Starting phenix.real_space_refine on Wed Feb 4 06:31:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d66_46586/02_2026/9d66_46586.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d66_46586/02_2026/9d66_46586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d66_46586/02_2026/9d66_46586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d66_46586/02_2026/9d66_46586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d66_46586/02_2026/9d66_46586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d66_46586/02_2026/9d66_46586.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.141 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 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9306 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "B" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "C" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' HG': 1, ' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP B 603 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' HG': 1, ' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP C 603 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 36.441 24.199 46.434 1.00 69.42 S ATOM 2858 SG CYS A 441 35.971 26.061 44.199 1.00 71.84 S ATOM 4662 SG CYS B 269 79.119 55.569 46.430 1.00 69.42 S ATOM 5943 SG CYS B 441 77.742 54.230 44.196 1.00 71.84 S ATOM 7747 SG CYS C 269 30.614 76.848 46.436 1.00 69.42 S ATOM 9028 SG CYS C 441 32.462 76.324 44.202 1.00 71.84 S Time building chain proxies: 2.60, per 1000 atoms: 0.28 Number of scatterers: 9306 At special positions: 0 Unit cell: (102.08, 107.88, 70.76, 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 1668 8.00 N 1479 7.00 C 6087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 407.9 milliseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 86.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.765A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.556A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.644A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 84 through 117 removed outlier: 4.385A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.636A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.829A 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 272 removed outlier: 4.064A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.672A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 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 removed outlier: 3.685A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) 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 366 removed outlier: 4.612A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.455A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 414 through 426 removed outlier: 3.564A pdb=" N THR A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.719A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 467 removed outlier: 3.588A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 removed outlier: 3.765A pdb=" N LEU B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.557A pdb=" N PHE B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 81 removed outlier: 3.644A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix Processing helix chain 'B' and resid 84 through 117 removed outlier: 4.385A pdb=" N ILE B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.636A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (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 272 removed outlier: 4.064A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.672A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 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 removed outlier: 3.684A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) 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 366 removed outlier: 4.612A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 4.454A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 390 through 408 Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.565A pdb=" N THR B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.719A pdb=" N VAL B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA B 438 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 467 removed outlier: 3.589A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 removed outlier: 3.766A pdb=" N LEU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.557A pdb=" N PHE C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 81 removed outlier: 3.644A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 84 through 117 removed outlier: 4.385A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.635A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.828A 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 272 removed outlier: 4.064A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.673A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 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 removed outlier: 3.684A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) 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 366 removed outlier: 4.613A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 4.455A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 390 through 408 Processing helix chain 'C' and resid 414 through 426 removed outlier: 3.564A pdb=" N THR C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.720A pdb=" N VAL C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 437 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA C 438 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 467 removed outlier: 3.587A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (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 167 725 hydrogen bonds defined for protein. 