Starting phenix.real_space_refine on Wed Mar 4 17:43:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usx_26742/03_2026/7usx_26742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usx_26742/03_2026/7usx_26742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7usx_26742/03_2026/7usx_26742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usx_26742/03_2026/7usx_26742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7usx_26742/03_2026/7usx_26742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usx_26742/03_2026/7usx_26742.map" } resolution = 3.09 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 4 5.49 5 S 78 5.16 5 C 9466 2.51 5 N 2282 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 14220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4883 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 18, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4883 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 18, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 353 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 353 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 264 Unusual residues: {' CA': 2, 'CLR': 1, 'D12': 12, 'NAG': 1, 'PEE': 1, 'R16': 4} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 264 Unusual residues: {' CA': 2, 'CLR': 1, 'D12': 12, 'NAG': 1, 'PEE': 1, 'R16': 4} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'3PE': 1, 'D12': 2, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'3PE': 1, 'D12': 2, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.15, per 1000 atoms: 0.22 Number of scatterers: 14220 At special positions: 0 Unit cell: (133.401, 103.197, 106.553, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 78 16.00 P 4 15.00 O 2382 8.00 N 2282 7.00 C 9466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 816 " 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=2, symmetry=0 Links applied NAG-ASN " NAG A1321 " - " ASN A 209 " " NAG B1321 " - " ASN B 209 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 496.8 milliseconds 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 2 sheets defined 74.2% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 99 through 118 Processing helix chain 'A' and resid 122 through 148 removed outlier: 3.989A pdb=" N TYR A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 167 through 191 removed outlier: 4.055A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.463A pdb=" N VAL A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 291 removed outlier: 3.574A pdb=" N PHE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.662A pdb=" N TRP A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 343 removed outlier: 3.647A pdb=" N LYS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 381 removed outlier: 3.616A pdb=" N SER A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 418 Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 420 through 459 removed outlier: 3.548A pdb=" N ASN A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 695 Processing helix chain 'A' and resid 695 through 706 Processing helix chain 'A' and resid 724 through 742 Processing helix chain 'A' and resid 748 through 772 removed outlier: 3.827A pdb=" N ILE A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 810 removed outlier: 4.166A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 826 through 834 removed outlier: 4.020A pdb=" N GLU A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 850 through 883 Proline residue: A 856 - end of helix removed outlier: 3.539A pdb=" N SER A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 880 " --> pdb=" O ARG A 876 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 881 " --> pdb=" O GLU A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 92 Processing helix chain 'B' and resid 99 through 118 Processing helix chain 'B' and resid 122 through 148 removed outlier: 4.006A pdb=" N TYR B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 167 through 191 removed outlier: 4.044A pdb=" N PHE B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 218 through 223 removed outlier: 4.468A pdb=" N VAL B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 261 through 291 removed outlier: 3.576A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.654A pdb=" N TRP B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 343 removed outlier: 3.671A pdb=" N LYS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 381 removed outlier: 3.613A pdb=" N SER B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 418 Proline residue: B 407 - end of helix Processing helix chain 'B' and resid 420 through 459 removed outlier: 3.533A pdb=" N ASN B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 695 Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 724 through 742 Processing helix chain 'B' and resid 748 through 772 removed outlier: 3.826A pdb=" N ILE B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN