Starting phenix.real_space_refine on Wed Mar 4 08:21:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7da7_30624/03_2026/7da7_30624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7da7_30624/03_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_30624/03_2026/7da7_30624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7da7_30624/03_2026/7da7_30624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7da7_30624/03_2026/7da7_30624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7da7_30624/03_2026/7da7_30624.map" } 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-5986/lib/python3.9/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: 935 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: 2.96, per 1000 atoms: 0.25 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: 0.90 Conformation dependent library (CDL) restraints added in 517.2 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: 1.24 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: 1.88 Time building geometry restraints manager: 1.24 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: 7410 33.93 - 67.86: 333 67.86 - 101.79: 36 101.79 - 135.72: 0 135.72 - 169.64: 2 Dihedral angle restraints: 7781 sinusoidal: 3841 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 7778 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: 3.650 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 17.749 169.644 5185 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 covalent geometry : bond 0.00731 (12136) covalent geometry : angle 0.96872 (16679) SS BOND : bond 0.15131 ( 8) SS BOND : angle 17.19117 ( 16) hydrogen bonds : bond 0.28454 ( 112) hydrogen bonds : angle 9.92393 ( 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 : 0.423 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: 0.1345 time to fit residues: 22.8157 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 : 0.644 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.106448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.077067 restraints weight = 27512.078| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.00 r_work: 0.3212 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12144 Z= 0.121 Angle : 0.617 9.832 16695 Z= 0.315 Chirality : 0.041 0.205 2083 Planarity : 0.004 0.046 1908 Dihedral : 16.710 171.005 2539 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.20 % Allowed : 10.40 % Favored : 88.40 % 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: -3.18 (0.21), residues: 1330 helix: -2.57 (0.48), residues: 66 sheet: -3.04 (0.32), residues: 238 loop : -1.99 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 435 TYR 0.010 0.001 TYR B 684 PHE 0.016 0.001 PHE A 122 TRP 0.010 0.001 TRP B 244 HIS 0.009 0.001 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00274 (12136) covalent geometry : angle 0.61536 (16679) SS BOND : bond 0.00337 ( 8) SS BOND : angle 1.46446 ( 16) hydrogen bonds : bond 0.05295 ( 112) hydrogen bonds : angle 7.52068 ( 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 80 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8003 (m-80) cc_final: 0.7031 (t80) REVERT: A 128 GLU cc_start: 0.8018 (tt0) cc_final: 0.7242 (tm-30) REVERT: A 153 LEU cc_start: 0.8237 (tt) cc_final: 0.8006 (tp) REVERT: A 331 LYS cc_start: 0.8886 (tttt) cc_final: 0.8654 (ttpp) REVERT: A 445 GLU cc_start: 0.8429 (tt0) cc_final: 0.7962 (pp20) REVERT: A 460 PHE cc_start: 0.7724 (t80) cc_final: 0.7097 (t80) REVERT: A 557 ASN cc_start: 0.8724 (t0) cc_final: 0.8457 (t0) REVERT: B 132 MET cc_start: 0.8326 (mmm) cc_final: 0.8058 (mmm) REVERT: B 152 LYS cc_start: 0.8091 (mppt) cc_final: 0.7839 (mppt) REVERT: B 178 LEU cc_start: 0.8171 (mp) cc_final: 0.7699 (tt) REVERT: B 447 LYS cc_start: 0.8583 (tttp) cc_final: 0.8305 (tttp) REVERT: B 460 PHE cc_start: 0.6595 (t80) cc_final: 0.6224 (m-80) REVERT: B 637 ASN cc_start: 0.8485 (t0) cc_final: 0.8168 (t0) REVERT: B 679 ASN cc_start: 0.8334 (m-40) cc_final: 0.7639 (t0) outliers start: 15 outliers final: 3 residues processed: 80 average time/residue: 0.0976 time to fit residues: 12.1774 