2130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.19 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: 1831 1.33 - 1.45: 1904 1.45 - 1.57: 5571 1.57 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 9417 Sorted by residual: bond pdb=" N VAL B 411 " pdb=" CA VAL B 411 " ideal model delta sigma weight residual 1.461 1.489 -0.029 8.70e-03 1.32e+04 1.09e+01 bond pdb=" N VAL C 411 " pdb=" CA VAL C 411 " ideal model delta sigma weight residual 1.461 1.488 -0.028 8.70e-03 1.32e+04 1.02e+01 bond pdb=" N VAL A 411 " pdb=" CA VAL A 411 " ideal model delta sigma weight residual 1.461 1.488 -0.028 8.70e-03 1.32e+04 1.00e+01 bond pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.30e+00 bond pdb=" N VAL B 417 " pdb=" CA VAL B 417 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.03e+00 ... (remaining 9412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 11953 1.22 - 2.45: 680 2.45 - 3.67: 108 3.67 - 4.89: 33 4.89 - 6.11: 9 Bond angle restraints: 12783 Sorted by residual: angle pdb=" N ALA A 414 " pdb=" CA ALA A 414 " pdb=" C ALA A 414 " ideal model delta sigma weight residual 113.50 107.79 5.71 1.23e+00 6.61e-01 2.16e+01 angle pdb=" N ALA C 414 " pdb=" CA ALA C 414 " pdb=" C ALA C 414 " ideal model delta sigma weight residual 113.50 107.81 5.69 1.23e+00 6.61e-01 2.14e+01 angle pdb=" N ALA B 414 " pdb=" CA ALA B 414 " pdb=" C ALA B 414 " ideal model delta sigma weight residual 113.50 107.83 5.67 1.23e+00 6.61e-01 2.13e+01 angle pdb=" C ALA A 414 " pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta sigma weight residual 119.98 124.14 -4.16 1.11e+00 8.12e-01 1.40e+01 angle pdb=" C ALA C 414 " pdb=" N GLY C 415 " pdb=" CA GLY C 415 " ideal model delta sigma weight residual 119.98 124.12 -4.14 1.11e+00 8.12e-01 1.39e+01 ... (remaining 12778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5183 17.18 - 34.35: 313 34.35 - 51.53: 85 51.53 - 68.70: 29 68.70 - 85.88: 12 Dihedral angle restraints: 5622 sinusoidal: 2127 harmonic: 3495 Sorted by residual: dihedral pdb=" CG ARG C 280 " pdb=" CD ARG C 280 " pdb=" NE ARG C 280 " pdb=" CZ ARG C 280 " ideal model delta sinusoidal sigma weight residual 90.00 41.36 48.64 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG B 280 " pdb=" CD ARG B 280 " pdb=" NE ARG B 280 " pdb=" CZ ARG B 280 " ideal model delta sinusoidal sigma weight residual 90.00 41.39 48.61 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG A 280 " pdb=" CD ARG A 280 " pdb=" NE ARG A 280 " pdb=" CZ ARG A 280 " ideal model delta sinusoidal sigma weight residual 90.00 41.48 48.52 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 5619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1146 0.039 - 0.077: 384 0.077 - 0.116: 68 0.116 - 0.154: 25 0.154 - 0.193: 3 Chirality restraints: 1626 Sorted by residual: chirality pdb=" CA VAL B 411 " pdb=" N VAL B 411 " pdb=" C VAL B 411 " pdb=" CB VAL B 411 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA VAL C 411 " pdb=" N VAL C 411 " pdb=" C VAL C 411 " pdb=" CB VAL C 411 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 1623 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 39 " 0.149 9.50e-02 1.11e+02 6.74e-02 3.34e+00 pdb=" NE ARG B 39 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 39 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 39 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 39 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 39 " -0.150 9.50e-02 1.11e+02 6.75e-02 3.30e+00 pdb=" NE ARG C 39 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 39 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 39 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 39 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 39 " 0.148 9.50e-02 1.11e+02 6.69e-02 3.26e+00 pdb=" NE ARG A 39 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 39 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 39 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 39 " 0.001 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 103 2.62 - 3.19: 9119 3.19 - 3.76: 14445 3.76 - 4.33: 21323 4.33 - 4.90: 34404 Nonbonded interactions: 79394 Sorted by model distance: nonbonded pdb=" OD1 ASP B 368 " pdb="NA NA B 601 " model vdw 2.055 2.470 nonbonded pdb=" OD1 ASP C 368 " pdb="NA NA C 601 " model vdw 2.056 2.470 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.056 2.470 nonbonded pdb=" SG CYS A 269 " pdb="HG HG A 604 " model vdw 2.078 2.880 nonbonded pdb=" SG CYS C 269 " pdb="HG HG C 605 " model vdw 2.078 2.880 ... (remaining 79389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 470 or resid 601)) selection = (chain 'B' and (resid 17 through 470 or resid 602)) selection = (chain 'C' and (resid 17 through 470 or resid 602)) } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.400 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 : 0.004 0.036 9417 Z= 0.222 Angle : 0.684 6.115 12783 Z= 0.428 Chirality : 0.041 0.193 1626 Planarity : 0.005 0.068 1557 Dihedral : 13.815 85.876 3366 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1200 helix: -1.15 (0.15), residues: 945 sheet: 0.17 (0.68), residues: 54 loop : -0.06 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 39 TYR 0.018 0.004 TYR A 98 PHE 0.018 0.002 PHE C 279 TRP 0.006 0.002 TRP C 19 HIS 0.003 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9417) covalent geometry : angle 0.68358 (12783) hydrogen bonds : bond 0.19943 ( 725) hydrogen bonds : angle 7.87612 ( 2130) *********************** 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 207 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.351 Fit side-chains REVERT: A 149 MET cc_start: 0.8956 (mtm) cc_final: 0.8741 (mtp) REVERT: A 205 MET cc_start: 0.8290 (ptm) cc_final: 0.7919 (ptt) REVERT: A 229 MET cc_start: 0.8831 (mtm) cc_final: 0.8544 (mtm) REVERT: A 256 TRP cc_start: 0.8195 (m100) cc_final: 0.7427 (m-10) REVERT: A 272 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7157 (mt-10) REVERT: A 278 ILE cc_start: 0.7780 (mt) cc_final: 0.7469 (mp) REVERT: A 280 ARG cc_start: 0.7260 (ttp80) cc_final: 0.6754 (ttm170) REVERT: A 281 LYS cc_start: 0.7194 (tttt) cc_final: 0.6412 (mmtp) REVERT: A 286 MET cc_start: 0.8152 (mtp) cc_final: 0.7786 (mtm) REVERT: A 318 MET cc_start: 0.7073 (tpt) cc_final: 0.6430 (ttp) REVERT: A 352 LYS cc_start: 0.7480 (tmtt) cc_final: 0.6913 (mttt) REVERT: A 445 ARG cc_start: 0.8356 (mtt90) cc_final: 0.8140 (mtt90) REVERT: B 205 MET cc_start: 0.8425 (ptm) cc_final: 0.8108 (ptt) REVERT: B 232 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7853 (ttpt) REVERT: B 249 LYS cc_start: 0.8344 (mttt) cc_final: 0.7931 (mttm) REVERT: B 258 MET cc_start: 0.8275 (ttt) cc_final: 0.8007 (ttt) REVERT: B 260 LEU cc_start: 0.7648 (tm) cc_final: 0.7430 (tt) REVERT: B 272 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7052 (mt-10) REVERT: B 278 ILE cc_start: 0.7933 (mt) cc_final: 0.7635 (OUTLIER) REVERT: B 280 ARG cc_start: 0.7193 (ttp80) cc_final: 0.6851 (ttm170) REVERT: B 281 LYS cc_start: 0.7258 (tttt) cc_final: 0.6261 (mmtp) REVERT: B 286 MET cc_start: 0.8260 (mtp) cc_final: 0.8046 (mtm) REVERT: B 304 ILE cc_start: 0.7938 (pt) cc_final: 0.7563 (mt) REVERT: B 315 ARG cc_start: 0.7620 (tpp-160) cc_final: 0.7094 (ttm110) REVERT: B 318 MET cc_start: 0.7126 (tpt) cc_final: 0.6394 (ttp) REVERT: B 352 LYS cc_start: 0.7692 (tmtt) cc_final: 0.7186 (mttt) REVERT: B 356 