Starting phenix.real_space_refine on Fri Jul 3 04:36:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7da7_30624/07_2026/7da7_30624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7da7_30624/07_2026/7da7_30624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2026/7da7_30624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2026/7da7_30624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2026/7da7_30624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2026/7da7_30624.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2026/7da7_30624.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7da7_30624/07_2026/7da7_30624.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.041 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: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 28 5.16 5 C 7309 2.51 5 N 1838 2.21 5 O 2560 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11825 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5372 Classifications: {'peptide': 669} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 640} Chain breaks: 1 Chain: "B" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5372 Classifications: {'peptide': 669} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 640} Chain breaks: 1 Chain: "C" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1081 Classifications: {'RNA': 90} Modifications used: {'rna3p_pur': 42, 'rna3p_pyr': 47} Link IDs: {'rna3p': 89} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 959 Unresolved non-hydrogen angles: 1518 Unresolved non-hydrogen dihedrals: 666 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {' U%rna3p_pyr:plan': 19, ' G%rna3p_pur:plan': 23, ' G%rna3p_pur:plan2': 23, ' A%rna3p_pur:plan': 19, ' A%rna3p_pur:plan2': 19, ' C%rna3p_pyr:plan': 28, ' C%rna3p_pyr:plan2': 28, ' U:plan': 1} Unresolved non-hydrogen planarities: 965 Time building chain proxies: 2.10, per 1000 atoms: 0.18 Number of scatterers: 11825 At special positions: 0 Unit cell: (104.14, 96.76, 166.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 90 15.00 O 2560 8.00 N 1838 7.00 C 7309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 123 " distance=1.84 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 678 " distance=2.02 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 697 " distance=2.03 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 38 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 123 " distance=1.65 Simple disulfide: pdb=" SG CYS B 650 " - pdb=" SG CYS B 678 " distance=2.00 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS B 697 " distance=2.03 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: 0.58 Conformation dependent library (CDL) restraints added in 398.0 milliseconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 18 sheets defined 12.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 92 through 98 removed outlier: 4.408A pdb=" N CYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 4.483A pdb=" N PHE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 removed outlier: 4.031A pdb=" N THR A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 removed outlier: 4.483A pdb=" N GLY A 271 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.119A pdb=" N PHE A 319 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.908A pdb=" N VAL A 403 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 404 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N HIS A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.537A pdb=" N TRP A 453 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 4.206A pdb=" N TRP A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 548' Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.953A pdb=" N PHE A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Proline residue: A 633 - end of helix Processing helix chain 'A' and resid 651 through 664 removed outlier: 3.674A pdb=" N SER A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TRP A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.341A pdb=" N PHE B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.631A pdb=" N TRP B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.525A pdb=" N GLY B 271 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP B 274 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 