B 772 " --> pdb=" O VAL B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 810 removed outlier: 4.175A pdb=" N LEU B 789 " --> pdb=" O SER B 785 " (cutoff:3.500A) Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 826 through 834 removed outlier: 4.010A pdb=" N GLU B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 846 Processing helix chain 'B' and resid 850 through 883 Proline residue: B 856 - end of helix removed outlier: 3.537A pdb=" N SER B 870 " --> pdb=" O TYR B 866 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 880 " --> pdb=" O ARG B 876 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 881 " --> pdb=" O GLU B 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.750A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.649A pdb=" N ASN C 50 " --> pdb=" O PHE C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 76 through 81 removed outlier: 4.391A pdb=" N GLU C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.685A pdb=" N PHE C 92 " --> pdb=" O ILE C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 155 through 171 Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'D' and resid 23 through 43 removed outlier: 3.720A pdb=" N LEU D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'E' and resid 21 through 32 removed outlier: 3.783A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 50 removed outlier: 3.687A pdb=" N ASN E 50 " --> pdb=" O PHE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.514A pdb=" N ILE E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 76 through 81 removed outlier: 4.415A pdb=" N GLU E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 92 removed outlier: 3.658A pdb=" N PHE E 92 " --> pdb=" O ILE E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 117 through 130 Processing helix chain 'E' and resid 138 through 151 Processing helix chain 'E' and resid 155 through 171 Processing helix chain 'E' and resid 179 through 188 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'F' and resid 23 through 43 removed outlier: 3.723A pdb=" N LEU F 27 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 63 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AA2, first strand: chain 'E' and resid 67 through 69 878 hydrogen bonds defined for protein. 2622 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: 1.94 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2100 1.31 - 1.43: 3916 1.43 - 1.56: 8342 1.56 - 1.68: 8 1.68 - 1.81: 130 Bond restraints: 14496 Sorted by residual: bond pdb=" C21 3PE F 201 " pdb=" O21 3PE F 201 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C21 3PE D 201 " pdb=" O21 3PE D 201 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C30 PEE B1303 " pdb=" O3 PEE B1303 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C30 PEE A1303 " pdb=" O3 PEE A1303 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C10 PEE B1303 " pdb=" O2 PEE B1303 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 18936 3.19 - 6.38: 469 6.38 - 9.56: 17 9.56 - 12.75: 2 12.75 - 15.94: 4 Bond angle restraints: 19428 Sorted by residual: angle pdb=" O3P PEE B1303 " pdb=" P PEE B1303 " pdb=" O4P PEE B1303 " ideal model delta sigma weight residual 92.91 108.85 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" O3P PEE A1303 " pdb=" P PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sigma weight residual 92.91 108.82 -15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" O12 3PE D 201 " pdb=" P 3PE D 201 " pdb=" O14 3PE D 201 " ideal model delta sigma weight residual 123.79 109.41 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE F 201 " pdb=" P 3PE F 201 " pdb=" O14 3PE F 201 " ideal model delta sigma weight residual 123.79 109.46 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C ARG B 334 " pdb=" N GLU B 335 " pdb=" CA GLU B 335 " ideal model delta sigma weight residual 120.72 114.36 6.36 1.67e+00 3.59e-01 1.45e+01 ... (remaining 19423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.07: 8426 31.07 - 62.15: 414 62.15 - 93.22: 32 93.22 - 124.29: 6 124.29 - 155.37: 2 Dihedral angle restraints: 8880 sinusoidal: 3952 harmonic: 4928 Sorted by residual: dihedral pdb=" CB CYS B 667 " pdb=" SG CYS B 667 " pdb=" SG CYS B 816 " pdb=" CB CYS B 816 " ideal model delta sinusoidal sigma weight residual -86.00 -142.54 56.54 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS A 667 " pdb=" SG CYS A 667 " pdb=" SG CYS A 816 " pdb=" CB CYS A 816 " ideal model delta sinusoidal sigma weight residual -86.00 -140.14 54.14 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" C4 PEE A1303 " pdb=" O4P PEE A1303 " pdb=" P PEE A1303 " pdb=" O2P PEE A1303 " ideal model delta sinusoidal sigma weight residual 284.22 128.85 155.37 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 8877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1566 0.041 - 0.081: 503 0.081 - 0.122: 79 0.122 - 0.162: 2 0.162 - 0.203: 10 