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 : 0.442 ------------------------------------------------------------------------------- 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: 0.9980 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 0.0370 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 71 ASN A 77 GLN A 157 HIS A 518 ASN B 86 ASN ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.100723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071379 restraints weight = 28758.531| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.00 r_work: 0.3087 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 12144 Z= 0.301 Angle : 0.739 10.026 16695 Z= 0.373 Chirality : 0.046 0.347 2083 Planarity : 0.005 0.050 1908 Dihedral : 16.425 161.193 2539 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.32 % Allowed : 13.92 % Favored : 83.76 % 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: -2.98 (0.22), residues: 1330 helix: -1.63 (0.65), residues: 54 sheet: -3.06 (0.31), residues: 240 loop : -1.86 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 490 TYR 0.019 0.002 TYR A 327 PHE 0.021 0.002 PHE A 635 TRP 0.022 0.002 TRP B 244 HIS 0.007 0.002 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00711 (12136) covalent geometry : angle 0.73893 (16679) SS BOND : bond 0.00580 ( 8) SS BOND : angle 1.10624 ( 16) hydrogen bonds : bond 0.06638 ( 112) hydrogen bonds : angle 7.30358 ( 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 82 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8027 (m-80) cc_final: 0.7195 (t80) REVERT: A 128 GLU cc_start: 0.8188 (tt0) cc_final: 0.7703 (tm-30) REVERT: A 460 PHE cc_start: 0.7710 (t80) cc_final: 0.7055 (t80) REVERT: B 130 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6180 (t0) REVERT: B 132 MET cc_start: 0.8352 (mmm) cc_final: 0.8020 (mmm) REVERT: B 152 LYS cc_start: 0.8425 (mppt) cc_final: 0.7961 (mppt) REVERT: B 158 ASN cc_start: 0.8225 (m-40) cc_final: 0.8015 (t0) REVERT: B 178 LEU cc_start: 0.8150 (mp) cc_final: 0.7842 (mp) REVERT: B 460 PHE cc_start: 0.6902 (t80) cc_final: 0.6634 (m-80) REVERT: B 461 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: B 511 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8630 (mt) REVERT: B 637 ASN cc_start: 0.8737 (t0) cc_final: 0.8375 (t0) REVERT: B 679 ASN cc_start: 0.8475 (m-40) cc_final: 0.7917 (t0) outliers start: 29 outliers final: 14 residues processed: 78 average time/residue: 0.0923 time to fit residues: 11.4734 Evaluate side-chains 63 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 71 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 0.0060 chunk 50 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 518 ASN B 71 ASN B 367 ASN ** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.103328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073974 restraints weight = 28128.823| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.02 r_work: 0.3146 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12144 Z= 0.119 Angle : 0.551 8.577 16695 Z= 0.278 Chirality : 0.040 0.267 2083 Planarity : 0.004 0.046 1908 Dihedral : 16.030 162.112 2539 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.36 % Allowed : 16.16 % Favored : 82.48 % 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: -2.44 (0.23), residues: 1330 helix: -0.06 (0.85), residues: 42 sheet: -2.87 (0.32), residues: 242 loop : -1.46 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 435 TYR 0.006 0.001 TYR B 684 PHE 0.013 0.001 PHE A 122 TRP 0.008 0.001 TRP B 244 HIS 0.004 0.001 HIS B 45 Details of bonding type rmsd covalent geometry : bond 0.00284 (12136) covalent geometry : angle 0.55006 (16679) SS BOND : bond 0.00279 ( 8) SS BOND : angle 0.91884 ( 16) hydrogen bonds : bond 0.04402 ( 112) hydrogen bonds : angle 6.69730 ( 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 69 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8134 (tt0) cc_final: 0.7670 (tm-30) REVERT: A 460 PHE cc_start: 0.7667 (t80) cc_final: 0.6998 (t80) REVERT: A 557 ASN cc_start: 0.8722 (t0) cc_final: 0.8472 (t0) REVERT: B 132 MET cc_start: 0.8387 (mmm) cc_final: 