Starting phenix.real_space_refine on Fri Jul 3 17:15:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7usx_26742/07_2026/7usx_26742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usx_26742/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7usx_26742/07_2026/7usx_26742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usx_26742/07_2026/7usx_26742.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7usx_26742/07_2026/7usx_26742.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7usx_26742/07_2026/7usx_26742.cif" model { file = "/net/cci-nas-00/data/ceres_data/7usx_26742/07_2026/7usx_26742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usx_26742/07_2026/7usx_26742.cif" } 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-6108/lib/python3.11/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: 39 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: 39 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: 2.57, per 1000 atoms: 0.18 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: 0.87 Conformation dependent library (CDL) restraints added in 388.5 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: 0.32 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: 1.87 Time building geometry restraints manager: 1.10 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 - 21.22: 7760 21.22 - 42.45: 765 42.45 - 63.67: 141 63.67 - 84.90: 9 84.90 - 106.12: 7 Dihedral angle restraints: 8682 sinusoidal: 3754 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=" C10 CLR A1308 " pdb=" C1 CLR A1308 " pdb=" C2 CLR A1308 " pdb=" C3 CLR A1308 " ideal model delta sinusoidal sigma weight residual -56.83 49.29 -106.12 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 8679 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: 5.000 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.800 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 16.308 106.121 5476 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/Z covalent geometry : bond 0.00390 / 0.18 (14496) covalent geometry : angle 0.86268 / 0.37 (19428) SS BOND : bond 0.00284 / 0.14 ( 2) SS BOND : angle 1.44313 / 0.81 ( 4) hydrogen bonds : bond 0.11544 / 7.55 ( 878) hydrogen bonds : angle 5.04012 / 3.66 ( 2622) Misc. bond : bond 0.10836 / 5.36 ( 2) link_NAG-ASN : bond 0.03440 / 1.74 ( 2) link_NAG-ASN : angle 3.54104 / 1.82 ( 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 : 0.479 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: 0.0954 time to fit residues: 23.6306 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 : 0.468 ------------------------------------------------------------------------------- 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... 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 = 0.4310 r_free = 0.4310 target = 0.206346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140225 restraints weight = 14284.718| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.67 r_work: 0.3462 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.0737 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 : 0.521 10.864 19438 Z= 0.263 Chirality : 0.039 0.156 2160 Planarity : 0.004 0.062 2340 Dihedral : 8.912 106.073 2273 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.34 % Allowed : 19.12 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.21), residues: 1654 helix: 2.56 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 189 TYR 0.018 0.001 TYR A 245 PHE 0.012 0.001 PHE A 717 TRP 0.011 0.001 TRP D 25 HIS 0.003 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14496) covalent geometry : angle 0.50386 / 0.26 (19428) SS BOND : bond 0.00222 / 0.11 ( 2) SS BOND : angle 1.05925 / 0.61 ( 4) hydrogen bonds : bond 0.04042 / 2.70 ( 878) hydrogen bonds : angle 3.72012 / 2.69 ( 2622) Misc. bond : bond 0.00031 / 0.02 ( 2) link_NAG-ASN : bond 0.01770 / 0.89 ( 2) link_NAG-ASN : angle 7.48880 / 3.74 ( 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 : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6207 (ttp) cc_final: 0.5490 (mmt) REVERT: A 335 GLU cc_start: 0.5718 (mp0) cc_final: 