ARG cc_start: 0.6689 (tpm170) cc_final: 0.6255 (ptp-170) REVERT: B 357 PHE cc_start: 0.7910 (t80) cc_final: 0.7585 (t80) REVERT: C 99 PHE cc_start: 0.7550 (t80) cc_final: 0.7295 (t80) REVERT: C 232 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7301 (tptm) REVERT: C 256 TRP cc_start: 0.8167 (m100) cc_final: 0.7421 (m-10) REVERT: C 258 MET cc_start: 0.8390 (ttt) cc_final: 0.7945 (ttt) REVERT: C 275 ASP cc_start: 0.6784 (m-30) cc_final: 0.6522 (t0) REVERT: C 278 ILE cc_start: 0.7815 (mt) cc_final: 0.7553 (mp) REVERT: C 280 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7006 (ttm170) REVERT: C 281 LYS cc_start: 0.7405 (tttt) cc_final: 0.6640 (mmtp) REVERT: C 286 MET cc_start: 0.8136 (mtp) cc_final: 0.7737 (mtt) REVERT: C 304 ILE cc_start: 0.7831 (pt) cc_final: 0.7382 (mt) REVERT: C 318 MET cc_start: 0.7420 (tpt) cc_final: 0.6849 (ttp) REVERT: C 322 GLN cc_start: 0.8159 (tt0) cc_final: 0.7752 (tt0) REVERT: C 325 LEU cc_start: 0.7877 (mt) cc_final: 0.7649 (tp) REVERT: C 352 LYS cc_start: 0.7483 (tmtt) cc_final: 0.7028 (mttt) REVERT: C 356 ARG cc_start: 0.6348 (tpm170) cc_final: 0.6131 (ptp-170) outliers start: 0 outliers final: 1 residues processed: 207 average time/residue: 0.5635 time to fit residues: 124.0529 Evaluate side-chains 167 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 252 GLN A 312 ASN A 348 ASN A 385 ASN B 211 ASN B 252 GLN C 211 ASN C 252 GLN C 312 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.185919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150085 restraints weight = 2532.073| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 0.70 r_work: 0.3129 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9417 Z= 0.147 Angle : 0.552 7.498 12783 Z= 0.293 Chirality : 0.041 0.151 1626 Planarity : 0.004 0.036 1557 Dihedral : 4.020 13.423 1281 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.47 % Allowed : 10.95 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1200 helix: 0.60 (0.16), residues: 954 sheet: 0.34 (0.75), residues: 54 loop : -0.07 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 280 TYR 0.010 0.002 TYR B 373 PHE 0.027 0.002 PHE B 222 TRP 0.006 0.001 TRP B 19 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9417) covalent geometry : angle 0.55233 (12783) hydrogen bonds : bond 0.05292 ( 725) hydrogen bonds : angle 5.00562 ( 2130) *********************** 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 197 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.332 Fit side-chains REVERT: A 40 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6807 (mt-10) REVERT: A 117 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7953 (mttm) REVERT: A 163 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7429 (pttp) REVERT: A 228 LYS cc_start: 0.8196 (mptt) cc_final: 0.6868 (mtpt) REVERT: A 229 MET cc_start: 0.8829 (mtm) cc_final: 0.8474 (mtm) REVERT: A 256 TRP cc_start: 0.8540 (m100) cc_final: 0.7731 (m-10) REVERT: A 272 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6748 (mt-10) REVERT: A 280 ARG cc_start: 0.7030 (ttp80) cc_final: 0.6524 (ttm170) REVERT: A 281 LYS cc_start: 0.6977 (tttt) cc_final: 0.6163 (mmtp) REVERT: A 286 MET cc_start: 0.8348 (mtp) cc_final: 0.8002 (mtm) REVERT: A 315 ARG cc_start: 0.7522 (tpp-160) cc_final: 0.7167 (ttm110) REVERT: A 318 MET cc_start: 0.7330 (tpt) cc_final: 0.6800 (ttm) REVERT: A 347 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7820 (m110) REVERT: A 352 LYS cc_start: 0.7093 (tmtt) cc_final: 0.6696 (mttt) REVERT: A 356 ARG cc_start: 0.6605 (tpm170) cc_final: 0.6200 (ptp-110) REVERT: A 357 PHE cc_start: 0.8275 (t80) cc_final: 0.8059 (t80) REVERT: A 359 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8219 (mp) REVERT: A 368 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: A 444 ASP cc_start: 0.7866 (t0) cc_final: 0.7638 (t0) REVERT: A 464 LYS cc_start: 0.7251 (tppp) cc_final: 0.6595 (tppt) REVERT: B 40 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: B 205 MET cc_start: 0.8495 (ptm) cc_final: 0.8182 (ptt) REVERT: B 232 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7445 (mtpt) REVERT: B 272 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6844 (mt-10) REVERT: B 281 LYS cc_start: 0.6786 (tttt) cc_final: 0.5877 (mmtp) REVERT: B 304 ILE cc_start: 0.7804 (pt) cc_final: 0.7372 (mt) REVERT: B 318 MET cc_start: 0.7198 (tpt) cc_final: 0.6558 (ttp) REVERT: B 329 MET cc_start: 0.8380 (mmt) cc_final: 0.8171 (mmt) REVERT: B 352 LYS cc_start: 0.7027 (tmtt) cc_final: 0.6644 (mttt) REVERT: B 356 ARG cc_start: 0.6828 (tpm170) cc_final: 0.6329 (ptp-110) REVERT: C 232 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7747 (mtmp) REVERT: C 256 TRP cc_start: 0.8531 (m100) cc_final: 0.7645 (m-10) REVERT: C 258 MET cc_start: 0.8200 (ttt) cc_final: 0.7894 (ttt) REVERT: C 280 ARG cc_start: 0.7375 (ttp80) cc_final: 0.6931 (ttm170) REVERT: C 281 LYS cc_start: 0.7184 (tttt) cc_final: 0.6428 (mmtp) REVERT: C 286 MET cc_start: 0.8289 (mtp) cc_final: 0.7946 (mtm) REVERT: C 304 ILE cc_start: 0.7529 (pt) cc_final: 0.7163 (mt) REVERT: C 318 MET cc_start: 0.7463 (tpt) cc_final: 0.6896 (ttp) REVERT: C 352 LYS cc_start: 0.7255 (tmtt) cc_final: 0.6808 (mttt) outliers start: 25 outliers final: 6 residues processed: 183 average time/residue: 0.5423 time to fit residues: 105.2783 Evaluate side-chains 173 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 368 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 116 optimal weight: 0.0670 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 312 ASN B 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.185427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149852 restraints weight = 2531.497| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 0.67 r_work: 0.3119 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9417 Z= 0.183 Angle : 0.564 6.868 12783 Z= 0.295 Chirality : 0.042 0.147 1626 Planarity : 0.004 0.037 1557 Dihedral : 3.926 12.186 1281 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.25 % Allowed : 11.74 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1200 helix: 0.77 (0.16), residues: 957 sheet: 0.44 (0.74), residues: 54 loop : -0.24 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 353 TYR 0.011 0.002 TYR B 373 PHE 0.016 0.002 PHE C 240 TRP 0.004 0.001 TRP B 276 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9417) covalent geometry : angle 0.56433 (12783) hydrogen bonds : bond 0.05257 ( 725) hydrogen bonds : angle 4.88388 ( 2130) *********************** 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 