0.8080 (mmm) REVERT: B 152 LYS cc_start: 0.8445 (mppt) cc_final: 0.7947 (mppt) REVERT: B 158 ASN cc_start: 0.8300 (m-40) cc_final: 0.7785 (t0) REVERT: B 211 LYS cc_start: 0.9310 (tppt) cc_final: 0.8219 (mtmt) REVERT: B 447 LYS cc_start: 0.8742 (tttp) cc_final: 0.8447 (tttp) REVERT: B 460 PHE cc_start: 0.6920 (t80) cc_final: 0.6500 (m-80) REVERT: B 637 ASN cc_start: 0.8730 (t0) cc_final: 0.8365 (t0) REVERT: B 679 ASN cc_start: 0.8465 (m-40) cc_final: 0.7788 (t0) outliers start: 17 outliers final: 7 residues processed: 69 average time/residue: 0.0903 time to fit residues: 9.9064 Evaluate side-chains 53 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR 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 404 SER 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: 5.9990 chunk 128 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN B 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.101321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.072242 restraints weight = 28245.071| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.00 r_work: 0.3108 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12144 Z= 0.210 Angle : 0.609 11.419 16695 Z= 0.306 Chirality : 0.042 0.283 2083 Planarity : 0.004 0.044 1908 Dihedral : 15.868 160.301 2539 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.00 % Allowed : 16.48 % Favored : 81.52 % 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: -2.47 (0.23), residues: 1330 helix: -1.50 (0.68), residues: 56 sheet: -2.75 (0.33), residues: 230 loop : -1.48 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.012 0.001 TYR A 327 PHE 0.011 0.001 PHE B 631 TRP 0.009 0.001 TRP B 244 HIS 0.007 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00502 (12136) covalent geometry : angle 0.60804 (16679) SS BOND : bond 0.00930 ( 8) SS BOND : angle 1.19640 ( 16) hydrogen bonds : bond 0.05055 ( 112) hydrogen bonds : angle 6.66921 ( 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 73 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8197 (tt0) cc_final: 0.7737 (tm-30) REVERT: A 246 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (tt) REVERT: A 460 PHE cc_start: 0.7705 (t80) cc_final: 0.7013 (t80) REVERT: A 557 ASN cc_start: 0.8780 (t0) cc_final: 0.8511 (t0) REVERT: B 152 LYS cc_start: 0.8482 (mppt) cc_final: 0.7903 (mppt) REVERT: B 176 GLU cc_start: 0.8083 (tt0) cc_final: 0.7822 (mp0) REVERT: B 447 LYS cc_start: 0.8702 (tttp) cc_final: 0.8486 (tttp) REVERT: B 460 PHE cc_start: 0.6939 (t80) cc_final: 0.6546 (m-80) REVERT: B 511 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8622 (mt) REVERT: B 637 ASN cc_start: 0.8801 (t0) cc_final: 0.8399 (t0) REVERT: B 679 ASN cc_start: 0.8544 (m-40) cc_final: 0.7897 (t0) outliers start: 25 outliers final: 15 residues processed: 70 average time/residue: 0.0887 time to fit residues: 10.1050 Evaluate side-chains 61 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 246 LEU 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 588 GLU 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 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: 5.9990 chunk 74 optimal weight: 20.0000 chunk 137 optimal weight: 50.0000 chunk 33 optimal weight: 0.8980 chunk 118 optimal weight: 0.0980 chunk 86 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 0.0270 chunk 56 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 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 = 0.3877 r_free = 0.3877 target = 0.104058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.075022 restraints weight = 28223.516| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.02 r_work: 0.3169 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12144 Z= 0.089 Angle : 0.526 11.116 16695 Z= 0.261 Chirality : 0.039 0.252 2083 Planarity : 0.004 0.041 1908 Dihedral : 15.479 162.094 2539 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.52 % Allowed : 17.76 % Favored : 80.72 % 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: -2.19 (0.23), residues: 1330 helix: -0.97 (0.72), residues: 56 sheet: -2.40 (0.36), residues: 204 loop : -1.39 (0.20), residues: 