removed outlier: 3.685A pdb=" N VAL B 403 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER B 404 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS B 407 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 454 removed outlier: 3.549A pdb=" N TRP B 453 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 removed outlier: 4.289A pdb=" N TRP B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 548 " --> pdb=" O ALA B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 543 through 548' Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.647A pdb=" N PHE B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 651 through 664 removed outlier: 3.562A pdb=" N SER B 656 " --> pdb=" O CYS B 652 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N TRP B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 692 removed outlier: 3.514A pdb=" N PHE B 692 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 7.068A pdb=" N ALA A 36 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 57 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 255 removed outlier: 7.084A pdb=" N LEU A 254 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A 304 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A 328 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 361 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU A 385 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 413 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 487 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 264 Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.611A pdb=" N LEU A 314 " --> pdb=" O ASN A 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA8, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.649A pdb=" N GLN A 446 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 470 " --> pdb=" O LYS A 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 37 removed outlier: 7.231A pdb=" N ALA B 36 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 57 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 129 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 186 through 187 Processing sheet with id=AB3, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AB4, first strand: chain 'B' and resid 253 through 255 removed outlier: 7.080A pdb=" N LEU B 254 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 304 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU B 328 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU B 361 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU B 385 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 413 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 487 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AB6, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.616A pdb=" N LEU B 314 " --> pdb=" O ASN B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 396 through 397 Processing sheet with id=AB8, first strand: chain 'B' and resid 445 through 447 removed outlier: 6.577A pdb=" N GLN B 446 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 470 " --> pdb=" O LYS B 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 640 through 641 112 hydrogen bonds defined for protein. 273 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: 1.40 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1774 1.31 - 1.44: 3186 1.44 - 1.57: 6962 1.57 - 1.70: 178 1.70 - 1.83: 36 Bond restraints: 12136 Sorted by residual: bond pdb=" C GLU A 653 " pdb=" O GLU A 653 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.33e-02 5.65e+03 2.11e+01 bond pdb=" O3' G C 18 " pdb=" P U C 19 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.50e-02 4.44e+03 1.66e+01 bond pdb=" O3' U C 29 " pdb=" P A C 30 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.48e+01 bond pdb=" O3' C C 242 " pdb=" P A C 243 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.50e-02 4.44e+03 1.43e+01 bond pdb=" O3' A C 34 " pdb=" P C C 35 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.50e-02 4.44e+03 1.41e+01 ... (remaining 12131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 16038 2.29 - 4.58: 567 4.58 - 6.87: 58 6.87 - 9.17: 14 9.17 - 11.46: 2 Bond angle restraints: 16679 Sorted by residual: angle pdb=" O3' G C 13 " pdb=" C3' G C 13 " pdb=" C2' G C 13 " ideal model delta sigma