197 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.359 Fit side-chains REVERT: A 40 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6881 (mt-10) REVERT: A 60 MET cc_start: 0.8563 (mmm) cc_final: 0.8232 (mmm) REVERT: A 229 MET cc_start: 0.8805 (mtm) cc_final: 0.8542 (mtm) REVERT: A 256 TRP cc_start: 0.8518 (m100) cc_final: 0.7727 (m-10) REVERT: A 272 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6744 (mt-10) REVERT: A 280 ARG cc_start: 0.7113 (ttp80) cc_final: 0.6611 (ttm170) REVERT: A 281 LYS cc_start: 0.7191 (tttt) cc_final: 0.6187 (mmtp) REVERT: A 286 MET cc_start: 0.8309 (mtp) cc_final: 0.8004 (mtm) REVERT: A 318 MET cc_start: 0.7259 (tpt) cc_final: 0.6824 (ttp) REVERT: A 352 LYS cc_start: 0.7146 (tmtt) cc_final: 0.6816 (mttt) REVERT: A 356 ARG cc_start: 0.6805 (tpm170) cc_final: 0.6344 (ptp-110) REVERT: A 368 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: A 419 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.6846 (tmm) REVERT: A 444 ASP cc_start: 0.7816 (t0) cc_final: 0.7589 (t0) REVERT: B 40 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6846 (mt-10) REVERT: B 205 MET cc_start: 0.8515 (ptm) cc_final: 0.8236 (ptt) REVERT: B 232 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7532 (mtpt) REVERT: B 269 CYS cc_start: 0.7143 (t) cc_final: 0.6817 (t) REVERT: B 272 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6821 (mm-30) REVERT: B 280 ARG cc_start: 0.7239 (ttp80) cc_final: 0.6861 (ttm170) REVERT: B 281 LYS cc_start: 0.6948 (tttt) cc_final: 0.5938 (mmtp) REVERT: B 304 ILE cc_start: 0.7762 (pt) cc_final: 0.7410 (mt) REVERT: B 315 ARG cc_start: 0.7415 (tpp-160) cc_final: 0.7171 (ttm170) REVERT: B 318 MET cc_start: 0.7279 (tpt) cc_final: 0.6873 (ttp) REVERT: B 352 LYS cc_start: 0.7058 (tmtt) cc_final: 0.6703 (mttt) REVERT: B 356 ARG cc_start: 0.6861 (tpm170) cc_final: 0.6426 (ptp-110) REVERT: B 357 PHE cc_start: 0.8195 (t80) cc_final: 0.7930 (t80) REVERT: C 75 MET cc_start: 0.8349 (mmt) cc_final: 0.8075 (mmp) REVERT: C 232 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7772 (mtmt) REVERT: C 256 TRP cc_start: 0.8601 (m100) cc_final: 0.7765 (m-10) REVERT: C 258 MET cc_start: 0.8272 (ttt) cc_final: 0.7987 (ttt) REVERT: C 280 ARG cc_start: 0.7403 (ttp80) cc_final: 0.6917 (ttm170) REVERT: C 281 LYS cc_start: 0.7212 (tttt) cc_final: 0.6470 (mmtp) REVERT: C 286 MET cc_start: 0.8285 (mtp) cc_final: 0.7991 (mtm) REVERT: C 304 ILE cc_start: 0.7498 (pt) cc_final: 0.7167 (mt) REVERT: C 315 ARG cc_start: 0.7645 (tpp-160) cc_final: 0.7242 (ttm110) REVERT: C 318 MET cc_start: 0.7662 (tpt) cc_final: 0.7105 (ttp) REVERT: C 352 LYS cc_start: 0.7241 (tmtt) cc_final: 0.6872 (mttt) REVERT: C 445 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8103 (mmt180) outliers start: 33 outliers final: 15 residues processed: 176 average time/residue: 0.5701 time to fit residues: 106.9864 Evaluate side-chains 182 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 0.0370 chunk 115 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 312 ASN C 312 ASN C 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.187603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.152043 restraints weight = 2692.705| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 0.68 r_work: 0.3118 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2458 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= 0.136 Angle : 0.496 5.842 12783 Z= 0.260 Chirality : 0.039 0.139 1626 Planarity : 0.004 0.036 1557 Dihedral : 3.701 11.900 1281 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.25 % Allowed : 12.82 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1200 helix: 1.05 (0.16), residues: 960 sheet: 1.61 (0.72), residues: 48 loop : -0.25 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 353 TYR 0.011 0.001 TYR B 373 PHE 0.014 0.002 PHE B 222 TRP 0.004 0.001 TRP A 276 HIS 0.001 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9417) covalent geometry : angle 0.49576 (12783) hydrogen bonds : bond 0.04557 ( 725) hydrogen bonds : angle 4.68370 ( 2130) *********************** 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 197 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.243 Fit side-chains REVERT: A 60 MET cc_start: 0.8564 (mmm) cc_final: 0.8241 (mmm) REVERT: A 229 MET cc_start: 0.8823 (mtm) cc_final: 0.8592 (mtm) REVERT: A 231 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: A 256 TRP cc_start: 0.8515 (m100) cc_final: 0.7721 (m-10) REVERT: A 272 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6771 (mt-10) REVERT: A 280 ARG cc_start: 0.7068 (ttp80) cc_final: 0.6589 (ttm170) REVERT: A 281 LYS cc_start: 0.7188 (tttt) cc_final: 0.6180 (mmtp) REVERT: A 286 MET cc_start: 0.8277 (mtp) cc_final: 0.8007 (mtm) REVERT: A 318 MET cc_start: 0.7249 (tpt) cc_final: 0.6866 (ttp) REVERT: A 347 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8093 (m110) REVERT: A 352 LYS cc_start: 0.7155 (tmtt) cc_final: 0.6920 (mttt) REVERT: A 356 ARG cc_start: 0.6825 (tpm170) cc_final: 0.6255 (ptp-110) REVERT: A 368 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: A 419 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.6839 (tmm) REVERT: B 40 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7057 (mt-10) REVERT: B 99 PHE cc_start: 0.7977 (t80) cc_final: 0.7617 (t80) REVERT: B 205 MET cc_start: 0.8526 (ptm) cc_final: 0.8237 (ptt) REVERT: B 232 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7417 (mtpt) REVERT: B 269 CYS cc_start: 0.7295 (t) cc_final: 0.6888 (t) REVERT: B 272 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6710 (mt-10) REVERT: B 281 LYS cc_start: 0.6994 (tttt) cc_final: 0.5937 (mmtp) REVERT: B 318 MET cc_start: 0.7210 (tpt) cc_final: 0.6962 (ttp) REVERT: B 352 LYS cc_start: 0.6974 (tmtt) cc_final: 0.6635 (mttt) REVERT: B 356 ARG cc_start: 0.6753 (tpm170) cc_final: 0.6218 (ptp-110) REVERT: B 357 PHE cc_start: 0.8132 (t80) cc_final: 0.7905 (t80) REVERT: B 419 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8008 (tpp) REVERT: B 444 ASP cc_start: 0.7675 (t0) cc_final: 0.7440 (t0) REVERT: C 40 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6940 (mp0) REVERT: C 232 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7593 (mtmt) REVERT: C 256 TRP cc_start: 0.8602 (m100) cc_final: 0.7763 (m-10) REVERT: C 258 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7940 (ttt) REVERT: C 280 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6963 (ttm170) REVERT: C 281 LYS cc_start: 0.7192 (tttt) cc_final: 0.6323 (mmmm) REVERT: C 286 MET cc_start: 0.8217 (mtp) cc_final: 0.7923 (mtm) REVERT: C 307 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7360 (mt) REVERT: C 315 ARG cc_start: 0.7602 (tpp-160) cc_final: 0.7266 (ttm170) REVERT: C 318 MET cc_start: 0.7536 (tpt) cc_final: 0.7130 (ttp) REVERT: C 352 LYS cc_start: 0.7207 (tmtt) cc_final: 0.6938 (mttt) REVERT: C 445 ARG cc_start: 0.8373 (mtt90) cc_final: 0.8069 (mmt180) outliers start: 33 outliers final: 13 residues processed: 176 average time/residue: 0.4629 time to fit residues: 87.1491 Evaluate side-chains 177 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 chunk 93 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.190887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.155031 restraints weight = 2752.168| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 0.71 r_work: 0.3131 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2626 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= 0.124 Angle : 0.477 5.179 12783 Z= 0.250 Chirality : 0.039 0.183 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.563 11.481 1281 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.25 % Allowed : 14.20 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1200 helix: 1.27 (0.17), residues: 960 sheet: 0.71 (0.78), residues: 54 loop : 0.11 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 353 TYR 0.009 0.001 TYR B 373 PHE 0.013 0.001 PHE B 222 TRP 0.003 0.001 TRP B 276 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9417) covalent geometry : angle 0.47659 (12783) hydrogen bonds : bond 0.04282 ( 725) hydrogen bonds : angle 4.59131 ( 2130) *********************** 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 191 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.357 Fit side-chains REVERT: A 40 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 60 MET cc_start: 0.8572 (mmm) cc_final: 0.8212 (mmm) REVERT: A 229 MET cc_start: 0.8766 (mtm) cc_final: 0.8517 (mtm) REVERT: A 256 TRP cc_start: 0.8508 (m100) cc_final: 0.7695 (m-10) REVERT: A 272 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6832 (mt-10) REVERT: A 280 ARG cc_start: 0.7222 (ttp80) cc_final: 0.6775 (ttm170) REVERT: A 281 LYS cc_start: 0.7167 (tttt) cc_final: 0.6141 (mmtp) REVERT: A 286 MET cc_start: 0.8262 (mtp) cc_final: 0.8004 (mtm) REVERT: A 318 MET cc_start: 0.7243 (tpt) cc_final: 0.6874 (ttp) REVERT: A 356 ARG cc_start: 0.6694 (tpm170) cc_final: 0.6129 (ptp-110) REVERT: A 368 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: A 444 ASP cc_start: 0.7488 (t0) cc_final: 0.7078 (t70) REVERT: B 99 PHE cc_start: 0.7967 (t80) cc_final: 0.7577 (t80) REVERT: B 205 MET cc_start: 0.8520 (ptm) cc_final: 0.8219 (ptt) REVERT: B 232 LYS cc_start: 0.7748 (ttpt) cc_final: 0.7441 (mtpt) REVERT: B 269 CYS cc_start: 0.7214 (t) cc_final: 0.6774 (t) REVERT: B 281 LYS cc_start: 0.7103 (tttt) cc_final: 0.5951 (mmtp) REVERT: B 318 MET cc_start: 0.7197 (tpt) cc_final: 0.6965 (ttp) REVERT: B 352 LYS cc_start: 0.6993 (tmtt) cc_final: 0.6716 (mttt) REVERT: B 356 ARG cc_start: 0.6788 (tpm170) cc_final: 0.6229 (ptp-110) REVERT: B 357 PHE cc_start: 0.8102 (t80) cc_final: 0.7851 (t80) REVERT: B 419 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7934 (tpp) REVERT: C 40 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6951 (mp0) REVERT: C 232 LYS cc_start: 0.7745 (ttpt) cc_final: 0.7506 (mtmt) REVERT: C 256 TRP cc_start: 0.8582 (m100) cc_final: 0.7713 (m-10) REVERT: C 258 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7941 (ttt) REVERT: C 280 ARG cc_start: 0.7423 (ttp80) cc_final: 0.7027 (ttm170) REVERT: C 281 LYS cc_start: 0.7223 (tttt) cc_final: 0.6350 (mmmm) REVERT: C 286 MET cc_start: 0.8206 (mtp) cc_final: 0.7933 (mtm) REVERT: C 307 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7347 (mt) REVERT: C 315 ARG cc_start: 0.7600 (tpp-160) cc_final: 0.7154 (ttm170) REVERT: C 318 MET cc_start: 0.7528 (tpt) cc_final: 0.7082 (ptt) REVERT: C 352 LYS cc_start: 0.7128 (tmtt) cc_final: 0.6760 (mttt) REVERT: C 353 ARG cc_start: 0.7793 (mpp80) cc_final: 0.7574 (mpp80) REVERT: C 368 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7622 (m-30) outliers start: 33 outliers final: 11 residues processed: 171 average time/residue: 0.4648 time to fit residues: 84.9878 Evaluate side-chains 170 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 114 optimal weight: 0.0000 chunk 62 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.177984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.136592 restraints weight = 2835.938| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 0.87 r_work: 0.3086 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2701 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= 0.138 Angle : 0.499 5.091 12783 Z= 0.261 Chirality : 0.040 0.187 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.552 11.466 1281 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.06 % Allowed : 14.60 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1200 helix: 1.31 (0.17), residues: 948 sheet: 0.79 (0.78), residues: 54 loop : -0.00 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 353 TYR 0.008 0.001 TYR B 285 PHE 0.012 0.001 PHE C 240 TRP 0.003 0.001 TRP A 276 HIS 0.001 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9417) covalent geometry : angle 0.49867 (12783) hydrogen bonds : bond 0.04412 ( 725) hydrogen bonds : angle 4.63235 ( 2130) *********************** 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 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.250 Fit side-chains REVERT: A 40 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7036 (mt-10) REVERT: A 60 MET cc_start: 0.8540 (mmm) cc_final: 0.8291 (mmm) REVERT: A 256 TRP cc_start: 0.8475 (m100) cc_final: 0.7611 (m-10) REVERT: A 272 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6806 (mt-10) REVERT: A 280 ARG cc_start: 0.7200 (ttp80) cc_final: 0.6732 (ttm170) REVERT: A 281 LYS cc_start: 0.7106 (tttt) cc_final: 0.6037 (mmtp) REVERT: A 286 MET cc_start: 0.8297 (mtp) cc_final: 0.8039 (mtm) REVERT: A 318 MET cc_start: 0.7202 (tpt) cc_final: 0.6778 (ttp) REVERT: A 347 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8042 (m110) REVERT: A 356 ARG cc_start: 0.6680 (tpm170) cc_final: 0.6052 (ptp-110) REVERT: A 368 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: A 444 ASP cc_start: 0.7478 (t0) cc_final: 0.7077 (t70) REVERT: B 99 PHE cc_start: 0.7916 (t80) cc_final: 0.7507 (t80) REVERT: B 205 MET cc_start: 0.8607 (ptm) cc_final: 0.8299 (ptt) REVERT: B 232 LYS cc_start: 0.7696 (ttpt) cc_final: 0.7318 (mtpt) REVERT: B 269 