Starting phenix.real_space_refine on Fri Jun 13 17:03:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usx_26742/06_2025/7usx_26742.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usx_26742/06_2025/7usx_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_26742/06_2025/7usx_26742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usx_26742/06_2025/7usx_26742.map" model { file = "/net/cci-nas-00/data/ceres_data/7usx_26742/06_2025/7usx_26742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usx_26742/06_2025/7usx_26742.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 5, '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: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 353 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 353 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 264 Unusual residues: {' CA': 2, 'CLR': 1, 'D12': 12, 'NAG': 1, 'PEE': 1, 'R16': 4} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 264 Unusual residues: {' CA': 2, 'CLR': 1, 'D12': 12, 'NAG': 1, 'PEE': 1, 'R16': 4} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'3PE': 1, 'D12': 2, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'3PE': 1, 'D12': 2, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 10.65, per 1000 atoms: 0.75 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: 4.19 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.17 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: 4.14 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2100 1.31 - 1.43: 3916 1.43 - 1.56: 8342 1.56 - 1.68: 8 1.68 - 1.81: 130 Bond restraints: 14496 Sorted by residual: bond pdb=" C21 3PE F 201 " pdb=" O21 3PE F 201 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C21 3PE D 201 " pdb=" O21 3PE D 201 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C30 PEE B1303 " pdb=" O3 PEE B1303 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C30 PEE A1303 " pdb=" O3 PEE A1303 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C10 PEE B1303 " pdb=" O2 PEE B1303 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 18936 3.19 - 6.38: 469 6.38 - 9.56: 17 9.56 - 12.75: 2 12.75 - 15.94: 4 Bond angle restraints: 19428 Sorted by residual: angle pdb=" O3P PEE B1303 " pdb=" P PEE B1303 " pdb=" O4P PEE B1303 " ideal model delta sigma weight residual 92.91 108.85 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" O3P PEE A1303 " pdb=" P PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sigma weight residual 92.91 108.82 -15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" O12 3PE D 201 " pdb=" P 3PE D 201 " pdb=" O14 3PE D 201 " ideal model delta sigma weight residual 123.79 109.41 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE F 201 " pdb=" P 3PE F 201 " pdb=" O14 3PE F 201 " ideal model delta sigma weight residual 123.79 109.46 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C ARG B 334 " pdb=" N GLU B 335 " pdb=" CA GLU B 335 " ideal model delta sigma weight residual 120.72 114.36 6.36 1.67e+00 3.59e-01 1.45e+01 ... (remaining 19423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.07: 8426 31.07 - 62.15: 414 62.15 - 93.22: 32 93.22 - 124.29: 6 124.29 - 155.37: 2 Dihedral angle restraints: 8880 sinusoidal: 3952 harmonic: 4928 Sorted by residual: dihedral pdb=" CB CYS B 667 " pdb=" SG CYS B 667 " pdb=" SG CYS B 816 " pdb=" CB CYS B 816 " ideal model delta sinusoidal sigma weight residual -86.00 -142.54 56.54 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS A 667 " pdb=" SG CYS A 667 " pdb=" SG CYS A 816 " pdb=" CB CYS A 816 " ideal model delta sinusoidal sigma weight residual -86.00 -140.14 54.14 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" C4 PEE A1303 " pdb=" O4P PEE A1303 " pdb=" P PEE A1303 " pdb=" O2P PEE A1303 " ideal model delta sinusoidal sigma weight residual 284.22 128.85 155.37 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 8877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1566 0.041 - 0.081: 503 0.081 - 0.122: 79 0.122 - 0.162: 2 0.162 - 0.203: 10 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA GLU B 335 " pdb=" N GLU B 335 " pdb=" C GLU B 335 " pdb=" CB GLU B 335 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA GLU A 335 " pdb=" N GLU A 335 " pdb=" C GLU A 335 " pdb=" CB GLU A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" C2 PEE A1303 " pdb=" C1 PEE A1303 " pdb=" C3 PEE A1303 " pdb=" O2 PEE A1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.50 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 2157 not shown) Planarity restraints: 