0.5305 (mp0) REVERT: A 372 TYR cc_start: 0.7433 (t80) cc_final: 0.7171 (t80) REVERT: A 720 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7347 (t80) REVERT: B 138 MET cc_start: 0.6199 (ttp) cc_final: 0.5439 (mmt) REVERT: B 372 TYR cc_start: 0.7386 (t80) cc_final: 0.7115 (t80) REVERT: B 720 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7487 (t80) REVERT: C 99 ASN cc_start: 0.6952 (m-40) cc_final: 0.6601 (m-40) REVERT: C 119 GLN cc_start: 0.6293 (OUTLIER) cc_final: 0.5782 (pt0) REVERT: C 180 PHE cc_start: 0.3831 (t80) cc_final: 0.2523 (p90) REVERT: D 23 ARG cc_start: 0.5642 (tpt90) cc_final: 0.5341 (mmm160) REVERT: E 99 ASN cc_start: 0.7390 (m-40) cc_final: 0.7067 (m-40) outliers start: 34 outliers final: 12 residues processed: 188 average time/residue: 0.0895 time to fit residues: 25.8795 Evaluate side-chains 177 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.204774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138620 restraints weight = 14481.895| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.33 r_work: 0.3469 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14502 Z= 0.134 Angle : 0.520 9.906 19438 Z= 0.263 Chirality : 0.039 0.121 2160 Planarity : 0.004 0.065 2340 Dihedral : 8.648 106.332 2270 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.68 % Allowed : 19.60 % Favored : 77.72 % 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: 1.88 (0.21), residues: 1654 helix: 2.52 (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 D 23 TYR 0.019 0.001 TYR B 245 PHE 0.012 0.001 PHE E 109 TRP 0.011 0.001 TRP F 25 HIS 0.003 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (14496) covalent geometry : angle 0.50724 / 0.26 (19428) SS BOND : bond 0.00315 / 0.16 ( 2) SS BOND : angle 1.38377 / 0.80 ( 4) hydrogen bonds : bond 0.04129 / 2.76 ( 878) hydrogen bonds : angle 3.66953 / 2.65 ( 2622) Misc. bond : bond 0.00049 / 0.02 ( 2) link_NAG-ASN : bond 0.02241 / 1.13 ( 2) link_NAG-ASN : angle 6.49974 / 3.33 ( 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 : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6118 (ttp) cc_final: 0.5403 (mmt) REVERT: A 335 GLU cc_start: 0.6023 (mp0) cc_final: 0.5576 (mp0) REVERT: A 372 TYR cc_start: 0.7295 (t80) cc_final: 0.7030 (t80) REVERT: A 435 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6943 (tp) REVERT: A 720 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.7330 (t80) REVERT: B 138 MET cc_start: 0.6078 (ttp) cc_final: 0.5292 (mmt) REVERT: B 335 GLU cc_start: 0.5806 (mp0) cc_final: 0.5351 (mp0) REVERT: B 372 TYR cc_start: 0.7294 (t80) cc_final: 0.7017 (t80) REVERT: B 435 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6936 (tp) REVERT: B 720 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7455 (t80) REVERT: B 814 ARG cc_start: 0.7450 (mmp80) cc_final: 0.7245 (mmt180) REVERT: C 99 ASN cc_start: 0.6800 (m-40) cc_final: 0.6454 (m-40) REVERT: C 119 GLN cc_start: 0.6191 (OUTLIER) cc_final: 0.5682 (pt0) REVERT: E 99 ASN cc_start: 0.7382 (m-40) cc_final: 0.7049 (m-40) outliers start: 39 outliers final: 19 residues processed: 191 average time/residue: 0.0926 time to fit residues: 27.1214 Evaluate side-chains 178 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 127 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 153 optimal weight: 0.0370 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4305 r_free = 0.4305 target = 0.205729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139985 restraints weight = 14457.636| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.73 r_work: 0.3464 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14502 Z= 0.109 Angle : 0.487 10.200 19438 Z= 0.248 Chirality : 0.038 0.121 2160 Planarity : 0.004 0.063 2340 Dihedral : 8.185 105.901 2270 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.16 % Allowed : 19.60 % Favored : 77.24 % 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: 2.09 (0.21), residues: 1654 helix: 2.71 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 23 TYR 0.015 0.001 TYR A 245 PHE 0.013 0.001 PHE C 105 TRP 0.012 0.001 TRP F 