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA GLU B 335 " pdb=" N GLU B 335 " pdb=" C GLU B 335 " pdb=" CB GLU B 335 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA GLU A 335 " pdb=" N GLU A 335 " pdb=" C GLU A 335 " pdb=" CB GLU A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" C2 PEE A1303 " pdb=" C1 PEE A1303 " pdb=" C3 PEE A1303 " pdb=" O2 PEE A1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.50 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 2157 not shown) Planarity restraints: 2342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1321 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG B1321 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1321 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG B1321 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG B1321 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1321 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG A1321 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1321 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG A1321 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1321 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 209 " 0.155 2.00e-02 2.50e+03 2.83e-01 9.98e+02 pdb=" CG ASN A 209 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A 209 " 0.104 2.00e-02 2.50e+03 pdb=" ND2 ASN A 209 " -0.501 2.00e-02 2.50e+03 pdb=" C1 NAG A1321 " 0.326 2.00e-02 2.50e+03 ... (remaining 2339 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2303 2.76 - 3.29: 13242 3.29 - 3.83: 23278 3.83 - 4.36: 25978 4.36 - 4.90: 47215 Nonbonded interactions: 112016 Sorted by model distance: nonbonded pdb=" O PRO E 63 " pdb=" OG SER E 101 " model vdw 2.223 3.040 nonbonded pdb=" O TYR E 28 " pdb=" OG1 THR E 32 " model vdw 2.248 3.040 nonbonded pdb=" NH2 ARG A 94 " pdb=" O GLN C 29 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP B 683 " pdb=" NZ LYS B 756 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG B 94 " pdb=" O GLN E 29 " model vdw 2.253 3.120 ... (remaining 112011 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 4.230 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.630 Find NCS groups from input model: 0.360 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 14502 Z= 0.223 Angle : 0.865 15.940 19438 Z= 0.370 Chirality : 0.040 0.203 2160 Planarity : 0.009 0.296 2340 Dihedral : 17.358 155.365 5674 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.14 % Allowed : 19.60 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.21), residues: 1654 helix: 2.28 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.72 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 165 TYR 0.015 0.001 TYR B 245 PHE 0.031 0.001 PHE A 376 TRP 0.010 0.001 TRP D 25 HIS 0.002 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00390 (14496) covalent geometry : angle 0.86268 (19428) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.44313 ( 4) hydrogen bonds : bond 0.11544 ( 878) hydrogen bonds : angle 5.04012 ( 2622) Misc. bond : bond 0.10836 ( 2) link_NAG-ASN : bond 0.03440 ( 2) link_NAG-ASN : angle 3.54104 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 88 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6651 (tt0) REVERT: A 138 MET cc_start: 0.6652 (ttp) cc_final: 0.5975 (mmt) REVERT: B 138 MET cc_start: 0.6653 (ttp) cc_final: 0.5940 (mmt) REVERT: C 99 ASN cc_start: 0.7248 (m-40) cc_final: 0.7026 (m-40) REVERT: E 99 ASN cc_start: 0.7668 (m-40) cc_final: 0.7360 (m-40) outliers start: 2 outliers final: 2 residues processed: 163 average time/residue: 0.1094 time to fit residues: 26.8070 Evaluate side-chains 162 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN B 144 ASN B 731 HIS C 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.206312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.140167 restraints weight = 14300.841| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.66 r_work: 0.3471 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14502 Z= 0.116 Angle : 0.531 10.342 19438 Z= 0.264 Chirality : 0.039 0.178 2160 Planarity : 0.004 0.062 2340 Dihedral : 11.268 155.025 2471 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.34 % Allowed : 19.19 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.21), residues: 1654 helix: 2.54 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.78 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 189 TYR 0.019 0.001 TYR A 245 PHE 0.012 0.001 PHE A 717 TRP 0.011 0.001 TRP F 25 HIS 0.004 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00258 (14496) covalent geometry : angle 0.51572 (19428) SS BOND : bond 0.00293 ( 2) SS BOND : angle 1.06852 ( 4) hydrogen bonds : bond 0.03999 ( 878) hydrogen bonds : angle 3.71036 ( 2622) Misc. bond : bond 0.00019 ( 2) link_NAG-ASN : bond 0.01138 ( 2) link_NAG-ASN : angle 7.09258 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6185 (ttp) cc_final: 0.5471 (mmt) REVERT: A 335 GLU cc_start: 0.5731 (mp0) cc_final: 