weight residual 113.70 125.16 -11.46 1.50e+00 4.44e-01 5.83e+01 angle pdb=" N PRO A 236 " pdb=" CA PRO A 236 " pdb=" C PRO A 236 " ideal model delta sigma weight residual 113.86 105.67 8.19 1.25e+00 6.40e-01 4.30e+01 angle pdb=" C4' G C 45 " pdb=" C3' G C 45 " pdb=" O3' G C 45 " ideal model delta sigma weight residual 113.00 122.59 -9.59 1.50e+00 4.44e-01 4.09e+01 angle pdb=" CA HIS A 237 " pdb=" C HIS A 237 " pdb=" O HIS A 237 " ideal model delta sigma weight residual 121.88 115.33 6.55 1.30e+00 5.92e-01 2.54e+01 angle pdb=" C4' A C 258 " pdb=" C3' A C 258 " pdb=" O3' A C 258 " ideal model delta sigma weight residual 113.00 120.48 -7.48 1.50e+00 4.44e-01 2.49e+01 ... (remaining 16674 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 7335 33.93 - 67.86: 267 67.86 - 101.79: 36 101.79 - 135.72: 0 135.72 - 169.64: 2 Dihedral angle restraints: 7640 sinusoidal: 3700 harmonic: 3940 Sorted by residual: dihedral pdb=" C5' U C 259 " pdb=" C4' U C 259 " pdb=" C3' U C 259 " pdb=" O3' U C 259 " ideal model delta sinusoidal sigma weight residual 82.00 166.03 -84.03 1 8.00e+00 1.56e-02 1.34e+02 dihedral pdb=" C4' U C 259 " pdb=" C3' U C 259 " pdb=" C2' U C 259 " pdb=" C1' U C 259 " ideal model delta sinusoidal sigma weight residual 36.00 -40.93 76.93 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" O4' U C 259 " pdb=" C4' U C 259 " pdb=" C3' U C 259 " pdb=" C2' U C 259 " ideal model delta sinusoidal sigma weight residual -35.00 38.01 -73.01 1 8.00e+00 1.56e-02 1.06e+02 ... (remaining 7637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 2027 0.177 - 0.354: 53 0.354 - 0.531: 2 0.531 - 0.708: 0 0.708 - 0.885: 1 Chirality restraints: 2083 Sorted by residual: chirality pdb=" C3' G C 13 " pdb=" C4' G C 13 " pdb=" O3' G C 13 " pdb=" C2' G C 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.59 -0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" CA PRO B 681 " pdb=" N PRO B 681 " pdb=" C PRO B 681 " pdb=" CB PRO B 681 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" C2' G C 13 " pdb=" C3' G C 13 " pdb=" O2' G C 13 " pdb=" C1' G C 13 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 2080 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 681 " -0.017 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C PRO B 681 " 0.064 2.00e-02 2.50e+03 pdb=" O PRO B 681 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS B 682 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 593 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASN B 593 " -0.061 2.00e-02 2.50e+03 pdb=" O ASN B 593 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 594 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 626 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C VAL B 626 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL B 626 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU B 627 " 0.013 2.00e-02 2.50e+03 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 202 2.64 - 3.20: 11020 3.20 - 3.77: 16869 3.77 - 4.33: 24683 4.33 - 4.90: 39765 Nonbonded interactions: 92539 Sorted by model distance: nonbonded pdb=" O HIS B 683 " pdb=" ND1 HIS B 683 " model vdw 2.072 3.120 nonbonded pdb=" O ASN A 679 " pdb=" OD1 ASN A 679 " model vdw 2.166 3.040 nonbonded pdb=" O PHE A 85 " pdb=" O2' G C 14 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN B 374 " pdb=" OG1 THR B 377 " model vdw 2.198 3.040 nonbonded pdb=" O ASN B 110 " pdb=" ND2 ASN B 134 " model vdw 2.222 3.120 ... (remaining 92534 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.090 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:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.008 0.379 12144 Z= 0.424 Angle : 1.105 47.090 16695 Z= 0.634 Chirality : 0.071 0.885 2083 Planarity : 0.005 0.049 1908 Dihedral : 16.866 169.644 5044 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.70 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -4.59 (0.19), residues: 1330 helix: -4.99 (0.17), residues: 66 sheet: -3.41 (0.32), residues: 208 loop : -3.12 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 490 TYR 0.015 0.002 TYR B 384 PHE 0.017 0.001 PHE B 687 TRP 0.031 0.002 TRP B 274 HIS 0.005 0.001 HIS B 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.38 (12136) covalent geometry : angle 0.96872 / 0.58 (16679) SS BOND : bond 