2342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1321 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG B1321 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1321 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG B1321 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG B1321 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1321 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG A1321 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1321 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG A1321 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1321 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 209 " 0.155 2.00e-02 2.50e+03 2.83e-01 9.98e+02 pdb=" CG ASN A 209 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A 209 " 0.104 2.00e-02 2.50e+03 pdb=" ND2 ASN A 209 " -0.501 2.00e-02 2.50e+03 pdb=" C1 NAG A1321 " 0.326 2.00e-02 2.50e+03 ... (remaining 2339 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2303 2.76 - 3.29: 13242 3.29 - 3.83: 23278 3.83 - 4.36: 25978 4.36 - 4.90: 47215 Nonbonded interactions: 112016 Sorted by model distance: nonbonded pdb=" O PRO E 63 " pdb=" OG SER E 101 " model vdw 2.223 3.040 nonbonded pdb=" O TYR E 28 " pdb=" OG1 THR E 32 " model vdw 2.248 3.040 nonbonded pdb=" NH2 ARG A 94 " pdb=" O GLN C 29 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP B 683 " pdb=" NZ LYS B 756 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG B 94 " pdb=" O GLN E 29 " model vdw 2.253 3.120 ... (remaining 112011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.010 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 14502 Z= 0.223 Angle : 0.865 15.940 19438 Z= 0.370 Chirality : 0.040 0.203 2160 Planarity : 0.009 0.296 2340 Dihedral : 17.358 155.365 5674 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP D 25 HIS 0.002 0.001 HIS E 198 PHE 0.031 0.001 PHE A 376 TYR 0.015 0.001 TYR B 245 ARG 0.003 0.000 ARG C 165 Details of bonding type rmsd link_NAG-ASN : bond 0.03440 ( 2) link_NAG-ASN : angle 3.54104 ( 6) hydrogen bonds : bond 0.11544 ( 878) hydrogen bonds : angle 5.04012 ( 2622) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.44313 ( 4) covalent geometry : bond 0.00390 (14496) covalent geometry : angle 0.86268 (19428) Misc. bond : bond 0.10836 ( 2) *********************** 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 : 1.453 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: 0.2491 time to fit residues: 61.3268 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 : 1.441 ------------------------------------------------------------------------------- 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 138 optimal weight: 0.6980 chunk 124 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN B 144 ASN B 731 HIS C 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.208604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144201 restraints weight = 14315.646| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.66 r_work: 0.3461 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.0731 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= 0.126 Angle : 0.548 10.598 19438 Z= 0.272 Chirality : 0.040 0.160 2160 Planarity : 0.004 0.064 2340 Dihedral : 11.384 155.640 2471 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.34 % Allowed : 19.19 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1654 helix: 2.49 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.77 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 25 HIS 0.004 0.001 HIS A 233 PHE 0.012 0.001 PHE A 717 TYR 0.020 0.001 TYR B 245 ARG 0.003 0.000 ARG C 189 Details of bonding type rmsd link_NAG-ASN : bond 0.01416 ( 2) link_NAG-ASN : angle 7.50378 ( 6) hydrogen bonds : bond 0.04195 ( 878) hydrogen bonds : angle 3.75187 ( 2622) SS BOND : bond 0.00321 ( 2) SS BOND : angle 1.21663 ( 4) covalent geometry : bond 0.00292 (14496) covalent geometry : angle 0.53167 (19428) Misc. bond : bond 0.00035 ( 2) *********************** 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 205 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6125 (ttp) cc_final: 0.5424 (mmt) REVERT: A 239 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6756 (ttp80) REVERT: A 335 GLU cc_start: 0.5646 (mp0) cc_final: 0.5241 (mp0) REVERT: A 372 TYR cc_start: 0.7284 (t80) cc_final: 0.7018 (t80) REVERT: A 720 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7268 (t80) REVERT: B 138 MET cc_start: 0.6113 (ttp) cc_final: 0.5372 (mmt) REVERT: B 372 TYR cc_start: 0.7248 (t80) cc_final: 0.6975 (t80) REVERT: B 720 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7356 (t80) REVERT: C 99 ASN cc_start: 0.6848 (m-40) cc_final: 0.6485 (m-40) REVERT: C 119 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5714 (pt0) REVERT: C 180 PHE cc_start: 0.3748 (t80) cc_final: 0.2411 (p90) REVERT: E 99 ASN cc_start: 0.7323 (m-40) cc_final: 0.6951 (m-40) outliers start: 34 outliers final: 13 residues processed: 190 average time/residue: 0.2386 time to fit residues: 69.3620 Evaluate side-chains 178 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 C residue 150 THR 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 81 optimal weight: 0.5980 chunk 123 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN B 144 ASN B 394 GLN C 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.204536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138180 restraints weight = 14396.403| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.86 r_work: 0.3435 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14502 Z= 0.128 Angle : 0.513 9.573 19438 Z= 0.260 Chirality : 0.039 0.120 2160 Planarity : 0.004 0.064 2340 Dihedral : 10.432 151.615 2468 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.82 % Allowed : 19.53 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.21), residues: 1654 helix: 2.52 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.84 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 25 HIS 0.003 0.001 HIS A 233 PHE 0.040 0.001 PHE B 208 TYR 0.018 0.001 TYR B 245 ARG 0.002 0.000 ARG C 189 Details of bonding type rmsd link_NAG-ASN : bond 0.01821 ( 2) link_NAG-ASN : angle 6.18906 ( 6) hydrogen bonds : bond 0.04085 ( 878) hydrogen bonds : angle 3.67029 ( 2622) SS BOND : bond 0.00391 ( 2) SS BOND : angle 1.30729 ( 4) covalent geometry : bond 0.00304 (14496) covalent geometry : angle 0.50155 (19428) Misc. bond : bond 0.00048 ( 2) *********************** 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 204 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6229 (ttp) cc_final: 0.5488 (mmt) REVERT: A 239 ARG cc_start: 0.7208 (ttp80) cc_final: 0.6932 (ttp80) REVERT: A 335 GLU cc_start: 0.6083 (mp0) cc_final: 0.5633 (mp0) REVERT: A 372 TYR cc_start: 0.7532 (t80) cc_final: 0.7280 (t80) REVERT: A 394 GLN cc_start: 0.7467 (mm110) cc_final: 0.7167 (mm-40) REVERT: A 720 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7412 (t80) REVERT: B 138 MET cc_start: 0.6193 (ttp) cc_final: 0.5379 (mmt) REVERT: B 239 ARG cc_start: 0.7256 (ttp80) cc_final: 0.6979 (ttp80) REVERT: B 335 GLU cc_start: 0.5872 (mp0) cc_final: 0.5399 (mp0) REVERT: B 394 GLN cc_start: 0.7381 (mm110) cc_final: 0.7098 (mm-40) REVERT: B 435 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7253 (tp) REVERT: B 720 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7533 (t80) REVERT: B 814 ARG cc_start: 0.7617 (mmp80) cc_final: 0.7408 (mmt180) REVERT: C 99 ASN cc_start: 0.6957 (m-40) cc_final: 0.6604 (m-40) REVERT: C 119 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.5806 (pt0) REVERT: E 99 ASN cc_start: 0.7499 (m-40) cc_final: 0.7171 (m-40) outliers start: 41 outliers final: 22 residues processed: 186 average time/residue: 0.2445 time to fit residues: 68.8263 Evaluate side-chains 180 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 444 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 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 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 14 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN B 144 ASN B 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.206254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141848 restraints weight = 14358.714| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.65 r_work: 0.3466 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1114 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= 0.117 Angle : 0.490 8.398 19438 Z= 0.251 Chirality : 0.038 0.121 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.922 145.391 2468 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.89 % Allowed : 19.