0.5315 (mp0) REVERT: A 372 TYR cc_start: 0.7412 (t80) cc_final: 0.7150 (t80) REVERT: A 720 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7372 (t80) REVERT: B 138 MET cc_start: 0.6172 (ttp) cc_final: 0.5415 (mmt) REVERT: B 372 TYR cc_start: 0.7361 (t80) cc_final: 0.7090 (t80) REVERT: B 720 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7393 (t80) REVERT: B 814 ARG cc_start: 0.7535 (mmp80) cc_final: 0.7308 (mmt180) REVERT: C 99 ASN cc_start: 0.6973 (m-40) cc_final: 0.6606 (m-40) REVERT: C 119 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.5731 (pt0) REVERT: C 180 PHE cc_start: 0.3837 (t80) cc_final: 0.2506 (p90) REVERT: E 99 ASN cc_start: 0.7377 (m-40) cc_final: 0.7055 (m-40) outliers start: 34 outliers final: 11 residues processed: 188 average time/residue: 0.1060 time to fit residues: 30.5048 Evaluate side-chains 174 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 57 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 125 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 731 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.205239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139096 restraints weight = 14470.568| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.33 r_work: 0.3471 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14502 Z= 0.128 Angle : 0.511 9.580 19438 Z= 0.259 Chirality : 0.039 0.120 2160 Planarity : 0.004 0.064 2340 Dihedral : 10.426 151.392 2468 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.68 % Allowed : 19.33 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.21), residues: 1654 helix: 2.55 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.83 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 189 TYR 0.019 0.001 TYR A 245 PHE 0.036 0.001 PHE B 208 TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00303 (14496) covalent geometry : angle 0.49873 (19428) SS BOND : bond 0.00358 ( 2) SS BOND : angle 1.30281 ( 4) hydrogen bonds : bond 0.04052 ( 878) hydrogen bonds : angle 3.65042 ( 2622) Misc. bond : bond 0.00049 ( 2) link_NAG-ASN : bond 0.01707 ( 2) link_NAG-ASN : angle 6.15508 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6113 (ttp) cc_final: 0.5401 (mmt) REVERT: A 335 GLU cc_start: 0.6035 (mp0) cc_final: 0.5596 (mp0) REVERT: A 372 TYR cc_start: 0.7282 (t80) cc_final: 0.7014 (t80) REVERT: A 435 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6913 (tp) REVERT: A 720 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7270 (t80) REVERT: A 814 ARG cc_start: 0.7468 (mmp80) cc_final: 0.7209 (mmt180) REVERT: B 138 MET cc_start: 0.6093 (ttp) cc_final: 0.5353 (mmt) REVERT: B 331 ILE cc_start: 0.6896 (mt) cc_final: 0.6028 (mp) REVERT: B 335 GLU cc_start: 0.5744 (mp0) cc_final: 0.5283 (mp0) REVERT: B 372 TYR cc_start: 0.7279 (t80) cc_final: 0.7000 (t80) REVERT: B 435 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6900 (tp) REVERT: B 720 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7396 (t80) REVERT: B 814 ARG cc_start: 0.7445 (mmp80) cc_final: 0.7235 (mmt180) REVERT: C 99 ASN cc_start: 0.6804 (m-40) cc_final: 0.6462 (m-40) REVERT: C 119 GLN cc_start: 0.6246 (OUTLIER) cc_final: 0.5750 (pt0) REVERT: E 99 ASN cc_start: 0.7376 (m-40) cc_final: 0.7016 (m-40) outliers start: 39 outliers final: 20 residues processed: 191 average time/residue: 0.1028 time to fit residues: 30.0640 Evaluate side-chains 181 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 58 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 731 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.206641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143639 restraints weight = 14524.655| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.74 r_work: 0.3461 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14502 Z= 0.114 Angle : 0.488 9.157 19438 Z= 0.249 Chirality : 0.038 0.121 2160 Planarity : 0.004 0.063 2340 Dihedral : 9.928 145.025 2468 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.03 % Allowed : 19.81 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.21), residues: 1654 helix: 2.65 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.81 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 349 TYR 0.017 0.001 TYR B 245 PHE 0.029 0.001 PHE B 208 TRP 0.012 0.001 TRP F 25 HIS 0.002 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00263 (14496) covalent geometry : angle 0.47709 (19428) SS BOND : bond 0.00322 ( 2) SS BOND : angle 1.14475 ( 4) hydrogen bonds : bond 0.03821 ( 878) hydrogen bonds : angle 3.57148 ( 2622) Misc. bond : bond 0.00024 ( 2) link_NAG-ASN : bond 0.01763 ( 2) link_NAG-ASN : angle 5.84824 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6125 (ttp) cc_final: 0.5406 (mmt) REVERT: A 335 GLU cc_start: 0.5952 (mp0) cc_final: 0.5595 (mp0) REVERT: A 372 TYR cc_start: 0.7362 (t80) cc_final: 0.7100 (t80) REVERT: A 394 GLN cc_start: 0.7317 (mm-40) cc_final: 0.7061 (mm-40) REVERT: A 435 