1070 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 0.012 0.001 PHE A 122 TRP 0.005 0.000 TRP A 657 HIS 0.003 0.000 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00208 (12136) covalent geometry : angle 0.52549 (16679) SS BOND : bond 0.00250 ( 8) SS BOND : angle 0.78776 ( 16) hydrogen bonds : bond 0.03579 ( 112) hydrogen bonds : angle 6.24341 ( 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 76 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8131 (tt0) cc_final: 0.7662 (tm-30) REVERT: A 208 ASN cc_start: 0.8685 (m-40) cc_final: 0.8404 (m110) REVERT: A 445 GLU cc_start: 0.8483 (tt0) cc_final: 0.8079 (pp20) REVERT: A 460 PHE cc_start: 0.7663 (t80) cc_final: 0.7012 (t80) REVERT: B 134 ASN cc_start: 0.5557 (OUTLIER) cc_final: 0.5081 (m-40) REVERT: B 152 LYS cc_start: 0.8475 (mppt) cc_final: 0.7968 (mppt) REVERT: B 211 LYS cc_start: 0.9326 (tppt) cc_final: 0.8145 (mtmt) REVERT: B 364 ASP cc_start: 0.7930 (m-30) cc_final: 0.7375 (m-30) REVERT: B 447 LYS cc_start: 0.8695 (tttp) cc_final: 0.8362 (tttp) REVERT: B 460 PHE cc_start: 0.6966 (t80) cc_final: 0.6552 (m-80) REVERT: B 511 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8589 (mt) REVERT: B 637 ASN cc_start: 0.8793 (t0) cc_final: 0.8427 (t0) REVERT: B 650 CYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8794 (m) REVERT: B 679 ASN cc_start: 0.8554 (m-40) cc_final: 0.7881 (t0) outliers start: 19 outliers final: 7 residues processed: 74 average time/residue: 0.0869 time to fit residues: 10.3452 Evaluate side-chains 61 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 SER 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: 9.9990 chunk 75 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.3980 chunk 136 optimal weight: 40.0000 chunk 14 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN B 109 HIS ** B 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.099012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070154 restraints weight = 28865.081| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.01 r_work: 0.3060 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 12144 Z= 0.347 Angle : 0.737 10.321 16695 Z= 0.368 Chirality : 0.046 0.148 2083 Planarity : 0.005 0.042 1908 Dihedral : 15.778 160.042 2539 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 2.40 % Allowed : 16.48 % Favored : 81.12 % 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: -2.56 (0.23), residues: 1330 helix: -1.61 (0.67), residues: 56 sheet: -2.67 (0.36), residues: 204 loop : -1.62 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 313 TYR 0.016 0.002 TYR A 327 PHE 0.018 0.002 PHE B 631 TRP 0.010 0.001 TRP B 244 HIS 0.009 0.001 HIS B 109 Details of bonding type rmsd covalent geometry : bond 0.00823 (12136) covalent geometry : angle 0.73640 (16679) SS BOND : bond 0.00645 ( 8) SS BOND : angle 1.11444 ( 16) hydrogen bonds : bond 0.06011 ( 112) hydrogen bonds : angle 6.85861 ( 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 77 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 47 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8222 (tt0) cc_final: 0.7764 (tm-30) REVERT: A 460 PHE cc_start: 0.7683 (t80) cc_final: 0.6966 (t80) REVERT: B 134 ASN cc_start: 0.5639 (OUTLIER) cc_final: 0.4899 (m110) REVERT: B 447 LYS cc_start: 0.8740 (tttp) cc_final: 0.8494 (tttp) REVERT: B 460 PHE cc_start: 0.7061 (t80) cc_final: 0.6614 (m-80) REVERT: B 511 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8655 (mt) REVERT: B 637 ASN cc_start: 0.8872 (t0) cc_final: 0.8547 (t0) outliers start: 30 outliers final: 21 residues processed: 74 average time/residue: 0.0772 time to fit residues: 9.5533 Evaluate side-chains 68 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 91 LEU 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 559 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 134 ASN 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 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: 3.9990 chunk 6 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN ** B 593 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 = 0.3850 