25 HIS 0.002 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14496) covalent geometry : angle 0.47350 / 0.24 (19428) SS BOND : bond 0.00299 / 0.15 ( 2) SS BOND : angle 1.07772 / 0.63 ( 4) hydrogen bonds : bond 0.03731 / 2.48 ( 878) hydrogen bonds : angle 3.55796 / 2.58 ( 2622) Misc. bond : bond 0.00014 / 0.01 ( 2) link_NAG-ASN : bond 0.01402 / 0.71 ( 2) link_NAG-ASN : angle 6.40681 / 3.31 ( 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 208 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6200 (ttp) cc_final: 0.5463 (mmt) REVERT: A 331 ILE cc_start: 0.7144 (mm) cc_final: 0.6409 (mt) REVERT: A 335 GLU cc_start: 0.6004 (mp0) cc_final: 0.5644 (mp0) REVERT: A 372 TYR cc_start: 0.7469 (t80) cc_final: 0.7211 (t80) REVERT: A 394 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7168 (mm-40) REVERT: A 435 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7235 (tp) REVERT: A 720 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7371 (t80) REVERT: A 814 ARG cc_start: 0.7612 (mmp80) cc_final: 0.7406 (mmt180) REVERT: B 138 MET cc_start: 0.6156 (ttp) cc_final: 0.5376 (mmt) REVERT: B 331 ILE cc_start: 0.7275 (mt) cc_final: 0.6226 (mp) REVERT: B 335 GLU cc_start: 0.6003 (mp0) cc_final: 0.5479 (mp0) REVERT: B 372 TYR cc_start: 0.7471 (t80) cc_final: 0.7197 (t80) REVERT: B 394 GLN cc_start: 0.7340 (mm-40) cc_final: 0.7099 (mm-40) REVERT: B 720 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7393 (t80) REVERT: C 99 ASN cc_start: 0.6941 (m-40) cc_final: 0.6591 (m-40) REVERT: C 119 GLN cc_start: 0.6279 (OUTLIER) cc_final: 0.5727 (pt0) REVERT: E 99 ASN cc_start: 0.7593 (m-40) cc_final: 0.6434 (m-40) outliers start: 46 outliers final: 25 residues processed: 191 average time/residue: 0.0891 time to fit residues: 26.4895 Evaluate side-chains 183 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 147 THR 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 C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 130 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.206001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144347 restraints weight = 14554.386| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.48 r_work: 0.3441 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1232 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= 0.123 Angle : 0.498 9.723 19438 Z= 0.254 Chirality : 0.038 0.123 2160 Planarity : 0.004 0.064 2340 Dihedral : 8.036 106.317 2270 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.78 % Allowed : 19.05 % 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: 1.98 (0.21), residues: 1654 helix: 2.60 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.86 (0.25), residues: 512 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 0.013 0.001 PHE E 109 TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (14496) covalent geometry : angle 0.48569 / 0.25 (19428) SS BOND : bond 0.00386 / 0.19 ( 2) SS BOND : angle 1.22359 / 0.70 ( 4) hydrogen bonds : bond 0.03910 / 2.61 ( 878) hydrogen bonds : angle 3.57751 / 2.60 ( 2622) Misc. bond : bond 0.00018 / 0.01 ( 2) link_NAG-ASN : bond 0.01400 / 0.71 ( 2) link_NAG-ASN : angle 6.32797 / 3.22 ( 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 218 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6282 (ttp) cc_final: 0.5465 (mmt) REVERT: A 254 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6946 (mp) REVERT: A 331 ILE cc_start: 0.7185 (mm) cc_final: 0.6412 (mt) REVERT: A 335 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5618 (mp0) REVERT: A 372 TYR cc_start: 0.7577 (t80) cc_final: 0.7321 (t80) REVERT: A 435 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7360 (tp) REVERT: A 720 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7506 (t80) REVERT: B 96 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.4929 (mp10) REVERT: B 138 MET cc_start: 0.6252 (ttp) cc_final: 0.5438 (mmt) REVERT: B 331 ILE cc_start: 0.7372 (mt) cc_final: 0.6298 (mp) REVERT: B 335 GLU cc_start: 0.6071 (mp0) cc_final: 0.5578 (mp0) REVERT: B 372 TYR cc_start: 0.7586 (t80) cc_final: 0.7321 (t80) REVERT: B 435 