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7063 (tp) REVERT: A 720 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7363 (t80) REVERT: A 814 ARG cc_start: 0.7527 (mmp80) cc_final: 0.7307 (mmt180) REVERT: B 138 MET cc_start: 0.6087 (ttp) cc_final: 0.5323 (mmt) REVERT: B 331 ILE cc_start: 0.7194 (mt) cc_final: 0.6198 (mp) REVERT: B 335 GLU cc_start: 0.5926 (mp0) cc_final: 0.5410 (mp0) REVERT: B 372 TYR cc_start: 0.7345 (t80) cc_final: 0.7069 (t80) REVERT: B 394 GLN cc_start: 0.7185 (mm-40) cc_final: 0.6958 (mm-40) REVERT: B 720 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7346 (t80) REVERT: C 99 ASN cc_start: 0.6836 (m-40) cc_final: 0.6495 (m-40) REVERT: C 119 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5754 (pt0) REVERT: E 99 ASN cc_start: 0.7434 (m-40) cc_final: 0.6285 (m-40) outliers start: 44 outliers final: 25 residues processed: 188 average time/residue: 0.1008 time to fit residues: 29.2736 Evaluate side-chains 182 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 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 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.206855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141184 restraints weight = 14512.830| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.33 r_work: 0.3473 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14502 Z= 0.127 Angle : 0.501 9.512 19438 Z= 0.256 Chirality : 0.039 0.122 2160 Planarity : 0.004 0.065 2340 Dihedral : 9.706 138.540 2468 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.85 % Allowed : 19.39 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.21), residues: 1654 helix: 2.60 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.018 0.001 TYR B 245 PHE 0.017 0.001 PHE B 208 TRP 0.011 0.001 TRP F 25 HIS 0.003 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00305 (14496) covalent geometry : angle 0.48996 (19428) SS BOND : bond 0.00411 ( 2) SS BOND : angle 1.29044 ( 4) hydrogen bonds : bond 0.03991 ( 878) hydrogen bonds : angle 3.59860 ( 2622) Misc. bond : bond 0.00022 ( 2) link_NAG-ASN : bond 0.01412 ( 2) link_NAG-ASN : angle 5.79262 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6023 (ttp) cc_final: 0.5311 (mmt) REVERT: A 254 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6679 (mp) REVERT: A 331 ILE cc_start: 0.6888 (mm) cc_final: 0.6238 (mt) REVERT: A 335 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5410 (mp0) REVERT: A 372 TYR cc_start: 0.7405 (t80) cc_final: 0.7147 (t80) REVERT: A 435 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7127 (tp) REVERT: A 720 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7499 (t80) REVERT: B 96 GLN cc_start: 0.5910 (OUTLIER) cc_final: 0.4749 (mp10) REVERT: B 138 MET cc_start: 0.5985 (ttp) cc_final: 0.5252 (mmt) REVERT: B 331 ILE cc_start: 0.7142 (mt) cc_final: 0.6211 (mp) REVERT: B 335 GLU cc_start: 0.5872 (mp0) cc_final: 0.5406 (mp0) REVERT: B 435 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7023 (tp) REVERT: B 720 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7513 (t80) REVERT: C 99 ASN cc_start: 0.6559 (m-40) cc_final: 0.6140 (m-40) REVERT: C 119 GLN cc_start: 0.6361 (OUTLIER) cc_final: 0.5834 (pt0) REVERT: E 99 ASN cc_start: 0.6547 (m-40) cc_final: 0.6235 (m-40) outliers start: 56 outliers final: 32 residues processed: 201 average time/residue: 0.1036 time to fit residues: 31.9284 Evaluate side-chains 193 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.206110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140771 restraints weight = 14453.041| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.29 r_work: 0.3468 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14502 Z= 0.135 Angle : 0.512 8.452 19438 Z= 0.261 Chirality : 0.039 0.122 2160 Planarity : 0.004 0.065 2340 Dihedral : 9.582 128.392 2468 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.99 % Allowed : 19.19 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.21), residues: 1654 helix: 2.52 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -1.84 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 764 TYR 0.018 0.001 TYR B 245 PHE 0.019 0.001 PHE B 208 TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00329 (14496) covalent geometry : angle 0.50394 (19428) SS BOND : bond 0.00414 ( 2) SS BOND : angle 1.29283 ( 4) hydrogen bonds : bond 0.04076 ( 878) hydrogen bonds : angle 3.61009 ( 2622) Misc. bond : bond 0.00024 ( 2) link_NAG-ASN : bond 0.01360 ( 2) link_NAG-ASN : angle 5.20869 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.5835 (OUTLIER) cc_final: 0.4743 (mp10) REVERT: A 138 MET cc_start: 0.6031 (ttp) cc_final: 0.5325 (mmt) REVERT: A 254 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6688 (mp) REVERT: A 291 MET cc_start: 0.7001 (ttp) cc_final: 0.6349 (mmm) REVERT: A 331 ILE cc_start: 0.6852 (mm) cc_final: 0.6299 (mt) REVERT: A 335 GLU cc_start: 0.5887 (OUTLIER) cc_final: 0.5571 (mp0) REVERT: A 349 ARG cc_start: 0.6254 (mmp80) cc_final: 0.6025 (mmp80) REVERT: A 372 TYR cc_start: 0.7456 (t80) cc_final: 0.7209 (t80) REVERT: A 435 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7004 (tp) REVERT: A 720 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7510 (t80) REVERT: B 96 GLN cc_start: 0.5905 (OUTLIER) cc_final: 0.4737 (mp10) REVERT: B 138 MET cc_start: 0.6047 (ttp) cc_final: 0.5340 (mmt) REVERT: B 254 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6848 (mp) REVERT: B 331 ILE cc_start: 0.7142 (mt) cc_final: 0.6240 (mp) REVERT: B 335 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5582 (mp0) REVERT: B 435 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7028 (tp) REVERT: B 720 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7546 (t80) REVERT: C 99 ASN cc_start: 0.6534 (m-40) cc_final: 0.6090 (m-40) REVERT: C 119 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.5806 (pt0) REVERT: E 99 ASN cc_start: 0.6656 (m-40) cc_final: 0.6350 (m-40) outliers start: 58 outliers final: 33 residues processed: 199 average time/residue: 0.0984 time to fit residues: 30.2015 Evaluate side-chains 202 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 150 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 394 GLN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.205499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.147101 restraints weight = 14539.748| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.26 r_work: 0.3448 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14502 Z= 0.116 Angle : 0.490 7.917 19438 Z= 0.252 Chirality : 0.038 0.123 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.417 113.897 2468 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.30 % Allowed : 19.88 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.21), residues: 1654 helix: 2.62 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 165 TYR 0.016 0.001 TYR A 245 PHE 0.014 0.001 PHE B 208 TRP 0.011 0.001 TRP D 25 HIS 0.002 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00275 (14496) covalent geometry : angle 0.48259 (19428) SS BOND : bond 0.00303 ( 2) SS BOND : angle 1.16882 ( 4) hydrogen bonds : bond 0.03826 ( 878) hydrogen bonds : angle 3.54996 ( 2622) Misc. bond : bond 0.00017 ( 2) link_NAG-ASN : bond 0.01200 ( 2) link_NAG-ASN : angle 4.78604 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.6013 (OUTLIER) cc_final: 0.4943 (mp10) REVERT: A 138 MET cc_start: 0.6281 (ttp) cc_final: 0.5550 (mmt) REVERT: A 254 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6876 (mp) REVERT: A 291 MET cc_start: 0.7017 (ttp) cc_final: 0.6401 (mmm) REVERT: A 324 ASN cc_start: 0.7092 (t0) cc_final: 0.6642 (t0) REVERT: A 331 ILE cc_start: 0.7161 (mm) cc_final: 0.6446 (mt) REVERT: A 335 GLU cc_start: 0.6083 (OUTLIER) cc_final: 0.5801 (mp0) REVERT: A 372 TYR cc_start: 0.7677 (t80) cc_final: 0.7433 (t80) REVERT: A 435 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7354 (tp) REVERT: A 720 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7541 (t80) REVERT: A 814 ARG cc_start: 0.7712 (mmp80) cc_final: 0.7399 (mmt180) REVERT: B 96 GLN cc_start: 0.6087 (OUTLIER) cc_final: 0.4975 (mp10) REVERT: B 138 MET cc_start: 0.6281 (ttp) cc_final: 0.5501 (mmt) REVERT: B 291 MET cc_start: 0.7067 (ttp) cc_final: 0.6428 (mmm) REVERT: B 324 ASN cc_start: 0.7083 (t0) cc_final: 0.6657 (t0) REVERT: B 331 ILE cc_start: 0.7410 (mt) cc_final: 0.6405 (mp) REVERT: B 335 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5819 (mp0) REVERT: B 435 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7380 (tp) REVERT: B 720 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7617 (t80) REVERT: C 99 ASN cc_start: 0.6801 (m-40) cc_final: 0.6342 (m-40) REVERT: C 119 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.5893 (pt0) REVERT: C 189 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.4831 (ptp-170) REVERT: E 99 ASN cc_start: 0.6853 (m-40) cc_final: 0.6514 (m-40) REVERT: E 119 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.6008 (pt0) outliers start: 48 outliers final: 31 residues processed: 194 average time/residue: 0.1040 time to fit residues: 31.1805 Evaluate side-chains 200 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 0.0870 chunk 58 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 394 GLN B 181 ASN B 394 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.207945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.153250 restraints weight = 14353.144| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.97 r_work: 0.3486 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14502 Z= 0.103 Angle : 0.476 7.382 19438 Z= 0.245 Chirality : 0.038 0.122 2160 Planarity : 0.004 0.063 2340 Dihedral : 9.225 127.270 2468 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.89 % Allowed : 20.43 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.21), residues: 1654 helix: 2.70 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.75 