r_free = 0.3850 target = 0.102432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.073577 restraints weight = 28307.238| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.02 r_work: 0.3136 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12144 Z= 0.106 Angle : 0.569 9.523 16695 Z= 0.280 Chirality : 0.039 0.149 2083 Planarity : 0.004 0.041 1908 Dihedral : 15.542 161.710 2539 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.52 % Allowed : 17.52 % Favored : 80.96 % 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: -2.21 (0.24), residues: 1330 helix: -0.97 (0.71), residues: 56 sheet: -2.70 (0.34), residues: 232 loop : -1.27 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.006 0.001 TYR B 684 PHE 0.012 0.001 PHE A 122 TRP 0.006 0.001 TRP B 244 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00254 (12136) covalent geometry : angle 0.56749 (16679) SS BOND : bond 0.00233 ( 8) SS BOND : angle 1.62310 ( 16) hydrogen bonds : bond 0.04171 ( 112) hydrogen bonds : angle 6.35736 ( 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 72 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6640 (t80) REVERT: A 128 GLU cc_start: 0.8165 (tt0) cc_final: 0.7692 (tm-30) REVERT: A 208 ASN cc_start: 0.8745 (m-40) cc_final: 0.8471 (m110) REVERT: A 445 GLU cc_start: 0.8497 (tt0) cc_final: 0.8126 (pp20) REVERT: A 460 PHE cc_start: 0.7636 (t80) cc_final: 0.6949 (t80) REVERT: B 134 ASN cc_start: 0.5673 (OUTLIER) cc_final: 0.5009 (m110) REVERT: B 211 LYS cc_start: 0.9347 (tppt) cc_final: 0.8135 (mtmt) REVERT: B 447 LYS cc_start: 0.8674 (tttp) cc_final: 0.8444 (tttp) REVERT: B 460 PHE cc_start: 0.7003 (t80) cc_final: 0.6581 (m-80) REVERT: B 511 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8593 (mt) REVERT: B 637 ASN cc_start: 0.8796 (t0) cc_final: 0.8443 (t0) outliers start: 19 outliers final: 14 residues processed: 71 average time/residue: 0.0826 time to fit residues: 9.6869 Evaluate side-chains 67 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 655 ILE 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 249 THR Chi-restraints excluded: chain B residue 404 SER 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: 10.0000 chunk 129 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 0.0170 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.100922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.072288 restraints weight = 28444.112| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.02 r_work: 0.3111 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12144 Z= 0.162 Angle : 0.589 9.013 16695 Z= 0.291 Chirality : 0.041 0.135 2083 Planarity : 0.004 0.041 1908 Dihedral : 15.313 159.770 2539 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 1.60 % Allowed : 17.76 % Favored : 80.64 % 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: -2.24 (0.24), residues: 1330 helix: -1.02 (0.71), residues: 56 sheet: -2.73 (0.33), residues: 232 loop : -1.29 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 485 TYR 0.010 0.001 TYR A 327 PHE 0.010 0.001 PHE A 607 TRP 0.006 0.001 TRP B 244 HIS 0.003 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00394 (12136) covalent geometry : angle 0.58735 (16679) SS BOND : bond 0.00334 ( 8) SS BOND : angle 1.42706 ( 16) hydrogen bonds : bond 0.04514 ( 112) hydrogen bonds : angle 6.41957 ( 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 74 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8125 (tt0) cc_final: 0.7645 (tm-30) REVERT: A 208 ASN cc_start: 0.8769 (m-40) cc_final: 0.8496 (m110) REVERT: A 445 GLU cc_start: 0.8541 (tt0) cc_final: 0.8154 (pp20) REVERT: A 460 PHE cc_start: 0.7711 (t80) cc_final: 0.7013 (t80) REVERT: B 107 LEU cc_start: 0.9050 (tp) cc_final: 0.8744 (tt) REVERT: B 134 ASN cc_start: 0.5702 (OUTLIER) cc_final: 0.4128 (m110) REVERT: B 211 LYS cc_start: 0.9359 (tppt) cc_final: 0.8117 (mtmt) REVERT: B 460 PHE cc_start: 0.7122 (t80) cc_final: 0.6663 (m-80) REVERT: B 471 GLN cc_start: 0.8910 (tt0) cc_final: 0.8493 (tt0) REVERT: B 511 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 637 ASN cc_start: 0.8823 (t0) cc_final: 