CYS cc_start: 0.7416 (t) cc_final: 0.7018 (t) REVERT: B 281 LYS cc_start: 0.7025 (tttt) cc_final: 0.5847 (mmtp) REVERT: B 307 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7173 (mt) REVERT: B 318 MET cc_start: 0.7194 (tpt) cc_final: 0.6901 (ttp) REVERT: B 352 LYS cc_start: 0.6880 (tmtt) cc_final: 0.6592 (mttt) REVERT: B 356 ARG cc_start: 0.6793 (tpm170) cc_final: 0.6120 (ptp-110) REVERT: B 357 PHE cc_start: 0.8054 (t80) cc_final: 0.7766 (t80) REVERT: B 419 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7923 (tpp) REVERT: C 40 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6872 (mp0) REVERT: C 92 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6766 (mm) REVERT: C 232 LYS cc_start: 0.7761 (ttpt) cc_final: 0.7490 (mtmt) REVERT: C 256 TRP cc_start: 0.8551 (m100) cc_final: 0.7635 (m-10) REVERT: C 258 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7930 (ttt) REVERT: C 280 ARG cc_start: 0.7383 (ttp80) cc_final: 0.6956 (ttm170) REVERT: C 281 LYS cc_start: 0.7134 (tttt) cc_final: 0.6194 (mmmm) REVERT: C 286 MET cc_start: 0.8162 (mtp) cc_final: 0.7872 (mtm) REVERT: C 307 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7251 (mt) REVERT: C 315 ARG cc_start: 0.7556 (tpp-160) cc_final: 0.7039 (ttm170) REVERT: C 318 MET cc_start: 0.7499 (tpt) cc_final: 0.6997 (ptt) REVERT: C 352 LYS cc_start: 0.7147 (tmtt) cc_final: 0.6711 (mttt) REVERT: C 353 ARG cc_start: 0.7697 (mpp80) cc_final: 0.7480 (mpp80) outliers start: 31 outliers final: 13 residues processed: 167 average time/residue: 0.4642 time to fit residues: 83.0944 Evaluate side-chains 172 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 106 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN C 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.190412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.155069 restraints weight = 2764.316| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 0.69 r_work: 0.3126 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9417 Z= 0.133 Angle : 0.489 5.239 12783 Z= 0.256 Chirality : 0.039 0.175 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.523 11.425 1281 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.06 % Allowed : 14.99 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.24), residues: 1200 helix: 1.37 (0.17), residues: 948 sheet: 0.79 (0.79), residues: 54 loop : 0.01 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 353 TYR 0.008 0.001 TYR B 285 PHE 0.012 0.001 PHE C 240 TRP 0.003 0.001 TRP A 276 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9417) covalent geometry : angle 0.48916 (12783) hydrogen bonds : bond 0.04332 ( 725) hydrogen bonds : angle 4.61510 ( 2130) *********************** 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 189 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.399 Fit side-chains REVERT: A 60 MET cc_start: 0.8566 (mmm) cc_final: 0.8329 (mmm) REVERT: A 256 TRP cc_start: 0.8527 (m100) cc_final: 0.7739 (m-10) REVERT: A 272 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6883 (mt-10) REVERT: A 280 ARG cc_start: 0.7244 (ttp80) cc_final: 0.6806 (ttm170) REVERT: A 281 LYS cc_start: 0.7215 (tttt) cc_final: 0.6171 (mmtp) REVERT: A 286 MET cc_start: 0.8389 (mtp) cc_final: 0.8138 (mtm) REVERT: A 318 MET cc_start: 0.7153 (tpt) cc_final: 0.6760 (ttp) REVERT: A 347 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8064 (m110) REVERT: A 356 ARG cc_start: 0.6748 (tpm170) cc_final: 0.6225 (ptp-110) REVERT: A 357 PHE cc_start: 0.8228 (t80) cc_final: 0.8011 (t80) REVERT: A 359 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8166 (mp) REVERT: A 368 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: A 444 ASP cc_start: 0.7627 (t0) cc_final: 0.7223 (t70) REVERT: B 40 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: B 42 SER cc_start: 0.8476 (t) cc_final: 0.8242 (m) REVERT: B 99 PHE cc_start: 0.8009 (t80) cc_final: 0.7613 (t80) REVERT: B 205 MET cc_start: 0.8563 (ptm) cc_final: 0.8263 (ptt) REVERT: B 232 LYS cc_start: 0.7728 (ttpt) cc_final: 0.7427 (mtpt) REVERT: B 269 CYS cc_start: 0.7639 (t) cc_final: 0.7218 (t) REVERT: B 272 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7003 (mt-10) REVERT: B 281 LYS cc_start: 0.7169 (tttt) cc_final: 0.5974 (mmtp) REVERT: B 307 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7339 (mt) REVERT: B 318 MET cc_start: 0.7328 (tpt) cc_final: 0.7079 (ttp) REVERT: B 352 LYS cc_start: 0.6992 (tmtt) cc_final: 0.6724 (mttt) REVERT: B 356 ARG cc_start: 0.6852 (tpm170) cc_final: 0.6280 (ptp-110) REVERT: B 357 PHE cc_start: 0.8159 (t80) cc_final: 0.7865 (t80) REVERT: B 419 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8012 (tpp) REVERT: C 40 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6898 (mp0) REVERT: C 92 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6800 (mm) REVERT: C 232 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7518 (mtmt) REVERT: C 256 TRP cc_start: 0.8600 (m100) cc_final: 0.7748 (m-10) REVERT: C 258 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7944 (ttt) REVERT: C 280 ARG cc_start: 0.7458 (ttp80) cc_final: 0.7071 (ttm170) REVERT: C 281 LYS cc_start: 0.7216 (tttt) cc_final: 0.6302 (mmmm) REVERT: C 286 MET cc_start: 0.8258 (mtp) cc_final: 0.7984 (mtm) REVERT: C 307 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7388 (mt) REVERT: C 315 ARG cc_start: 0.7620 (tpp-160) cc_final: 0.7122 (ttm170) REVERT: C 318 MET cc_start: 0.7509 (tpt) cc_final: 0.7102 (ptt) REVERT: C 352 LYS cc_start: 0.7248 (tmtt) cc_final: 0.6852 (mttt) REVERT: C 368 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7696 (m-30) outliers start: 31 outliers final: 12 residues processed: 172 average time/residue: 0.5026 time to fit residues: 92.7871 Evaluate side-chains 174 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.178338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138043 restraints weight = 2847.941| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 0.83 r_work: 0.3096 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9417 Z= 0.140 Angle : 0.497 5.899 12783 Z= 0.260 Chirality : 0.040 0.198 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.527 11.446 1281 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.86 % Allowed : 15.68 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1200 helix: 1.33 (0.17), residues: 948 sheet: 1.78 (0.75), residues: 48 loop : -0.25 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.008 0.001 TYR A 285 PHE 0.013 0.001 PHE C 240 TRP 0.004 0.001 TRP A 276 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9417) covalent