0.15131 / 5.58 ( 8) SS BOND : angle 17.19117 / 9.66 ( 16) hydrogen bonds : bond 0.28454 / 19.47 ( 112) hydrogen bonds : angle 9.92393 / 6.83 ( 273) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7802 (mmm) cc_final: 0.7180 (tpp) REVERT: A 208 ASN cc_start: 0.8118 (m-40) cc_final: 0.7872 (m110) REVERT: A 460 PHE cc_start: 0.7221 (t80) cc_final: 0.6909 (t80) REVERT: A 557 ASN cc_start: 0.8682 (t0) cc_final: 0.8396 (t0) REVERT: B 178 LEU cc_start: 0.8047 (mp) cc_final: 0.7726 (tt) REVERT: B 679 ASN cc_start: 0.7986 (m-40) cc_final: 0.7662 (t0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1247 time to fit residues: 21.1561 Evaluate side-chains 48 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 62 ASN A 97 GLN A 109 HIS A 118 GLN A 137 HIS A 142 ASN A 146 ASN A 451 GLN A 467 ASN A 471 GLN A 495 ASN A 518 ASN A 585 ASN ** A 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN A 637 ASN A 646 ASN B 61 HIS B 62 ASN B 63 GLN B 71 ASN B 97 GLN B 118 GLN B 142 ASN B 146 ASN B 158 ASN B 419 HIS B 451 GLN B 467 ASN B 471 GLN B 518 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN B 646 ASN B 660 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.106404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.077054 restraints weight = 27522.465| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.00 r_work: 0.3212 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12144 Z= 0.120 Angle : 0.619 9.958 16695 Z= 0.316 Chirality : 0.041 0.240 2083 Planarity : 0.004 0.047 1908 Dihedral : 14.397 171.742 2398 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.20 % Allowed : 10.48 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -3.17 (0.21), residues: 1330 helix: -2.58 (0.48), residues: 66 sheet: -3.00 (0.32), residues: 240 loop : -1.98 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 32 TYR 0.010 0.001 TYR B 684 PHE 0.019 0.001 PHE A 122 TRP 0.009 0.001 TRP B 244 HIS 0.008 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (12136) covalent geometry : angle 0.61792 / 0.32 (16679) SS BOND : bond 0.00541 / 0.22 ( 8) SS BOND : angle 1.49725 / 0.90 ( 16) hydrogen bonds : bond 0.05316 / 3.73 ( 112) hydrogen bonds : angle 7.55096 / 5.06 ( 273) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7974 (m-80) cc_final: 0.7027 (t80) REVERT: A 128 GLU cc_start: 0.8025 (tt0) cc_final: 0.7282 (tm-30) REVERT: A 153 LEU cc_start: 0.8279 (tt) cc_final: 0.8041 (tp) REVERT: A 331 LYS cc_start: 0.8956 (tttt) cc_final: 0.8732 (ttpp) REVERT: A 445 GLU cc_start: 0.8400 (tt0) cc_final: 0.7978 (pp20) REVERT: A 460 PHE cc_start: 0.7748 (t80) cc_final: 0.7137 (t80) REVERT: A 557 ASN cc_start: 0.8737 (t0) cc_final: 0.8472 (t0) REVERT: B 132 MET cc_start: 0.8301 (mmm) cc_final: 0.8021 (mmm) REVERT: B 152 LYS cc_start: 0.8117 (mppt) cc_final: 0.7894 (mppt) REVERT: B 178 LEU cc_start: 0.8197 (mp) cc_final: 0.7716 (tt) REVERT: B 447 LYS cc_start: 0.8598 (tttp) cc_final: 0.8290 (tttp) REVERT: B 460 PHE cc_start: 0.6659 (t80) cc_final: 0.6278 (m-80) REVERT: B 637 ASN cc_start: 0.8458 (t0) cc_final: 0.8141 (t0) REVERT: B 679 ASN cc_start: 0.8325 (m-40) cc_final: 0.7673 (t0) outliers start: 15 outliers final: 3 residues processed: 81 average time/residue: 0.0832 time to fit residues: 10.5210 Evaluate side-chains 51 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 404 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 112 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 71 ASN A 77 GLN A 518 ASN B 86 ASN B 367 ASN B 682 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.101096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071783 restraints weight = 28638.887| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.01 r_work: 0.3096 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 12144 Z= 0.290 Angle : 0.713 9.721 16695 Z= 0.360 Chirality : 0.045 0.327 2083 Planarity : 0.005 0.050 1908 Dihedral : 13.953 161.158 2398 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.24 % Allowed : 13.52 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.95 (0.22), residues: 1330 helix: -1.34 (0.65), residues: 54 sheet: -3.04 (0.32), residues: 240 loop : -1.85 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 490 TYR 0.016 0.002 TYR A 327 PHE 0.019 0.002 PHE A 635 TRP 0.020 0.002 TRP B 244 HIS 0.006 