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7344 (tp) REVERT: B 720 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7521 (t80) REVERT: C 99 ASN cc_start: 0.7056 (m-40) cc_final: 0.6605 (m-40) REVERT: C 119 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.5832 (pt0) REVERT: E 99 ASN cc_start: 0.7009 (m-40) cc_final: 0.6607 (m-40) outliers start: 55 outliers final: 33 residues processed: 200 average time/residue: 0.0864 time to fit residues: 27.0009 Evaluate side-chains 197 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 67 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 106 optimal weight: 0.0670 chunk 161 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN 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 = 0.4324 r_free = 0.4324 target = 0.207533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142547 restraints weight = 14462.551| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.64 r_work: 0.3456 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14502 Z= 0.115 Angle : 0.491 9.251 19438 Z= 0.250 Chirality : 0.038 0.122 2160 Planarity : 0.004 0.063 2340 Dihedral : 7.835 106.126 2270 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.71 % Allowed : 19.33 % Favored : 76.96 % 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: 2.06 (0.21), residues: 1654 helix: 2.65 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.016 0.001 TYR B 245 PHE 0.012 0.001 PHE C 105 TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (14496) covalent geometry : angle 0.48011 / 0.25 (19428) SS BOND : bond 0.00343 / 0.17 ( 2) SS BOND : angle 1.13932 / 0.66 ( 4) hydrogen bonds : bond 0.03786 / 2.52 ( 878) hydrogen bonds : angle 3.54024 / 2.57 ( 2622) Misc. bond : bond 0.00017 / 0.01 ( 2) link_NAG-ASN : bond 0.01387 / 0.70 ( 2) link_NAG-ASN : angle 5.81161 / 2.95 ( 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 216 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.5707 (OUTLIER) cc_final: 0.4609 (mp10) REVERT: A 138 MET cc_start: 0.6105 (ttp) cc_final: 0.5392 (mmt) REVERT: A 189 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7872 (tp) REVERT: A 254 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6737 (mp) REVERT: A 291 MET cc_start: 0.6972 (ttp) cc_final: 0.6336 (mmm) REVERT: A 324 ASN cc_start: 0.6772 (t0) cc_final: 0.6304 (t0) REVERT: A 331 ILE cc_start: 0.6883 (mm) cc_final: 0.6173 (mt) REVERT: A 335 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5515 (mp0) REVERT: A 349 ARG cc_start: 0.6431 (mmp80) cc_final: 0.6197 (mmp80) REVERT: A 372 TYR cc_start: 0.7333 (t80) cc_final: 0.7073 (t80) REVERT: A 435 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6969 (tp) REVERT: A 720 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7434 (t80) REVERT: A 814 ARG cc_start: 0.7544 (mmp80) cc_final: 0.7198 (mmt180) REVERT: B 96 GLN cc_start: 0.5813 (OUTLIER) cc_final: 0.4670 (mp10) REVERT: B 138 MET cc_start: 0.6113 (ttp) cc_final: 0.5341 (mmt) REVERT: B 254 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6809 (mp) REVERT: B 331 ILE cc_start: 0.7134 (mt) cc_final: 0.6192 (mp) REVERT: B 335 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5654 (mp0) REVERT: B 372 TYR cc_start: 0.7327 (t80) cc_final: 0.7054 (t80) REVERT: B 435 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6935 (tp) REVERT: B 720 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7414 (t80) REVERT: C 99 ASN cc_start: 0.6669 (m-40) cc_final: 0.6209 (m-40) REVERT: C 119 GLN cc_start: 0.6255 (OUTLIER) cc_final: 0.5705 (pt0) REVERT: E 99 ASN cc_start: 0.6804 (m-40) cc_final: 0.6445 (m-40) outliers start: 54 outliers final: 30 residues processed: 197 average time/residue: 0.0947 time to fit residues: 28.6842 Evaluate side-chains 195 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.9990 chunk 4 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN A 394 GLN B 144 ASN B 181 ASN B 394 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.207551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142430 restraints weight = 14553.698| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.30 