geometry : angle 0.49679 (12783) hydrogen bonds : bond 0.04425 ( 725) hydrogen bonds : angle 4.62589 ( 2130) *********************** 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 191 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.359 Fit side-chains REVERT: A 60 MET cc_start: 0.8559 (mmm) cc_final: 0.8302 (mmm) REVERT: A 256 TRP cc_start: 0.8477 (m100) cc_final: 0.7641 (m-10) REVERT: A 272 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6825 (mt-10) REVERT: A 280 ARG cc_start: 0.7221 (ttp80) cc_final: 0.6772 (ttm170) REVERT: A 281 LYS cc_start: 0.7160 (tttt) cc_final: 0.6083 (mmtp) REVERT: A 286 MET cc_start: 0.8332 (mtp) cc_final: 0.8067 (mtm) REVERT: A 318 MET cc_start: 0.7119 (tpt) cc_final: 0.6688 (ttp) REVERT: A 347 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7986 (m110) REVERT: A 356 ARG cc_start: 0.6720 (tpm170) cc_final: 0.6104 (ptp-110) REVERT: A 359 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8116 (mp) REVERT: A 368 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7509 (m-30) REVERT: A 444 ASP cc_start: 0.7481 (t0) cc_final: 0.7072 (t70) REVERT: B 42 SER cc_start: 0.8461 (t) cc_final: 0.8207 (m) REVERT: B 99 PHE cc_start: 0.7932 (t80) cc_final: 0.7550 (t80) REVERT: B 205 MET cc_start: 0.8568 (ptm) cc_final: 0.8257 (ptt) REVERT: B 269 CYS cc_start: 0.7407 (t) cc_final: 0.6951 (t) REVERT: B 272 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6978 (mt-10) REVERT: B 281 LYS cc_start: 0.6994 (tttt) cc_final: 0.5804 (mmtp) REVERT: B 307 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7212 (mt) REVERT: B 318 MET cc_start: 0.7191 (tpt) cc_final: 0.6933 (ttp) REVERT: B 352 LYS cc_start: 0.6883 (tmtt) cc_final: 0.6613 (mttt) REVERT: B 356 ARG cc_start: 0.6823 (tpm170) cc_final: 0.6188 (ptp-110) REVERT: B 357 PHE cc_start: 0.7999 (t80) cc_final: 0.7637 (t80) REVERT: B 419 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7968 (tpp) REVERT: C 40 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6826 (mp0) REVERT: C 42 SER cc_start: 0.8507 (t) cc_final: 0.8302 (t) REVERT: C 92 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6792 (mm) REVERT: C 232 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7490 (mtmt) REVERT: C 256 TRP cc_start: 0.8549 (m100) cc_final: 0.7647 (m-10) REVERT: C 258 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7912 (ttt) REVERT: C 280 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7011 (ttm170) REVERT: C 281 LYS cc_start: 0.7170 (tttt) cc_final: 0.6232 (mmmm) REVERT: C 286 MET cc_start: 0.8197 (mtp) cc_final: 0.7910 (mtm) REVERT: C 307 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7288 (mt) REVERT: C 315 ARG cc_start: 0.7549 (tpp-160) cc_final: 0.7030 (ttm170) REVERT: C 318 MET cc_start: 0.7375 (tpt) cc_final: 0.6895 (ptt) REVERT: C 352 LYS cc_start: 0.7133 (tmtt) cc_final: 0.6739 (mttt) REVERT: C 368 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7659 (m-30) REVERT: C 385 ASN cc_start: 0.8132 (m-40) cc_final: 0.7867 (m110) outliers start: 29 outliers final: 13 residues processed: 176 average time/residue: 0.4926 time to fit residues: 93.1431 Evaluate side-chains 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN C 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.175102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.134536 restraints weight = 2726.787| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.82 r_work: 0.3086 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2854 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= 0.136 Angle : 0.498 7.364 12783 Z= 0.260 Chirality : 0.040 0.167 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.513 11.432 1281 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.86 % Allowed : 15.68 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1200 helix: 1.35 (0.17), residues: 948 sheet: 1.64 (0.75), residues: 48 loop : -0.28 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.008 0.001 TYR A 285 PHE 0.012 0.001 PHE C 240 TRP 0.003 0.001 TRP B 276 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9417) covalent geometry : angle 0.49758 (12783) hydrogen bonds : bond 0.04355 ( 725) hydrogen bonds : angle 4.61016 ( 2130) *********************** 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 188 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.325 Fit side-chains REVERT: A 60 MET cc_start: 0.8536 (mmm) cc_final: 0.8278 (mmm) REVERT: A 92 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6409 (mm) REVERT: A 231 GLU cc_start: 0.7939 (tt0) cc_final: 0.7422 (tm-30) REVERT: A 256 TRP cc_start: 0.8446 (m100) cc_final: 0.7577 (m-10) REVERT: A 272 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6815 (mt-10) REVERT: A 280 ARG cc_start: 0.7192 (ttp80) cc_final: 0.6744 (ttm170) REVERT: A 281 LYS cc_start: 0.7113 (tttt) cc_final: 0.6023 (mmtp) REVERT: A 286 MET cc_start: 0.8273 (mtp) cc_final: 0.8003 (mtm) REVERT: A 307 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7171 (mt) REVERT: A 318 MET cc_start: 0.7027 (tpt) cc_final: 0.6611 (ttp) REVERT: A 347 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7967 (m110) REVERT: A 356 ARG cc_start: 0.6727 (tpm170) cc_final: 0.6043 (ptp-110) REVERT: A 359 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8071 (mp) REVERT: A 368 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: A 444 ASP cc_start: 0.7500 (t0) cc_final: 0.7084 (t70) REVERT: B 42 SER cc_start: 0.8434 (t) cc_final: 0.8211 (m) REVERT: B 99 PHE cc_start: 0.7880 (t80) cc_final: 0.7490 (t80) REVERT: B 205 MET cc_start: 0.8574 (ptm) cc_final: 0.8258 (ptt) REVERT: B 269 CYS cc_start: 0.7349 (t) cc_final: 0.6889 (t) REVERT: B 272 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6891 (mt-10) REVERT: B 281 LYS cc_start: 0.6875 (tttt) cc_final: 0.5711 (mmtp) REVERT: B 307 ILE cc_start: 0.7386 (OUTLIER) cc_final: 0.7135 (mt) REVERT: B 318 MET cc_start: 0.7125 (tpt) cc_final: 0.6869 (ttp) REVERT: B 352 LYS cc_start: 0.6824 (tmtt) cc_final: 0.6562 (mttt) REVERT: B 356 ARG cc_start: 0.6690 (tpm170) cc_final: 0.6059 (ptp-110) REVERT: B 357 PHE cc_start: 0.7900 (t80) cc_final: 0.7572 (t80) REVERT: B 419 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7912 (tpp) REVERT: C 40 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6806 (mp0) REVERT: C 42 SER cc_start: 0.8516 (t) cc_final: 0.8303 (t) REVERT: C 92 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6727 (mm) REVERT: C 232 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7446 (mtmt) REVERT: C 256 TRP cc_start: 0.8521 (m100) cc_final: 0.7584 (m-10) REVERT: C 258 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7927 (ttt) REVERT: C 280 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6966 (ttm170) REVERT: C 281 LYS cc_start: 0.7118 (tttt) cc_final: 0.6169 (mmmm) REVERT: C 286 MET cc_start: 0.8125 (mtp) cc_final: 0.7819 (mtm) REVERT: C 307 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7223 (mt) REVERT: C 315 ARG cc_start: 0.7513 (tpp-160) cc_final: 0.6994 (ttm170) REVERT: C 318 MET cc_start: 0.7287 (tpt) cc_final: 0.6764 (ptt) REVERT: C 352 LYS cc_start: 0.7087 (tmtt) cc_final: 0.6700 (mttt) REVERT: C 368 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: C 385 ASN cc_start: 0.8084 (m-40) cc_final: 0.7835 (m110) REVERT: C 419 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.6988 (tmm) outliers start: 29 outliers final: 10 residues processed: 172 average time/residue: 0.4952 time to fit residues: 91.5645 Evaluate side-chains 174 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 419 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.175475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134334 restraints weight = 2744.372| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 0.84 r_work: 0.3080 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2909 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= 0.132 Angle : 0.496 8.798 12783 Z= 0.259 Chirality : 0.040 0.199 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.466 11.476 1281 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.37 % Allowed : 16.07 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1200 helix: 1.38 (0.17), residues: 948 sheet: 1.53 (0.75), residues: 48 loop : -0.24 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.008 0.001 TYR A 285 PHE 0.012 0.001 PHE C 240 TRP 0.003 0.001 TRP A 276 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9417) covalent geometry : angle 0.49638 (12783) hydrogen bonds : bond 0.04299 ( 725) hydrogen bonds : angle 4.61390 ( 2130) ********************** 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 186 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.214 Fit side-chains REVERT: A 60 MET cc_start: 0.8558 (mmm) cc_final: 0.8301 (mmm) REVERT: A 92 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6437 (mm) REVERT: A 231 GLU cc_start: 0.7965 (tt0) cc_final: 0.7451 (tm-30) REVERT: A 256 TRP cc_start: 0.8520 (m100) cc_final: 0.7660 (m-10) REVERT: A 272 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6812 (mt-10) REVERT: A 274 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6901 (tp30) REVERT: A 280 ARG cc_start: 0.7209 (ttp80) cc_final: 0.6762 (ttm170) REVERT: A 281 LYS cc_start: 0.7145 (tttt) cc_final: 0.6055 (mmtp) REVERT: A 286 MET cc_start: 0.8303 (mtp) cc_final: 0.8038 (mtm) REVERT: A 307 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7191 (mt) REVERT: A 318 MET cc_start: 0.7172 (tpt) cc_final: 0.6808 (ttp) REVERT: A 347 ASN cc_start: 0.8270 (m110) cc_final: 0.7975 (m110) REVERT: A 356 ARG cc_start: 0.6659 (tpm170) cc_final: 0.6026 (ptp-110) REVERT: A 359 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8138 (mp) REVERT: A 368 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: A 444 ASP cc_start: 0.7521 (t0) cc_final: 0.7090 (t70) REVERT: B 42 SER cc_start: 0.8461 (t) cc_final: 0.8209 (m) REVERT: B 99 PHE cc_start: 0.7919 (t80) cc_final: 0.7531 (t80) REVERT: B 205 MET cc_start: 0.8592 (ptm) cc_final: 0.8281 (ptt) REVERT: B 269 CYS cc_start: 0.7425 (t) cc_final: 0.6956 (t) REVERT: B 272 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6947 (mt-10) REVERT: B 281 LYS cc_start: 0.6905 (tttt) cc_final: 0.5737 (mmtp) REVERT: B 307 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7181 (mt) REVERT: B 318 MET cc_start: 0.7143 (tpt) cc_final: 0.6897 (ttp) REVERT: B 352 LYS cc_start: 0.6844 (tmtt) cc_final: 0.6577 (mttt) REVERT: B 356 ARG cc_start: 0.6737 (tpm170) cc_final: 0.6102 (ptp-110) REVERT: B 357 PHE cc_start: 0.7956 (t80) cc_final: 0.7606 (t80) REVERT: B 419 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7918 (tpp) REVERT: C 40 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6747 (mp0) REVERT: C 42 SER cc_start: 0.8518 (t) cc_final: 0.8303 (t) REVERT: C 92 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6686 (mm) REVERT: C 232 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7471 (mtmt) REVERT: C 256 TRP cc_start: 0.8554 (m100) cc_final: 0.7633 (m-10) REVERT: C 258 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7905 (ttt) REVERT: C 280 ARG cc_start: 0.7416 (ttp80) cc_final: 0.6982 (ttm170) REVERT: C 281 LYS cc_start: 0.7138 (tttt) cc_final: 0.6188 (mmmm) REVERT: C 286 MET cc_start: 0.8169 (mtp) cc_final: 0.7869 (mtm) REVERT: C 307 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7269 (mt) REVERT: C 315 ARG cc_start: 0.7520 (tpp-160) cc_final: 0.7012 (ttm170) REVERT: C 318 MET cc_start: 0.7324 (tpt) cc_final: 0.6777 (ptt) REVERT: C 352 LYS cc_start: 0.7111 (tmtt) cc_final: 0.6721 (mttt) REVERT: C 368 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: C 385 ASN cc_start: 0.8106 (m-40) cc_final: 0.7850 (m110) outliers start: 24 outliers final: 11 residues processed: 173 average time/residue: 0.5178 time to fit residues: 95.7044 Evaluate side-chains 181 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 0.0060 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 0.0270 chunk 108 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 413 GLN B 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.177770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136957 restraints weight = 2728.250| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 0.84 r_work: 0.3134 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9417 Z= 0.113 Angle : 0.490 10.147 12783 Z= 0.255 Chirality : 0.039 0.166 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.358 11.272 1281 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.76 % Allowed : 16.17 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.24), residues: 1200 helix: 1.58 (0.17), residues: 948 sheet: 0.49 (0.79), residues: 54 loop : 0.07 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.008 0.001 TYR A 162 PHE 0.011 0.001 PHE B 222 TRP 0.007 0.001 TRP C 276 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9417) covalent geometry : angle 0.49041 (12783) hydrogen bonds : bond 0.03932 ( 725) hydrogen bonds : angle 4.51095 ( 2130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.17 seconds wall clock time: 52 minutes 28.10 seconds (3148.10 seconds total)