0.8424 (t0) outliers start: 20 outliers final: 15 residues processed: 73 average time/residue: 0.0804 time to fit residues: 9.9652 Evaluate side-chains 68 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 262 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 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 249 THR Chi-restraints excluded: chain B residue 404 SER 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: 3.9990 chunk 29 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 128 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 HIS ** B 593 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 = 0.3860 r_free = 0.3860 target = 0.102766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.074168 restraints weight = 28564.609| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.05 r_work: 0.3151 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12144 Z= 0.097 Angle : 0.547 8.868 16695 Z= 0.266 Chirality : 0.039 0.145 2083 Planarity : 0.004 0.040 1908 Dihedral : 15.137 161.194 2539 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.44 % Allowed : 18.16 % 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: -2.05 (0.24), residues: 1330 helix: -0.64 (0.74), residues: 56 sheet: -2.55 (0.34), residues: 230 loop : -1.18 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 435 TYR 0.005 0.001 TYR B 303 PHE 0.010 0.001 PHE A 122 TRP 0.006 0.001 TRP A 657 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00230 (12136) covalent geometry : angle 0.54574 (16679) SS BOND : bond 0.00193 ( 8) SS BOND : angle 1.08631 ( 16) hydrogen bonds : bond 0.03611 ( 112) hydrogen bonds : angle 6.10945 ( 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 73 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7097 (t80) REVERT: A 128 GLU cc_start: 0.8099 (tt0) cc_final: 0.7645 (tm-30) REVERT: A 208 ASN cc_start: 0.8734 (m-40) cc_final: 0.8473 (m110) REVERT: A 445 GLU cc_start: 0.8496 (tt0) cc_final: 0.8126 (pp20) REVERT: A 460 PHE cc_start: 0.7643 (t80) cc_final: 0.6974 (t80) REVERT: B 107 LEU cc_start: 0.9024 (tp) cc_final: 0.8743 (tt) REVERT: B 134 ASN cc_start: 0.5639 (OUTLIER) cc_final: 0.4041 (m110) REVERT: B 211 LYS cc_start: 0.9349 (tppt) cc_final: 0.8123 (mtmt) REVERT: B 460 PHE cc_start: 0.7156 (t80) cc_final: 0.6709 (m-80) REVERT: B 471 GLN cc_start: 0.8896 (tt0) cc_final: 0.8497 (tt0) REVERT: B 511 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8592 (mt) REVERT: B 637 ASN cc_start: 0.8783 (t0) cc_final: 0.8452 (t0) outliers start: 18 outliers final: 13 residues processed: 72 average time/residue: 0.0793 time to fit residues: 9.7192 Evaluate side-chains 67 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 64 LEU 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 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: 4.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 182 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 = 0.3822 r_free = 0.3822 target = 0.100564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.072086 restraints weight = 28710.864| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.03 r_work: 0.3107 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12144 Z= 0.181 Angle : 0.595 9.123 16695 Z= 0.293 Chirality : 0.041 0.141 2083 Planarity : 0.004 0.040 1908 Dihedral : 15.208 159.556 2539 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 1.52 % Allowed : 18.32 % Favored : 80.16 % 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: -2.07 (0.24), residues: 1330 helix: -0.19 (0.85), residues: 42 sheet: -2.66 (0.33), residues: 230 loop : -1.19 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 485 TYR 0.009 0.001 TYR A 327 PHE 0.011 0.001 PHE B 631 TRP 0.007 0.001 TRP B 244 HIS 0.004 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00437 (12136) covalent geometry : angle 0.59413 (16679) SS BOND : bond 0.00365 ( 8) SS BOND : angle 1.19527 ( 16) hydrogen bonds : bond 0.04589 ( 112) hydrogen bonds : angle 6.36815 ( 273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.96 seconds wall clock time: 47 minutes 52.06 seconds (2872.06 seconds total)