r_work: 0.3458 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1408 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 8.668 19438 Z= 0.250 Chirality : 0.038 0.121 2160 Planarity : 0.004 0.064 2340 Dihedral : 7.711 106.262 2270 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.44 % Allowed : 19.53 % Favored : 77.03 % 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: 2.08 (0.21), residues: 1654 helix: 2.67 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 165 TYR 0.016 0.001 TYR A 245 PHE 0.012 0.001 PHE C 105 TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (14496) covalent geometry : angle 0.47915 / 0.25 (19428) SS BOND : bond 0.00269 / 0.14 ( 2) SS BOND : angle 1.14012 / 0.66 ( 4) hydrogen bonds : bond 0.03771 / 2.51 ( 878) hydrogen bonds : angle 3.52285 / 2.56 ( 2622) Misc. bond : bond 0.00014 / 0.01 ( 2) link_NAG-ASN : bond 0.01264 / 0.63 ( 2) link_NAG-ASN : angle 5.36461 / 2.73 ( 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 203 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 153 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.5695 (OUTLIER) cc_final: 0.4608 (mp10) REVERT: A 138 MET cc_start: 0.6010 (ttp) cc_final: 0.5360 (mmt) REVERT: A 189 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7845 (tp) REVERT: A 254 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6693 (mp) REVERT: A 291 MET cc_start: 0.6828 (ttp) cc_final: 0.6183 (mmm) REVERT: A 324 ASN cc_start: 0.6695 (t0) cc_final: 0.6225 (t0) REVERT: A 331 ILE cc_start: 0.6836 (mm) cc_final: 0.6295 (mt) REVERT: A 335 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.5541 (mp0) REVERT: A 372 TYR cc_start: 0.7293 (t80) cc_final: 0.7030 (t80) REVERT: A 435 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6913 (tp) REVERT: A 720 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7489 (t80) REVERT: A 814 ARG cc_start: 0.7448 (mmp80) cc_final: 0.7110 (mmt180) REVERT: B 96 GLN cc_start: 0.5798 (OUTLIER) cc_final: 0.4651 (mp10) REVERT: B 138 MET cc_start: 0.6005 (ttp) cc_final: 0.5272 (mmt) REVERT: B 189 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7833 (tp) REVERT: B 291 MET cc_start: 0.6924 (ttp) cc_final: 0.6250 (mmm) REVERT: B 331 ILE cc_start: 0.7015 (mt) cc_final: 0.6124 (mp) REVERT: B 335 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: B 372 TYR cc_start: 0.7284 (t80) cc_final: 0.7010 (t80) REVERT: B 435 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6886 (tp) REVERT: B 720 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7470 (t80) REVERT: B 810 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7873 (mtt) REVERT: C 99 ASN cc_start: 0.6532 (m-40) cc_final: 0.6077 (m-40) REVERT: C 119 GLN cc_start: 0.6324 (OUTLIER) cc_final: 0.5798 (pt0) REVERT: C 189 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.4572 (ptp-170) REVERT: E 99 ASN cc_start: 0.6495 (m-40) cc_final: 0.6172 (m-40) REVERT: E 119 GLN cc_start: 0.6200 (OUTLIER) cc_final: 0.5874 (pt0) outliers start: 50 outliers final: 33 residues processed: 184 average time/residue: 0.0935 time to fit residues: 26.8690 Evaluate side-chains 201 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 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 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 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 810 MET 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 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 Chi-restraints excluded: chain F residue 48 ILE 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: 0.7980 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN A 394 GLN B 144 ASN B 181 ASN B 394 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.204117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147169 restraints weight = 14501.563| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.17 r_work: 0.3457 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14502 Z= 0.112 Angle : 0.484 8.267 19438 Z= 0.248 Chirality : 0.038 0.122 2160 Planarity : 0.004 0.064 2340 Dihedral : 7.653 106.271 2270 