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.015 0.001 TYR A 245 PHE 0.015 0.001 PHE B 208 TRP 0.012 0.001 TRP F 25 HIS 0.002 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00232 (14496) covalent geometry : angle 0.46984 (19428) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.96799 ( 4) hydrogen bonds : bond 0.03615 ( 878) hydrogen bonds : angle 3.49199 ( 2622) Misc. bond : bond 0.00010 ( 2) link_NAG-ASN : bond 0.01149 ( 2) link_NAG-ASN : angle 4.41975 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.6017 (OUTLIER) cc_final: 0.4948 (mp10) REVERT: A 138 MET cc_start: 0.6292 (ttp) cc_final: 0.5562 (mmt) REVERT: A 189 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8038 (tp) REVERT: A 291 MET cc_start: 0.7036 (ttp) cc_final: 0.6437 (mmm) REVERT: A 331 ILE cc_start: 0.7172 (mm) cc_final: 0.6427 (mt) REVERT: A 335 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: A 372 TYR cc_start: 0.7608 (t80) cc_final: 0.7359 (t80) REVERT: A 435 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7321 (tp) REVERT: A 720 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7520 (t80) REVERT: A 814 ARG cc_start: 0.7697 (mmp80) cc_final: 0.7400 (mmt180) REVERT: B 96 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.4950 (mp10) REVERT: B 138 MET cc_start: 0.6300 (ttp) cc_final: 0.5483 (mmt) REVERT: B 189 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8038 (tp) REVERT: B 291 MET cc_start: 0.7115 (ttp) cc_final: 0.6468 (mmm) REVERT: B 331 ILE cc_start: 0.7447 (mt) cc_final: 0.6396 (mp) REVERT: B 335 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: B 435 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7296 (tp) REVERT: B 720 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7534 (t80) REVERT: C 99 ASN cc_start: 0.6878 (m-40) cc_final: 0.6421 (m-40) REVERT: C 119 GLN cc_start: 0.6413 (OUTLIER) cc_final: 0.5869 (pt0) REVERT: C 189 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.4771 (ptp-170) REVERT: E 99 ASN cc_start: 0.6870 (m-40) cc_final: 0.6538 (m-40) REVERT: E 119 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.5982 (pt0) outliers start: 42 outliers final: 25 residues processed: 184 average time/residue: 0.1024 time to fit residues: 29.3685 Evaluate side-chains 193 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 778 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 158 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.204428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145907 restraints weight = 14551.916| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.31 r_work: 0.3437 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14502 Z= 0.133 Angle : 0.505 7.202 19438 Z= 0.259 Chirality : 0.039 0.122 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.373 148.592 2468 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.09 % Allowed : 20.36 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.21), residues: 1654 helix: 2.56 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 764 TYR 0.018 0.001 TYR A 245 PHE 0.013 0.001 PHE C 105 TRP 0.011 0.001 TRP D 25 HIS 0.002 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00326 (14496) covalent geometry : angle 0.49912 (19428) SS BOND : bond 0.00333 ( 2) SS BOND : angle 1.23829 ( 4) hydrogen bonds : bond 0.04029 ( 878) hydrogen bonds : angle 3.56578 ( 2622) Misc. bond : bond 0.00019 ( 2) link_NAG-ASN : bond 0.01110 ( 2) link_NAG-ASN : angle 4.26221 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.6077 (OUTLIER) cc_final: 0.4984 (mp10) REVERT: A 138 MET cc_start: 0.6283 (ttp) cc_final: 0.5508 (mmt) REVERT: A 254 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6903 (mp) REVERT: A 291 MET cc_start: 0.7083 (ttp) cc_final: 0.6449 (mmm) REVERT: A 324 ASN cc_start: 0.7112 (t0) cc_final: 0.6649 (t0) REVERT: A 331 ILE cc_start: 0.7185 (mm) cc_final: 0.6423 (mt) REVERT: A 335 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5808 (mp0) REVERT: A 372 TYR cc_start: 0.7684 (t80) cc_final: 0.7449 (t80) REVERT: A 435 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7355 (tp) REVERT: A 720 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7620 (t80) REVERT: B 96 GLN cc_start: 0.6068 (OUTLIER) cc_final: 0.4926 (mp10) REVERT: B 138 MET cc_start: 0.6310 (ttp) cc_final: 0.5519 (mmt) REVERT: B 254 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6962 (mp) REVERT: B 291 MET cc_start: 0.7154 (ttp) cc_final: 0.6478 (mmm) REVERT: B 324 ASN cc_start: 0.7169 (t0) cc_final: 0.6728 (t0) REVERT: B 331 ILE cc_start: 0.7460 (mt) cc_final: 0.6422 (mp) REVERT: B 335 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5799 (mp0) REVERT: B 435 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7384 (tp) REVERT: B 720 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7627 (t80) REVERT: C 99 ASN cc_start: 0.6811 (m-40) cc_final: 0.6379 (m-40) REVERT: C 119 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.5953 (pt0) REVERT: C 189 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.4831 (ptp-170) REVERT: E 99 ASN cc_start: 0.6909 (m-40) cc_final: 0.6580 (m-40) REVERT: E 119 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.6006 (pt0) outliers start: 45 outliers final: 27 residues processed: 190 average time/residue: 0.1004 time to fit residues: 29.5295 Evaluate side-chains 200 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 91 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 181 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN ** B 394 GLN ** 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 = 0.4302 r_free = 0.4302 target = 0.207376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150989 restraints weight = 14400.126| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.13 r_work: 0.3443 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14502 Z= 0.125 Angle : 0.505 9.200 19438 Z= 0.258 Chirality : 0.039 0.131 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.408 155.308 2468 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.16 % Allowed : 20.50 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.21), residues: 1654 helix: 2.56 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 22 TYR 0.017 0.001 TYR A 245 PHE 0.013 0.001 PHE B 208 TRP 0.012 0.001 TRP F 25 HIS 0.002 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00299 (14496) covalent geometry : angle 0.49961 (19428) SS BOND : bond 0.00350 ( 2) SS BOND : angle 1.25359 ( 4) hydrogen bonds : bond 0.03953 ( 878) hydrogen bonds : angle 3.55597 ( 2622) Misc. bond : bond 0.00019 ( 2) link_NAG-ASN : bond 0.01109 ( 2) link_NAG-ASN : angle 4.15727 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.4968 (mp10) REVERT: A 138 MET cc_start: 0.6272 (ttp) cc_final: 0.5556 (mmt) REVERT: A 254 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6901 (mp) REVERT: A 291 MET cc_start: 0.7107 (ttp) cc_final: 0.6461 (mmm) REVERT: A 324 ASN cc_start: 0.7115 (t0) cc_final: 0.6673 (t0) REVERT: A 331 ILE cc_start: 0.7163 (mm) cc_final: 0.6389 (mt) REVERT: A 335 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5774 (mp0) REVERT: A 372 TYR cc_start: 0.7672 (t80) cc_final: 0.7438 (t80) REVERT: A 435 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7345 (tp) REVERT: A 720 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7595 (t80) REVERT: B 96 GLN cc_start: 0.6078 (OUTLIER) cc_final: 0.4952 (mp10) REVERT: B 138 MET cc_start: 0.6268 (ttp) cc_final: 0.5495 (mmt) REVERT: B 254 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6961 (mp) REVERT: B 291 MET cc_start: 0.7121 (ttp) cc_final: 0.6436 (mmm) REVERT: B 324 ASN cc_start: 0.7112 (t0) cc_final: 0.6676 (t0) REVERT: B 331 ILE cc_start: 0.7433 (mt) cc_final: 0.6404 (mp) REVERT: B 335 GLU cc_start: 0.6180 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: B 435 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7375 (tp) REVERT: B 720 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.7698 (t80) REVERT: C 99 ASN cc_start: 0.6795 (m-40) cc_final: 0.6369 (m-40) REVERT: C 119 GLN cc_start: 0.6503 (OUTLIER) cc_final: 0.5937 (pt0) REVERT: C 189 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.4829 (ptp-170) REVERT: E 99 ASN cc_start: 0.6906 (m-40) cc_final: 0.6580 (m-40) REVERT: E 119 GLN cc_start: 0.6351 (OUTLIER) cc_final: 0.5994 (pt0) outliers start: 46 outliers final: 30 residues processed: 188 average time/residue: 0.1009 time to fit residues: 29.8488 Evaluate side-chains 201 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 59 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 181 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN ** B 394 GLN ** 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 = 0.4250 r_free = 0.4250 target = 0.203185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141241 restraints weight = 14641.087| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.25 r_work: 0.3447 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14502 Z= 0.131 Angle : 0.510 9.183 19438 Z= 0.261 Chirality : 0.039 0.124 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.479 160.269 2468 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.23 % Allowed : 20.56 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.21), residues: 1654 helix: 2.52 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 764 TYR 0.018 0.001 TYR A 245 PHE 0.013 0.001 PHE E 109 TRP 0.015 0.001 TRP F 25 HIS 0.002 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00318 (14496) covalent geometry : angle 0.50422 (19428) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.31170 ( 4) hydrogen bonds : bond 0.04014 ( 878) hydrogen bonds : angle 3.57133 ( 2622) Misc. bond : bond 0.00021 ( 2) link_NAG-ASN : bond 0.01089 ( 2) link_NAG-ASN : angle 4.08983 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.25 seconds wall clock time: 68 minutes 29.97 seconds (4109.97 seconds total)