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1654 helix: 2.65 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.81 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 25 HIS 0.003 0.001 HIS A 233 PHE 0.030 0.001 PHE B 208 TYR 0.017 0.001 TYR B 245 ARG 0.002 0.000 ARG B 349 Details of bonding type rmsd link_NAG-ASN : bond 0.01659 ( 2) link_NAG-ASN : angle 5.62421 ( 6) hydrogen bonds : bond 0.03862 ( 878) hydrogen bonds : angle 3.58464 ( 2622) SS BOND : bond 0.00340 ( 2) SS BOND : angle 1.20011 ( 4) covalent geometry : bond 0.00271 (14496) covalent geometry : angle 0.48010 (19428) Misc. bond : bond 0.00036 ( 2) *********************** 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 213 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.6158 (ttp) cc_final: 0.5429 (mmt) REVERT: A 254 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 331 ILE cc_start: 0.7050 (mm) cc_final: 0.6229 (mt) REVERT: A 335 GLU cc_start: 0.5963 (mp0) cc_final: 0.5528 (mp0) REVERT: A 372 TYR cc_start: 0.7378 (t80) cc_final: 0.7114 (t80) REVERT: A 435 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7111 (tp) REVERT: A 720 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7318 (t80) REVERT: B 138 MET cc_start: 0.6101 (ttp) cc_final: 0.5332 (mmt) REVERT: B 331 ILE cc_start: 0.7201 (mt) cc_final: 0.6182 (mp) REVERT: B 335 GLU cc_start: 0.5947 (mp0) cc_final: 0.5420 (mp0) REVERT: B 349 ARG cc_start: 0.6598 (mmp80) cc_final: 0.6378 (mmp80) REVERT: B 720 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7402 (t80) REVERT: C 99 ASN cc_start: 0.6856 (m-40) cc_final: 0.6528 (m-40) REVERT: C 119 GLN cc_start: 0.6270 (OUTLIER) cc_final: 0.5724 (pt0) REVERT: E 99 ASN cc_start: 0.7468 (m-40) cc_final: 0.6338 (m-40) outliers start: 42 outliers final: 23 residues processed: 196 average time/residue: 0.2424 time to fit residues: 72.4103 Evaluate side-chains 185 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 209 ASN Chi-restraints excluded: chain A residue 254 LEU 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 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 189 LEU 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 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 44 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.207388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142034 restraints weight = 14480.208| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.33 r_work: 0.3484 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1230 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= 0.120 Angle : 0.492 8.747 19438 Z= 0.253 Chirality : 0.038 0.121 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.651 139.141 2468 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.71 % Allowed : 19.39 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1654 helix: 2.65 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS A 233 PHE 0.017 0.001 PHE B 208 TYR 0.017 0.001 TYR B 245 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd link_NAG-ASN : bond 0.01579 ( 2) link_NAG-ASN : angle 5.58013 ( 6) hydrogen bonds : bond 0.03874 ( 878) hydrogen bonds : angle 3.57291 ( 2622) SS BOND : bond 0.00358 ( 2) SS BOND : angle 1.14907 ( 4) covalent geometry : bond 0.00284 (14496) covalent geometry : angle 0.48231 (19428) Misc. bond : bond 0.00020 ( 2) *********************** 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 216 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6064 (ttp) cc_final: 0.5362 (mmt) REVERT: A 254 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6772 (mp) REVERT: A 331 ILE cc_start: 0.6915 (mm) cc_final: 0.6235 (mt) REVERT: A 335 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5457 (mp0) REVERT: A 372 TYR cc_start: 0.7394 (t80) cc_final: 0.7134 (t80) REVERT: A 435 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7089 (tp) REVERT: A 720 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7471 (t80) REVERT: B 96 GLN cc_start: 0.5945 (OUTLIER) cc_final: 0.4797 (mp10) REVERT: B 138 MET cc_start: 0.5996 (ttp) cc_final: 0.5259 (mmt) REVERT: B 254 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6846 (mp) REVERT: B 331 ILE cc_start: 0.7134 (mt) cc_final: 0.6182 (mp) REVERT: B 335 GLU cc_start: 0.5932 (mp0) cc_final: 0.5448 (mp0) REVERT: B 435 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7071 (tp) REVERT: B 720 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7487 (t80) REVERT: C 99 ASN cc_start: 0.6644 (m-40) cc_final: 0.6252 (m-40) REVERT: C 119 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.5840 (pt0) REVERT: E 99 ASN cc_start: 0.6636 (m-40) cc_final: 0.6264 (m-40) outliers start: 54 outliers final: 30 residues processed: 197 average time/residue: 0.2326 time to fit residues: 71.1520 Evaluate side-chains 193 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 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 209 ASN Chi-restraints excluded: chain B residue 254 LEU 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 