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.44 % Allowed : 19.88 % 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: 2.10 (0.21), residues: 1654 helix: 2.68 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 175 TYR 0.016 0.001 TYR A 245 PHE 0.012 0.001 PHE C 105 TRP 0.011 0.001 TRP D 25 HIS 0.002 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (14496) covalent geometry : angle 0.47504 / 0.25 (19428) SS BOND : bond 0.00320 / 0.16 ( 2) SS BOND : angle 1.08878 / 0.63 ( 4) hydrogen bonds : bond 0.03742 / 2.49 ( 878) hydrogen bonds : angle 3.51040 / 2.55 ( 2622) Misc. bond : bond 0.00014 / 0.01 ( 2) link_NAG-ASN : bond 0.01218 / 0.61 ( 2) link_NAG-ASN : angle 5.09774 / 2.60 ( 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 206 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.6056 (OUTLIER) cc_final: 0.4965 (mp10) REVERT: A 138 MET cc_start: 0.6298 (ttp) cc_final: 0.5565 (mmt) REVERT: A 189 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8111 (tp) REVERT: A 254 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6892 (mp) REVERT: A 291 MET cc_start: 0.7061 (ttp) cc_final: 0.6457 (mmm) REVERT: A 324 ASN cc_start: 0.7136 (t0) cc_final: 0.6660 (t0) REVERT: A 331 ILE cc_start: 0.7218 (mm) cc_final: 0.6483 (mt) REVERT: A 335 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5830 (mp0) REVERT: A 372 TYR cc_start: 0.7620 (t80) cc_final: 0.7372 (t80) REVERT: A 435 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7343 (tp) REVERT: A 720 TYR cc_start: 0.8334 (OUTLIER) cc_final: 0.7615 (t80) REVERT: A 814 ARG cc_start: 0.7714 (mmp80) cc_final: 0.7385 (mmt180) REVERT: B 96 GLN cc_start: 0.6061 (OUTLIER) cc_final: 0.4941 (mp10) REVERT: B 138 MET cc_start: 0.6313 (ttp) cc_final: 0.5491 (mmt) REVERT: B 189 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8109 (tp) REVERT: B 254 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6950 (mp) REVERT: B 291 MET cc_start: 0.7134 (ttp) cc_final: 0.6500 (mmm) REVERT: B 331 ILE cc_start: 0.7382 (mt) cc_final: 0.6362 (mp) REVERT: B 335 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5777 (mp0) REVERT: B 372 TYR cc_start: 0.7620 (t80) cc_final: 0.7357 (t80) REVERT: B 435 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7420 (tp) REVERT: B 720 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7598 (t80) REVERT: C 99 ASN cc_start: 0.6897 (m-40) cc_final: 0.6434 (m-40) REVERT: C 119 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.5896 (pt0) REVERT: C 189 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.4779 (ptp-170) REVERT: E 99 ASN cc_start: 0.6895 (m-40) cc_final: 0.6566 (m-40) REVERT: E 119 GLN cc_start: 0.6314 (OUTLIER) cc_final: 0.5971 (pt0) outliers start: 50 outliers final: 30 residues processed: 188 average time/residue: 0.0955 time to fit residues: 27.9003 Evaluate side-chains 199 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 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 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 57 ASN Chi-restraints excluded: chain E residue 119 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 158 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 126 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 127 optimal weight: 0.0470 chunk 64 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.205449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.145249 restraints weight = 14644.256| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.32 r_work: 0.3464 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14502 Z= 0.107 Angle : 0.476 7.507 19438 Z= 0.244 Chirality : 0.038 0.122 2160 Planarity : 0.004 0.063 2340 Dihedral : 7.510 106.191 2270 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.09 % Allowed : 20.15 % 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: 2.14 (0.21), residues: 1654 helix: 2.68 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -1.77 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 23 TYR 0.015 0.001 TYR A 245 PHE 0.012 0.001 PHE C 105 TRP 0.012 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14496) covalent