers start: 34 outliers final: 10 residues processed: 195 average time/residue: 1.2454 time to fit residues: 258.9980 Evaluate side-chains 178 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 272 GLU 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 235 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 0.0270 chunk 116 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 0.0060 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 overall best weight: 0.3454 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.196363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.166166 restraints weight = 2242.936| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 0.49 r_work: 0.3463 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9417 Z= 0.164 Angle : 0.486 5.638 12783 Z= 0.248 Chirality : 0.038 0.142 1626 Planarity : 0.003 0.033 1557 Dihedral : 3.678 34.345 1287 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.77 % Allowed : 24.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1200 helix: 1.84 (0.16), residues: 906 sheet: -0.24 (0.64), residues: 48 loop : -0.77 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.010 0.001 PHE C 240 TYR 0.010 0.001 TYR B 162 ARG 0.002 0.000 ARG A 39 *********************** 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 194 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.7923 (t80) cc_final: 0.7527 (t80) REVERT: A 117 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7610 (mttp) REVERT: A 167 GLU cc_start: 0.7373 (pp20) cc_final: 0.7018 (pp20) REVERT: A 272 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6901 (mp0) REVERT: A 303 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7548 (tp) REVERT: A 315 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7355 (ttm110) REVERT: A 356 ARG cc_start: 0.7158 (mmt180) cc_final: 0.6834 (mmt180) REVERT: A 444 ASP cc_start: 0.7766 (t0) cc_final: 0.7440 (t70) REVERT: B 68 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7414 (tp) REVERT: B 99 PHE cc_start: 0.7977 (t80) cc_final: 0.7706 (t80) REVERT: B 228 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7580 (mmtm) REVERT: B 258 MET cc_start: 0.8347 (tpp) cc_final: 0.8081 (tpt) REVERT: B 272 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: B 303 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7578 (tp) REVERT: B 315 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7355 (ttm170) REVERT: C 68 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7308 (tp) REVERT: C 117 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7752 (mttm) REVERT: C 205 MET cc_start: 0.8141 (ptt) cc_final: 0.7843 (ptm) REVERT: C 228 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7526 (mtmt) REVERT: C 235 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8006 (tt) REVERT: C 419 MET cc_start: 0.8957 (mmm) cc_final: 0.8541 (tpp) REVERT: C 444 ASP cc_start: 0.7907 (t0) cc_final: 0.7628 (t70) outliers start: 28 outliers final: 11 residues processed: 185 average time/residue: 1.1474 time to fit residues: 227.4055 Evaluate side-chains 174 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 272 GLU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.194458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.159190 restraints weight = 2501.265| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 0.67 r_work: 0.3590 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9417 Z= 0.322 Angle : 0.597 6.810 12783 Z= 0.304 Chirality : 0.042 0.152 1626 Planarity : 0.004 0.035 1557 Dihedral : 4.097 35.777 1287 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.97 % Allowed : 24.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1200 helix: 1.42 (0.16), residues: 936 sheet: -0.14 (0.65), residues: 48 loop : -1.23 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 256 HIS 0.003 0.001 HIS C 296 PHE 0.020 0.002 PHE C 240 TYR 0.010 0.001 TYR A 162 ARG 0.003 0.000 ARG A 353 *********************** 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 198 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.8062 (t80) cc_final: 0.7566 (t80) REVERT: A 117 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7635 (mttp) REVERT: A 167 GLU cc_start: 0.7460 (pp20) cc_final: 0.6962 (pp20) REVERT: A 272 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6884 (mp0) REVERT: A 303 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7529 (tp) REVERT: A 315 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7376 (ttm110) REVERT: A 444 ASP cc_start: 0.8054 (t0) cc_final: 0.7833 (t0) REVERT: B 68 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7264 (tp) REVERT: B 114 VAL cc_start: 0.8057 (t) cc_final: 0.7856 (m) REVERT: B 167 GLU cc_start: 0.7812 (pp20) cc_final: 0.7540 (pp20) REVERT: B 228 LYS cc_start: 0.8399 (mmtt) cc_final: 0.7691 (mmtm) REVERT: B 258 MET cc_start: 0.8400 (tpp) cc_final: 0.8140 (tpt) REVERT: B 272 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: B 315 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7314 (ttm170) REVERT: B 445 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7775 (mtt90) REVERT: C 68 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7221 (tp) REVERT: C 114 VAL cc_start: 0.8236 (t) cc_final: 0.7979 (m) REVERT: C 117 LYS cc_start: 0.8268 (mtmm) cc_final: 0.6556 (tmtt) REVERT: C 205 MET cc_start: 0.8258 (ptt) cc_final: 0.7958 (ptm) REVERT: C 228 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7552 (mtmt) REVERT: C 304 ILE cc_start: 0.7808 (tt) cc_final: 0.7513 (mt) REVERT: C 315 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7411 (ttm110) REVERT: C 419 MET cc_start: 0.9014 (mmm) cc_final: 0.8650 (tpp) outliers start: 30 outliers final: 10 residues processed: 183 average time/residue: 1.3538 time to fit residues: 263.6173 Evaluate side-chains 168 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 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 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 272 GLU 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 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 396 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.192990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.161281 restraints weight = 2441.747| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 0.54 r_work: 0.3548 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9417 Z= 0.202 Angle : 0.525 7.605 12783 Z= 0.266 Chirality : 0.039 0.146 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.821 32.584 1287 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.68 % Allowed : 25.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1200 helix: 1.67 (0.16), residues: 924 sheet: -0.33 (0.64), residues: 48 loop : -1.08 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 256 HIS 0.002 0.001 HIS B 296 PHE 0.015 0.002 PHE C 240 TYR 0.011 0.001 TYR B 162 ARG 0.004 0.000 ARG A 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7967 (ttp80) cc_final: 0.7722 (ttp80) REVERT: A 99 PHE cc_start: 0.8050 (t80) cc_final: 0.7659 (t80) REVERT: A 117 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7662 (mttp) REVERT: A 167 GLU cc_start: 0.7373 (pp20) cc_final: 0.6955 (pp20) REVERT: A 248 MET cc_start: 0.8571 (mmm) cc_final: 0.8162 (mmm) REVERT: A 272 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6892 (mp0) REVERT: A 303 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7655 (tp) REVERT: A 315 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7388 (ttm110) REVERT: A 444 ASP cc_start: 0.7899 (t0) cc_final: 0.7598 (t70) REVERT: B 68 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7416 (tp) REVERT: B 99 PHE cc_start: 0.8017 (t80) cc_final: 0.7774 (t80) REVERT: B 228 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7721 (mmtm) REVERT: B 258 MET cc_start: 0.8401 (tpp) cc_final: 0.8103 (tpt) REVERT: B 272 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: B 277 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6514 (mp0) REVERT: B 315 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7356 (ttm170) REVERT: B 440 ASP cc_start: 0.7770 (t70) cc_final: 0.7470 (t0) REVERT: B 445 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7413 (mmt180) REVERT: C 22 LEU cc_start: 0.8267 (mp) cc_final: 0.7917 (mt) REVERT: C 68 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7412 (tp) REVERT: C 114 VAL cc_start: 0.8289 (t) cc_final: 0.8067 (m) REVERT: C 117 LYS cc_start: 0.8306 (mtmm) cc_final: 0.6642 (tmtt) REVERT: C 205 MET cc_start: 0.8232 (ptt) cc_final: 0.7930 (ptm) REVERT: C 228 LYS cc_start: 0.8241 (mmtt) cc_final: 0.7695 (mmtm) REVERT: C 277 GLU cc_start: 0.6628 (tm-30) cc_final: 0.6369 (pm20) REVERT: C 304 ILE cc_start: 0.7902 (tt) cc_final: 0.7618 (mt) REVERT: C 315 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7431 (ttm110) REVERT: C 357 PHE cc_start: 0.8012 (t80) cc_final: 0.7785 (t80) REVERT: C 419 MET cc_start: 0.9031 (mmm) cc_final: 0.8751 (mmm) outliers start: 17 outliers final: 10 residues processed: 169 average time/residue: 1.5260 time to fit residues: 275.9207 Evaluate side-chains 166 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 235 ILE Chi-restraints excluded: chain B residue 269 CYS Chi-restraints excluded: chain B residue 272 GLU 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 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 115 optimal weight: 0.0030 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.193665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.161827 restraints weight = 2506.623| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 0.54 r_work: 0.3519 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9417 Z= 0.199 Angle : 0.526 8.504 12783 Z= 0.267 Chirality : 0.039 0.145 1626 Planarity : 0.004 0.036 1557 Dihedral : 3.792 32.071 1287 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.98 % Allowed : 25.02 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.23), residues: 1200 helix: 1.73 (0.16), residues: 924 sheet: -0.40 (0.64), residues: 48 loop : -1.04 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 256 HIS 0.001 0.000 HIS B 296 PHE 0.013 0.002 PHE C 240 TYR 0.011 0.001 TYR B 162 ARG 0.004 0.000 ARG A 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7434.91 seconds wall clock time: 131 minutes 5.64 seconds (7865.64 seconds total)