C residue 150 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 136 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.205480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.139128 restraints weight = 14629.802| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.34 r_work: 0.3445 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14502 Z= 0.124 Angle : 0.500 8.283 19438 Z= 0.256 Chirality : 0.039 0.122 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.503 130.294 2468 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.99 % Allowed : 19.12 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1654 helix: 2.59 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 PHE 0.018 0.001 PHE B 208 TYR 0.017 0.001 TYR A 245 ARG 0.002 0.000 ARG A 349 Details of bonding type rmsd link_NAG-ASN : bond 0.01407 ( 2) link_NAG-ASN : angle 5.18852 ( 6) hydrogen bonds : bond 0.03933 ( 878) hydrogen bonds : angle 3.56990 ( 2622) SS BOND : bond 0.00390 ( 2) SS BOND : angle 1.23741 ( 4) covalent geometry : bond 0.00296 (14496) covalent geometry : angle 0.49180 (19428) Misc. bond : bond 0.00021 ( 2) *********************** 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 220 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.5737 (OUTLIER) cc_final: 0.4639 (mp10) REVERT: A 138 MET cc_start: 0.6030 (ttp) cc_final: 0.5337 (mmt) REVERT: A 254 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6703 (mp) REVERT: A 291 MET cc_start: 0.6938 (ttp) cc_final: 0.6301 (mmm) REVERT: A 331 ILE cc_start: 0.6818 (mm) cc_final: 0.6301 (mt) REVERT: A 335 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5538 (mp0) REVERT: A 349 ARG cc_start: 0.6302 (mmp80) cc_final: 0.6065 (mmp80) REVERT: A 372 TYR cc_start: 0.7353 (t80) cc_final: 0.7099 (t80) REVERT: A 435 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6920 (tp) REVERT: A 720 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7405 (t80) REVERT: A 814 ARG cc_start: 0.7492 (mmp80) cc_final: 0.7140 (mmt180) REVERT: B 96 GLN cc_start: 0.5837 (OUTLIER) cc_final: 0.4682 (mp10) REVERT: B 138 MET cc_start: 0.6035 (ttp) cc_final: 0.5323 (mmt) REVERT: B 254 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6792 (mp) REVERT: B 331 ILE cc_start: 0.7076 (mt) cc_final: 0.6180 (mp) REVERT: B 335 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5553 (mp0) REVERT: B 435 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6937 (tp) REVERT: B 720 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7514 (t80) REVERT: C 99 ASN cc_start: 0.6458 (m-40) cc_final: 0.5979 (m-40) REVERT: C 119 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.5755 (pt0) REVERT: C 189 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.4639 (ptp-170) REVERT: E 99 ASN cc_start: 0.6543 (m-40) cc_final: 0.6216 (m-40) REVERT: E 119 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5892 (pt0) outliers start: 58 outliers final: 32 residues processed: 197 average time/residue: 0.2505 time to fit residues: 74.8398 Evaluate side-chains 204 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 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 C residue 150 THR Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 30 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 98 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 394 GLN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.204478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143090 restraints weight = 14629.869| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.09 r_work: 0.3465 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1427 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= 0.115 Angle : 0.488 7.683 19438 Z= 0.250 Chirality : 0.038 0.122 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.345 115.579 2468 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.09 % Allowed : 20.