geometry : angle 0.46890 / 0.24 (19428) SS BOND : bond 0.00276 / 0.14 ( 2) SS BOND : angle 1.02945 / 0.60 ( 4) hydrogen bonds : bond 0.03639 / 2.42 ( 878) hydrogen bonds : angle 3.47704 / 2.53 ( 2622) Misc. bond : bond 0.00011 / 0.01 ( 2) link_NAG-ASN : bond 0.01095 / 0.55 ( 2) link_NAG-ASN : angle 4.54623 / 2.33 ( 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 203 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.5986 (OUTLIER) cc_final: 0.4904 (mp10) REVERT: A 138 MET cc_start: 0.6252 (ttp) cc_final: 0.5531 (mmt) REVERT: A 189 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8047 (tp) REVERT: A 291 MET cc_start: 0.7043 (ttp) cc_final: 0.6418 (mmm) REVERT: A 331 ILE cc_start: 0.7082 (mm) cc_final: 0.6350 (mt) REVERT: A 335 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5871 (mp0) REVERT: A 372 TYR cc_start: 0.7583 (t80) cc_final: 0.7327 (t80) REVERT: A 394 GLN cc_start: 0.7652 (mm-40) cc_final: 0.6389 (mt0) REVERT: A 435 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7270 (tp) REVERT: A 720 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7559 (t80) REVERT: A 814 ARG cc_start: 0.7694 (mmp80) cc_final: 0.7377 (mmt180) REVERT: B 96 GLN cc_start: 0.6000 (OUTLIER) cc_final: 0.4880 (mp10) REVERT: B 138 MET cc_start: 0.6225 (ttp) cc_final: 0.5436 (mmt) REVERT: B 189 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8043 (tp) REVERT: B 254 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6920 (mp) REVERT: B 291 MET cc_start: 0.7070 (ttp) cc_final: 0.6410 (mmm) REVERT: B 331 ILE cc_start: 0.7338 (mt) cc_final: 0.6326 (mp) REVERT: B 335 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5720 (mp0) REVERT: B 372 TYR cc_start: 0.7585 (t80) cc_final: 0.7324 (t80) REVERT: B 394 GLN cc_start: 0.7658 (mm-40) cc_final: 0.6388 (mt0) REVERT: B 435 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7278 (tp) REVERT: B 720 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7547 (t80) REVERT: C 99 ASN cc_start: 0.6851 (m-40) cc_final: 0.6390 (m-40) REVERT: C 119 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5878 (pt0) REVERT: C 189 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.4786 (ptp-170) REVERT: E 99 ASN cc_start: 0.6821 (m-40) cc_final: 0.6464 (m-40) REVERT: E 119 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.6018 (pt0) outliers start: 45 outliers final: 27 residues processed: 187 average time/residue: 0.1012 time to fit residues: 29.5498 Evaluate side-chains 194 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 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 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 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 452 THR 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 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 57 ASN Chi-restraints excluded: chain E residue 119 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 91 optimal weight: 5.9990 chunk 160 optimal weight: 0.0870 chunk 57 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN A 181 ASN A 394 GLN B 181 ASN B 394 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.207057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149737 restraints weight = 14504.234| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.10 r_work: 0.3482 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1582 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= 0.105 Angle : 0.474 7.106 19438 Z= 0.244 Chirality : 0.038 0.127 2160 Planarity : 0.004 0.062 2340 Dihedral : 7.451 106.256 2270 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.16 % Allowed : 20.29 % 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: 2.17 (0.21), residues: 1654 helix: 2.62 (0.15), residues: 1162 sheet: None (None), residues: 0 loop : -1.65 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 23 TYR 0.015 0.001 TYR A 245 PHE 0.014 0.001 PHE A 376 TRP 0.019 0.001 TRP F 25 HIS 0.002 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (14496) covalent geometry : angle 0.46817 / 0.24 (19428) SS BOND : bond 0.00289 / 0.15 ( 2) SS