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.29 (12136) covalent geometry : angle 0.71203 / 0.36 (16679) SS BOND : bond 0.00568 / 0.26 ( 8) SS BOND : angle 1.30879 / 0.69 ( 16) hydrogen bonds : bond 0.06455 / 4.56 ( 112) hydrogen bonds : angle 7.30111 / 4.91 ( 273) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7951 (m-80) cc_final: 0.7036 (t80) REVERT: A 128 GLU cc_start: 0.8150 (tt0) cc_final: 0.7692 (tm-30) REVERT: A 460 PHE cc_start: 0.7741 (t80) cc_final: 0.7095 (t80) REVERT: B 130 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6231 (t0) REVERT: B 132 MET cc_start: 0.8363 (mmm) cc_final: 0.8042 (mmm) REVERT: B 152 LYS cc_start: 0.8386 (mppt) cc_final: 0.7882 (mppt) REVERT: B 158 ASN cc_start: 0.8344 (m-40) cc_final: 0.8014 (t0) REVERT: B 178 LEU cc_start: 0.8171 (mp) cc_final: 0.7840 (mp) REVERT: B 460 PHE cc_start: 0.6910 (t80) cc_final: 0.6660 (m-80) REVERT: B 461 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: B 511 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8643 (mt) REVERT: B 637 ASN cc_start: 0.8712 (t0) cc_final: 0.8361 (t0) REVERT: B 679 ASN cc_start: 0.8476 (m-40) cc_final: 0.7905 (t0) outliers start: 28 outliers final: 15 residues processed: 77 average time/residue: 0.0831 time to fit residues: 10.1576 Evaluate side-chains 65 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 40 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 518 ASN B 367 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.102688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.073406 restraints weight = 28282.172| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.02 r_work: 0.3133 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12144 Z= 0.151 Angle : 0.571 8.858 16695 Z= 0.288 Chirality : 0.041 0.277 2083 Planarity : 0.004 0.047 1908 Dihedral : 13.650 161.639 2398 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.60 % Allowed : 15.52 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.52 (0.23), residues: 1330 helix: -0.20 (0.85), residues: 42 sheet: -2.93 (0.32), residues: 242 loop : -1.51 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 435 TYR 0.007 0.001 TYR A 327 PHE 0.013 0.001 PHE A 122 TRP 0.010 0.001 TRP B 244 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (12136) covalent geometry : angle 0.57066 / 0.29 (16679) SS BOND : bond 0.00338 / 0.15 ( 8) SS BOND : angle 1.00812 / 0.54 ( 16) hydrogen bonds : bond 0.04708 / 3.30 ( 112) hydrogen bonds : angle 6.80071 / 4.56 ( 273) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8149 (tt0) cc_final: 0.7680 (tm-30) REVERT: A 460 PHE cc_start: 0.7670 (t80) cc_final: 0.7043 (t80) REVERT: A 557 ASN cc_start: 0.8746 (t0) cc_final: 0.8482 (t0) REVERT: B 132 MET cc_start: 0.8358 (mmm) cc_final: 0.8052 (mmm) REVERT: B 152 LYS cc_start: 0.8432 (mppt) cc_final: 0.7891 (mppt) REVERT: B 158 ASN cc_start: 0.8346 (m-40) cc_final: 0.7846 (t0) REVERT: B 178 LEU cc_start: 0.8147 (mp) cc_final: 0.7932 (mp) REVERT: B 211 LYS cc_start: 0.9339 (tppt) cc_final: 0.8213 (mtmt) REVERT: B 447 LYS cc_start: 0.8729 (tttp) cc_final: 0.8440 (tttp) REVERT: B 460 PHE cc_start: 0.6933 (t80) cc_final: 0.6508 (m-80) REVERT: B 637 ASN cc_start: 0.8754 (t0) cc_final: 0.8370 (t0) REVERT: B 679 ASN cc_start: 0.8498 (m-40) cc_final: 0.7784 (t0) outliers start: 20 outliers final: 10 residues processed: 73 average time/residue: 0.0925 time to fit residues: 10.3627 Evaluate side-chains 56 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 0.0170 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.0020 chunk 83 optimal weight: 5.9990 overall best weight: 0.8630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 ASN B 367 ASN B 518 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.103690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.074525 restraints weight = 28024.315| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.01 r_work: 0.3160 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12144 Z= 0.108 Angle : 0.537 12.145 16695 Z= 0.269 Chirality : 0.040 0.260 2083 Planarity : 0.004 0.045 1908 Dihedral : 13.314 161.193 2398 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.52 % Allowed : 16.80 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.31 (0.23), residues: 1330 helix: -1.10 (0.72), residues: 56 sheet: -2.68 (0.34), residues: 232 loop : -1.37 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 435 TYR 0.005 0.001 TYR A 308 PHE 0.012 0.001 PHE A 122 TRP 0.007 0.001 TRP B 244 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (12136) covalent geometry : angle 0.53672 / 0.27 (16679) SS BOND : bond 0.00477 / 0.34 ( 8) SS BOND : angle 1.05281 / 0.61 ( 16) hydrogen bonds : bond 0.03985 / 2.79 ( 112) hydrogen bonds : angle 6.40820 / 4.29 ( 273) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8131 (tt0) cc_final: 0.7677 (tm-30) REVERT: A 445 GLU cc_start: 0.8478 (tt0) cc_final: 0.8073 (pp20) REVERT: A 460 PHE cc_start: 0.7621 (t80) cc_final: 0.6937 (t80) REVERT: A 557 ASN cc_start: 0.8694 (t0) cc_final: 0.8487 (t0) REVERT: B 132 MET cc_start: 0.8278 (mmm) cc_final: 0.8038 (mmm) REVERT: B 152 LYS cc_start: 0.8483 (mppt) cc_final: 0.7980 (mppt) REVERT: B 158 ASN cc_start: 0.8213 (m-40) cc_final: 0.7745 (t0) REVERT: B 447 LYS cc_start: 0.8671 (tttp) cc_final: 0.8361 (tttp) REVERT: B 461 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: B 511 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8622 (mt) REVERT: B 637 ASN cc_start: 0.8779 (t0) cc_final: 0.8418 (t0) REVERT: B 650 CYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8795 (m) REVERT: B 679 ASN cc_start: 0.8484 (m-40) cc_final: 0.7794 (t0) outliers start: 19 outliers final: 9 residues processed: 70 average time/residue: 0.0895 time to fit residues: 9.6891 Evaluate side-chains 59 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 8 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 137 optimal weight: 50.0000 chunk 33 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.101303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072257 restraints weight = 28415.780| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.02 r_work: 0.3110 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12144 Z= 0.195 Angle : 0.594 11.097 16695 Z= 0.297 Chirality : 0.042 0.269 2083 Planarity : 0.004 0.043 1908 Dihedral : 13.267 159.926 2398 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.16 % Allowed : 16.80 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.34 (0.23), residues: 1330 helix: -1.32 (0.69), residues: 56 sheet: -2.71 (0.33), residues: 230 loop : -1.37 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 435 TYR 0.011 0.001 TYR A 327 PHE 0.011 0.001 PHE A 635 TRP 0.009 0.001 TRP B 244 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (12136) covalent geometry : angle 0.59309 / 0.30 (16679) SS BOND : bond 0.00421 / 0.20 ( 8) SS BOND : angle 1.01114 / 0.57 ( 16) hydrogen bonds : bond 0.04914 / 3.41 ( 112) hydrogen bonds : angle 6.56637 / 4.42 ( 273) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8161 (tt0) cc_final: 0.7681 (tm-30) REVERT: A 445 GLU cc_start: 0.8523 (tt0) cc_final: 0.8113 (pp20) REVERT: A 460 PHE cc_start: 0.7717 (t80) cc_final: 0.7061 (t80) REVERT: A 557 ASN cc_start: 0.8807 (t0) cc_final: 0.8554 (t0) REVERT: B 132 MET cc_start: 0.8157 (mmm) cc_final: 0.7916 (mmm) REVERT: B 134 ASN cc_start: 0.5549 (OUTLIER) cc_final: 0.4719 (m110) REVERT: B 511 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8619 (mt) REVERT: B 637 ASN cc_start: 0.8831 (t0) cc_final: 0.8415 (t0) outliers start: 27 outliers final: 15 residues processed: 69 average time/residue: 0.0788 time to fit residues: 9.1682 Evaluate side-chains 59 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 6 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.0670 chunk 136 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070441 restraints weight = 28882.505| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.02 r_work: 0.3060 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 12144 Z= 0.329 Angle : 0.723 10.141 16695 Z= 0.366 Chirality : 0.046 0.296 2083 Planarity : 0.005 0.048 1908 Dihedral : 13.765 159.909 2398 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 2.40 % Allowed : 17.04 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.65 (0.23), residues: 1330 helix: -1.73 (0.67), residues: 56 sheet: -2.68 (0.35), residues: 214 loop : -1.68 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 457 TYR 0.017 0.002 TYR A 327 PHE 0.015 0.002 PHE B 635 TRP 0.012 0.001 TRP B 244 HIS 0.006 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.33 (12136) covalent geometry : angle 0.72144 / 0.37 (16679) SS BOND : bond 0.00764 / 0.36 ( 8) SS BOND : angle 1.84123 / 1.02 ( 16) hydrogen bonds : bond 0.06069 / 4.19 ( 112) hydrogen bonds : angle 7.04773 / 4.80 ( 273) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 46 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6770 (t80) REVERT: A 128 GLU cc_start: 0.8212 (tt0) cc_final: 0.7732 (tm-30) REVERT: A 460 PHE cc_start: 0.7651 (t80) cc_final: 0.6969 (t80) REVERT: B 132 MET cc_start: 0.8122 (mmm) cc_final: 0.7881 (mmm) REVERT: B 134 ASN cc_start: 0.5741 (OUTLIER) cc_final: 0.4917 (m110) REVERT: B 176 GLU cc_start: 0.8008 (tt0) cc_final: 0.7764 (mp0) REVERT: B 511 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8667 (mt) REVERT: B 637 ASN cc_start: 0.8920 (t0) cc_final: 0.8599 (t0) outliers start: 30 outliers final: 19 residues processed: 72 average time/residue: 0.0844 time to fit residues: 9.9025 Evaluate side-chains 66 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.101904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073274 restraints weight = 28356.746| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.01 r_work: 0.3133 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12144 Z= 0.116 Angle : 0.551 9.563 16695 Z= 0.275 Chirality : 0.040 0.252 2083 Planarity : 0.004 0.041 1908 Dihedral : 13.469 161.573 2398 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.68 % Allowed : 17.84 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.29 (0.24), residues: 1330 helix: -0.97 (0.72), residues: 56 sheet: -2.72 (0.34), residues: 230 loop : -1.34 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 435 TYR 0.006 0.001 TYR B 684 PHE 0.011 0.001 PHE A 122 TRP 0.005 0.001 TRP B 244 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (12136) covalent geometry : angle 0.55023 / 0.27 (16679) SS BOND : bond 0.00270 / 0.14 ( 8) SS BOND : angle 1.29806 / 0.74 ( 16) hydrogen bonds : bond 0.04066 / 2.83 ( 112) hydrogen bonds : angle 6.41568 / 4.35 ( 273) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7033 (t80) REVERT: A 128 GLU cc_start: 0.8131 (tt0) cc_final: 0.7712 (tm-30) REVERT: A 208 ASN cc_start: 0.8753 (m-40) cc_final: 0.8451 (m110) REVERT: A 445 GLU cc_start: 0.8522 (tt0) cc_final: 0.8144 (pp20) REVERT: A 460 PHE cc_start: 0.7629 (t80) cc_final: 0.6909 (t80) REVERT: A 557 ASN cc_start: 0.8735 (t0) cc_final: 0.8517 (t0) REVERT: B 130 ASP cc_start: 0.7151 (t0) cc_final: 0.6425 (t0) REVERT: B 132 MET cc_start: 0.8126 (mmm) cc_final: 0.7804 (mmm) REVERT: B 134 ASN cc_start: 0.5468 (OUTLIER) cc_final: 0.4616 (m110) REVERT: B 211 LYS cc_start: 0.9350 (tppt) cc_final: 0.8121 (mtmt) REVERT: B 364 ASP cc_start: 0.8091 (m-30) cc_final: 0.7587 (m-30) REVERT: B 447 LYS cc_start: 0.8576 (tttp) cc_final: 0.7592 (tptt) REVERT: B 471 GLN cc_start: 0.8955 (tt0) cc_final: 0.8448 (tt0) REVERT: B 511 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8604 (mt) REVERT: B 637 ASN cc_start: 0.8818 (t0) cc_final: 0.8464 (t0) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.0892 time to fit residues: 10.8389 Evaluate side-chains 66 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 7 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.099688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071321 restraints weight = 28641.958| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.01 r_work: 0.3089 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12144 Z= 0.214 Angle : 0.613 8.999 16695 Z= 0.306 Chirality : 0.042 0.280 2083 Planarity : 0.004 0.041 1908 Dihedral : 13.521 159.534 2398 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 1.76 % Allowed : 17.84 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.39 (0.24), residues: 1330 helix: -1.14 (0.72), residues: 56 sheet: -2.81 (0.33), residues: 230 loop : -1.40 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.011 0.001 TYR B 284 PHE 0.011 0.001 PHE A 607 TRP 0.008 0.001 TRP B 244 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (12136) covalent geometry : angle 0.61150 / 0.31 (16679) SS BOND : bond 0.00433 / 0.20 ( 8) SS BOND : angle 1.29381 / 0.73 ( 16) hydrogen bonds : bond 0.05055 / 3.50 ( 112) hydrogen bonds : angle 6.63176 / 4.49 ( 273) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7135 (t80) REVERT: A 128 GLU cc_start: 0.8184 (tt0) cc_final: 0.7749 (tm-30) REVERT: A 445 GLU cc_start: 0.8530 (tt0) cc_final: 0.8157 (pp20) REVERT: A 460 PHE cc_start: 0.7683 (t80) cc_final: 0.6961 (t80) REVERT: A 557 ASN cc_start: 0.8834 (t0) cc_final: 0.8597 (t0) REVERT: B 132 MET cc_start: 0.8119 (mmm) cc_final: 0.7849 (mmm) REVERT: B 134 ASN cc_start: 0.5483 (OUTLIER) cc_final: 0.4595 (m110) REVERT: B 211 LYS cc_start: 0.9362 (tppt) cc_final: 0.8132 (mtmt) REVERT: B 511 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8632 (mt) REVERT: B 637 ASN cc_start: 0.8878 (t0) cc_final: 0.8485 (t0) outliers start: 22 outliers final: 17 residues processed: 67 average time/residue: 0.0895 time to fit residues: 10.0161 Evaluate side-chains 65 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 56 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 131 optimal weight: 0.0570 chunk 128 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.101986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.073530 restraints weight = 28467.521| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.04 r_work: 0.3144 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12144 Z= 0.092 Angle : 0.535 8.908 16695 Z= 0.264 Chirality : 0.039 0.243 2083 Planarity : 0.004 0.041 1908 Dihedral : 13.339 160.969 2398 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.52 % Allowed : 17.92 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.13 (0.24), residues: 1330 helix: -0.76 (0.73), residues: 56 sheet: -2.66 (0.34), residues: 232 loop : -1.21 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 435 TYR 0.006 0.001 TYR B 303 PHE 0.013 0.001 PHE B 122 TRP 0.006 0.001 TRP A 657 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.09 (12136) covalent geometry : angle 0.53423 / 0.26 (16679) SS BOND : bond 0.00195 / 0.11 ( 8) SS BOND : angle 1.06060 / 0.60 ( 16) hydrogen bonds : bond 0.03765 / 2.61 ( 112) hydrogen bonds : angle 6.20216 / 4.18 ( 273) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7136 (t80) REVERT: A 128 GLU cc_start: 0.8111 (tt0) cc_final: 0.7728 (tm-30) REVERT: A 208 ASN cc_start: 0.8731 (m-40) cc_final: 0.8457 (m110) REVERT: A 445 GLU cc_start: 0.8484 (tt0) cc_final: 0.8136 (pp20) REVERT: A 460 PHE cc_start: 0.7621 (t80) cc_final: 0.6948 (t80) REVERT: B 130 ASP cc_start: 0.7150 (t0) cc_final: 0.6417 (t0) REVERT: B 132 MET cc_start: 0.8046 (mmm) cc_final: 0.7732 (mmm) REVERT: B 134 ASN cc_start: 0.5461 (OUTLIER) cc_final: 0.4594 (m110) REVERT: B 211 LYS cc_start: 0.9342 (tppt) cc_final: 0.8129 (mtmt) REVERT: B 364 ASP cc_start: 0.8006 (m-30) cc_final: 0.7446 (m-30) REVERT: B 447 LYS cc_start: 0.8571 (tttp) cc_final: 0.8190 (tptp) REVERT: B 511 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8591 (mt) REVERT: B 637 ASN cc_start: 0.8828 (t0) cc_final: 0.8489 (t0) outliers start: 19 outliers final: 16 residues processed: 70 average time/residue: 0.0870 time to fit residues: 10.1271 Evaluate side-chains 70 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 32 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 0.0670 chunk 72 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.101998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.073504 restraints weight = 28419.356| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.04 r_work: 0.3144 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12144 Z= 0.100 Angle : 0.526 8.569 16695 Z= 0.259 Chirality : 0.039 0.241 2083 Planarity : 0.004 0.041 1908 Dihedral : 13.138 159.998 2398 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.52 % Allowed : 18.16 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.06 (0.24), residues: 1330 helix: -0.62 (0.75), residues: 56 sheet: -2.58 (0.34), residues: 232 loop : -1.18 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.006 0.001 TYR B 303 PHE 0.011 0.001 PHE B 122 TRP 0.005 0.001 TRP A 657 HIS 0.003 0.000 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (12136) covalent geometry : angle 0.52572 / 0.26 (16679) SS BOND : bond 0.00212 / 0.11 ( 8) SS BOND : angle 0.99770 / 0.56 ( 16) hydrogen bonds : bond 0.03667 / 2.53 ( 112) hydrogen bonds : angle 6.07579 / 4.10 ( 273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2628.50 seconds wall clock time: 46 minutes 0.36 seconds (2760.36 seconds total)