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.21), residues: 1654 helix: 2.64 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.75 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 25 HIS 0.002 0.001 HIS C 198 PHE 0.013 0.001 PHE B 208 TYR 0.016 0.001 TYR A 245 ARG 0.004 0.000 ARG E 165 Details of bonding type rmsd link_NAG-ASN : bond 0.01219 ( 2) link_NAG-ASN : angle 4.70610 ( 6) hydrogen bonds : bond 0.03776 ( 878) hydrogen bonds : angle 3.52981 ( 2622) SS BOND : bond 0.00368 ( 2) SS BOND : angle 1.07792 ( 4) covalent geometry : bond 0.00268 (14496) covalent geometry : angle 0.48127 (19428) Misc. bond : bond 0.00016 ( 2) *********************** 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 207 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.5987 (OUTLIER) cc_final: 0.4898 (mp10) REVERT: A 138 MET cc_start: 0.6262 (ttp) cc_final: 0.5502 (mmt) REVERT: A 189 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8101 (tp) REVERT: A 254 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6869 (mp) REVERT: A 291 MET cc_start: 0.7015 (ttp) cc_final: 0.6395 (mmm) REVERT: A 324 ASN cc_start: 0.7090 (t0) cc_final: 0.6639 (t0) REVERT: A 331 ILE cc_start: 0.7140 (mm) cc_final: 0.6514 (mt) REVERT: A 335 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5718 (mp0) REVERT: A 372 TYR cc_start: 0.7604 (t80) cc_final: 0.7353 (t80) REVERT: A 435 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7358 (tp) REVERT: A 720 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7514 (t80) REVERT: A 814 ARG cc_start: 0.7701 (mmp80) cc_final: 0.7377 (mmt180) REVERT: B 96 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.4955 (mp10) REVERT: B 138 MET cc_start: 0.6272 (ttp) cc_final: 0.5459 (mmt) REVERT: B 189 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8110 (tp) REVERT: B 324 ASN cc_start: 0.7056 (t0) cc_final: 0.6623 (t0) REVERT: B 331 ILE cc_start: 0.7378 (mt) cc_final: 0.6376 (mp) REVERT: B 335 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5704 (mp0) REVERT: B 435 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7344 (tp) REVERT: B 720 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7599 (t80) REVERT: C 99 ASN cc_start: 0.6836 (m-40) cc_final: 0.6368 (m-40) REVERT: C 119 GLN cc_start: 0.6435 (OUTLIER) cc_final: 0.5884 (pt0) REVERT: C 189 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.4818 (ptp-170) REVERT: E 99 ASN cc_start: 0.6891 (m-40) cc_final: 0.6557 (m-40) outliers start: 45 outliers final: 30 residues processed: 191 average time/residue: 0.2244 time to fit residues: 66.5509 Evaluate side-chains 198 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 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 B residue 778 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 112 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 181 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.204331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142926 restraints weight = 14548.587| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.22 r_work: 0.3472 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1483 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= 0.108 Angle : 0.479 7.384 19438 Z= 0.246 Chirality : 0.038 0.122 2160 Planarity : 0.004 0.063 2340 Dihedral : 9.273 122.019 2468 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.21), residues: 1654 helix: 2.68 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 25 HIS 0.002 0.001 HIS A 233 PHE 0.014 0.001 PHE B 208 TYR 0.016 0.001 TYR A 245 ARG 0.001 0.000 ARG E 62 Details of bonding type rmsd link_NAG-ASN : bond 0.01202 ( 2) link_NAG-ASN : angle 4.52836 ( 6) hydrogen bonds : bond 0.03694 ( 878) hydrogen bonds : angle 3.50067 ( 2622) SS BOND : bond 0.00299 ( 2) SS BOND : angle 1.01732 ( 4) covalent geometry : bond 0.00246 (14496) covalent geometry : angle 0.47190 (19428) Misc. bond : bond 0.00012 ( 2) *********************** 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 207 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.6030 (OUTLIER) cc_final: 0.4953 (mp10) REVERT: A 138 MET cc_start: 0.6258 (ttp) cc_final: 0.5507 (mmt) REVERT: A 189 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8091 (tp) REVERT: A 291 MET cc_start: 0.7058 (ttp) cc_final: 0.6458 (mmm) REVERT: A 331 ILE cc_start: 0.7193 (mm) cc_final: 0.6475 (mt) REVERT: A 335 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5791 (mp0) REVERT: A 372 TYR cc_start: 0.7607 (t80) cc_final: 0.7357 (t80) REVERT: A 435 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7320 (tp) REVERT: A 720 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7577 (t80) REVERT: A 814 ARG cc_start: 0.7719 (mmp80) cc_final: 0.7401 (mmt180) REVERT: B 96 GLN cc_start: 0.6071 (OUTLIER) cc_final: 0.4957 (mp10) REVERT: B 138 MET cc_start: 0.6263 (ttp) cc_final: 0.5454 (mmt) REVERT: B 189 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8077 (tp) REVERT: B 254 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6935 (mp) REVERT: B 291 MET cc_start: 0.7110 (ttp) cc_final: 0.6473 (mmm) REVERT: B 324 ASN cc_start: 0.7059 (t0) cc_final: 0.6626 (t0) REVERT: B 331 ILE cc_start: 0.7367 (mt) cc_final: 0.6350 (mp) REVERT: B 335 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5752 (mp0) REVERT: B 435 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7306 (tp) REVERT: B 720 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7608 (t80) REVERT: C 99 ASN cc_start: 0.6862 (m-40) cc_final: 0.6432 (m-40) REVERT: C 119 GLN cc_start: 0.6443 (OUTLIER) cc_final: 0.5892 (pt0) REVERT: C 189 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.4883 (ptp-170) REVERT: E 99 ASN cc_start: 0.6871 (m-40) cc_final: 0.6553 (m-40) REVERT: E 119 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.5999 (pt0) outliers start: 50 outliers final: 30 residues processed: 187 average time/residue: 0.2346 time to fit residues: 68.5313 Evaluate side-chains 198 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 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 A residue 778 ILE Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 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 778 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 117 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 181 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.203867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143011 restraints weight = 14485.000| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.06 r_work: 0.3466 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14502 Z= 0.130 Angle : 0.499 7.260 19438 Z= 0.256 Chirality : 0.039 0.123 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.307 136.017 2468 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.58 % Allowed : 19.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.21), residues: 1654 helix: 2.58 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.77 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 PHE 0.013 0.001 PHE C 105 TYR 0.018 0.001 TYR A 245 ARG 0.001 0.000 ARG B 764 Details of bonding type rmsd link_NAG-ASN : bond 0.01156 ( 2) link_NAG-ASN : angle 4.41795 ( 6) hydrogen bonds : bond 0.03961 ( 878) hydrogen bonds : angle 3.55361 ( 2622) SS BOND : bond 0.00384 ( 2) SS BOND : angle 1.25128 ( 4) covalent geometry : bond 0.00315 (14496) covalent geometry : angle 0.49322 (19428) Misc. bond : bond 0.00020 ( 2) *********************** 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 210 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.6092 (OUTLIER) cc_final: 0.4992 (mp10) REVERT: A 138 MET cc_start: 0.6302 (ttp) cc_final: 0.5570 (mmt) REVERT: A 254 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6902 (mp) REVERT: A 291 MET cc_start: 0.7090 (ttp) cc_final: 0.6467 (mmm) REVERT: A 324 ASN cc_start: 0.7107 (t0) cc_final: 0.6649 (t0) REVERT: A 331 ILE cc_start: 0.7159 (mm) cc_final: 0.6417 (mt) REVERT: A 335 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5762 (mp0) REVERT: A 372 TYR cc_start: 0.7675 (t80) cc_final: 0.7439 (t80) REVERT: A 435 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7377 (tp) REVERT: A 720 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7587 (t80) REVERT: B 96 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.4958 (mp10) REVERT: B 138 MET cc_start: 0.6307 (ttp) cc_final: 0.5515 (mmt) REVERT: B 254 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6961 (mp) REVERT: B 291 MET cc_start: 0.7160 (ttp) cc_final: 0.6489 (mmm) REVERT: B 324 ASN cc_start: 0.7102 (t0) cc_final: 0.6657 (t0) REVERT: B 331 ILE cc_start: 0.7418 (mt) cc_final: 0.6377 (mp) REVERT: B 335 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5762 (mp0) REVERT: B 435 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7367 (tp) REVERT: B 720 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7611 (t80) REVERT: C 99 ASN cc_start: 0.6823 (m-40) cc_final: 0.6359 (m-40) REVERT: C 119 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.5893 (pt0) REVERT: C 189 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.4884 (ptp-170) REVERT: E 99 ASN cc_start: 0.6904 (m-40) cc_final: 0.6585 (m-40) REVERT: E 119 GLN cc_start: 0.6330 (OUTLIER) cc_final: 0.5983 (pt0) outliers start: 52 outliers final: 34 residues processed: 193 average time/residue: 0.2313 time to fit residues: 69.4302 Evaluate side-chains 204 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE 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 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP 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 97 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 181 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.204692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145926 