BOND : angle 0.97381 / 0.57 ( 4) hydrogen bonds : bond 0.03600 / 2.39 ( 878) hydrogen bonds : angle 3.46312 / 2.52 ( 2622) Misc. bond : bond 0.00010 / 0.01 ( 2) link_NAG-ASN : bond 0.01080 / 0.54 ( 2) link_NAG-ASN : angle 4.25752 / 2.19 ( 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 202 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.4917 (mp10) REVERT: A 138 MET cc_start: 0.6263 (ttp) cc_final: 0.5549 (mmt) REVERT: A 189 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8056 (tp) REVERT: A 291 MET cc_start: 0.7054 (ttp) cc_final: 0.6432 (mmm) REVERT: A 324 ASN cc_start: 0.7105 (t0) cc_final: 0.6660 (t0) REVERT: A 331 ILE cc_start: 0.7105 (mm) cc_final: 0.6360 (mt) REVERT: A 335 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5879 (mp0) REVERT: A 372 TYR cc_start: 0.7598 (t80) cc_final: 0.7289 (t80) REVERT: A 394 GLN cc_start: 0.7692 (mm110) cc_final: 0.6457 (mt0) REVERT: A 435 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7399 (tp) REVERT: A 720 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7548 (t80) REVERT: A 814 ARG cc_start: 0.7713 (mmp80) cc_final: 0.7400 (mmt180) REVERT: B 96 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.4890 (mp10) REVERT: B 138 MET cc_start: 0.6255 (ttp) cc_final: 0.5457 (mmt) REVERT: B 189 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8054 (tp) REVERT: B 254 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6940 (mp) REVERT: B 291 MET cc_start: 0.7080 (ttp) cc_final: 0.6423 (mmm) REVERT: B 331 ILE cc_start: 0.7368 (mt) cc_final: 0.6331 (mp) REVERT: B 335 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5741 (mp0) REVERT: B 372 TYR cc_start: 0.7599 (t80) cc_final: 0.7288 (t80) REVERT: B 394 GLN cc_start: 0.7672 (mm110) cc_final: 0.6448 (mt0) REVERT: B 435 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7282 (tp) REVERT: B 720 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7655 (t80) REVERT: C 99 ASN cc_start: 0.6871 (m-40) cc_final: 0.6414 (m-40) REVERT: C 119 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.5925 (pt0) REVERT: C 189 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.4800 (ptp-170) REVERT: E 99 ASN cc_start: 0.6860 (m-40) cc_final: 0.6506 (m-40) REVERT: E 119 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.6016 (pt0) outliers start: 46 outliers final: 27 residues processed: 185 average time/residue: 0.0934 time to fit residues: 27.3621 Evaluate side-chains 194 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 720 TYR 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 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 Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 59 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN A 181 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.204575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148310 restraints weight = 14641.160| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.12 r_work: 0.3465 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1587 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= 0.121 Angle : 0.493 7.026 19438 Z= 0.254 Chirality : 0.038 0.122 2160 Planarity : 0.004 0.063 2340 Dihedral : 7.544 106.608 2270 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.03 % Allowed : 20.70 % Favored : 76.27 % 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: 2.07 (0.21), residues: 1654 helix: 2.60 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -1.75 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 165 TYR 0.017 0.001 TYR A 245 PHE 0.016 0.001 PHE A 376 TRP 0.017 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (14496) covalent geometry : angle 0.48702 / 0.25 (19428) SS BOND : bond 0.00355 / 0.18 ( 2) SS BOND : angle 1.15548 / 0.66 ( 4) hydrogen bonds : bond 0.03808 / 2.54 ( 878) hydrogen bonds : angle 3.50522 / 2.55 ( 2622) Misc. bond : bond 0.00016 / 0.01 ( 2) link_NAG-ASN : bond 0.01050 / 0.53 ( 2) link_NAG-ASN : angle 4.18963 / 2.16 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3615.85 seconds wall clock time: 62 minutes 34.87 seconds (3754.87 seconds total)