restraints weight = 14439.702| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.22 r_work: 0.3440 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14502 Z= 0.133 Angle : 0.504 7.111 19438 Z= 0.260 Chirality : 0.039 0.142 2160 Planarity : 0.004 0.064 2340 Dihedral : 9.377 148.051 2468 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.44 % Allowed : 20.08 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.21), residues: 1654 helix: 2.56 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 PHE 0.013 0.001 PHE E 109 TYR 0.018 0.001 TYR A 245 ARG 0.002 0.000 ARG E 62 Details of bonding type rmsd link_NAG-ASN : bond 0.01143 ( 2) link_NAG-ASN : angle 4.31618 ( 6) hydrogen bonds : bond 0.04026 ( 878) hydrogen bonds : angle 3.57102 ( 2622) SS BOND : bond 0.00293 ( 2) SS BOND : angle 1.35500 ( 4) covalent geometry : bond 0.00323 (14496) covalent geometry : angle 0.49842 (19428) Misc. bond : bond 0.00022 ( 2) ********************** 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 211 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLN cc_start: 0.6116 (OUTLIER) cc_final: 0.5017 (mp10) REVERT: A 138 MET cc_start: 0.6309 (ttp) cc_final: 0.5576 (mmt) REVERT: A 254 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6941 (mp) REVERT: A 291 MET cc_start: 0.7097 (ttp) cc_final: 0.6464 (mmm) REVERT: A 324 ASN cc_start: 0.7131 (t0) cc_final: 0.6668 (t0) REVERT: A 331 ILE cc_start: 0.7176 (mm) cc_final: 0.6428 (mt) REVERT: A 335 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5800 (mp0) REVERT: A 372 TYR cc_start: 0.7685 (t80) cc_final: 0.7452 (t80) REVERT: A 435 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7460 (tp) REVERT: A 720 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.7606 (t80) REVERT: B 96 GLN cc_start: 0.6098 (OUTLIER) cc_final: 0.4968 (mp10) REVERT: B 138 MET cc_start: 0.6293 (ttp) cc_final: 0.5516 (mmt) REVERT: B 254 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6966 (mp) REVERT: B 291 MET cc_start: 0.7157 (ttp) cc_final: 0.6476 (mmm) REVERT: B 324 ASN cc_start: 0.7115 (t0) cc_final: 0.6670 (t0) REVERT: B 331 ILE cc_start: 0.7430 (mt) cc_final: 0.6400 (mp) REVERT: B 335 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5792 (mp0) REVERT: B 435 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7386 (tp) REVERT: B 720 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7629 (t80) REVERT: C 99 ASN cc_start: 0.6812 (m-40) cc_final: 0.6384 (m-40) REVERT: C 119 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.5956 (pt0) REVERT: C 189 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.4877 (ptp-170) REVERT: E 99 ASN cc_start: 0.6914 (m-40) cc_final: 0.6595 (m-40) REVERT: E 119 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.6014 (pt0) outliers start: 50 outliers final: 33 residues processed: 193 average time/residue: 0.2331 time to fit residues: 69.2978 Evaluate side-chains 206 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE 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 189 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 720 TYR Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 192 ASP 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 63 optimal weight: 1.9990 chunk 152 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 106 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 181 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142984 restraints weight = 14737.160| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.10 r_work: 0.3469 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14502 Z= 0.114 Angle : 0.490 6.916 19438 Z= 0.252 Chirality : 0.038 0.123 2160 Planarity : 0.004 0.063 2340 Dihedral : 9.292 158.653 2468 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.37 % Allowed : 20.15 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.21), residues: 1654 helix: 2.64 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 25 HIS 0.002 0.001 HIS E 198 PHE 0.013 0.001 PHE B 208 TYR 0.016 0.001 TYR A 245 ARG 0.002 0.000 ARG D 23 Details of bonding type rmsd link_NAG-ASN : bond 0.01100 ( 2) link_NAG-ASN : angle 4.07568 ( 6) hydrogen bonds : bond 0.03780 ( 878) hydrogen bonds : angle 3.51527 ( 2622) SS BOND : bond 0.00336 ( 2) SS BOND : angle 1.13221 ( 4) covalent geometry : bond 0.00265 (14496) covalent geometry : angle 0.48422 (19428) Misc. bond : bond 0.00014 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9394.95 seconds wall clock time: 164 minutes 53.87 seconds (9893.87 seconds total)