Starting phenix.real_space_refine on Sun May 3 22:37:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uj4_64213/05_2026/9uj4_64213_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uj4_64213/05_2026/9uj4_64213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uj4_64213/05_2026/9uj4_64213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uj4_64213/05_2026/9uj4_64213.map" model { file = "/net/cci-nas-00/data/ceres_data/9uj4_64213/05_2026/9uj4_64213_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uj4_64213/05_2026/9uj4_64213_neut.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 4 5.49 5 S 80 5.16 5 C 10316 2.51 5 N 2696 2.21 5 O 2860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15968 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2827 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 7, 'TRANS': 341} Chain breaks: 2 Chain: "B" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2827 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 7, 'TRANS': 341} Chain breaks: 2 Chain: "F" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2827 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 7, 'TRANS': 341} Chain breaks: 2 Chain: "D" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2827 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 7, 'TRANS': 341} Chain breaks: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 58 Unusual residues: {' K': 4, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" 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: "H" 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: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "F" 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: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "D" 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: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.27, per 1000 atoms: 0.27 Number of scatterers: 15968 At special positions: 0 Unit cell: (114.939, 114.939, 121.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 80 16.00 P 4 15.00 O 2860 8.00 N 2696 7.00 C 10316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 689.1 milliseconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 78.3% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.921A pdb=" N GLY A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 144 removed outlier: 3.763A pdb=" N THR A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 178 removed outlier: 4.673A pdb=" N ALA A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 258 through 285 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 341 through 359 removed outlier: 3.664A pdb=" N GLY A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 384 removed outlier: 4.223A pdb=" N ALA A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.600A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 533 Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.633A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 21 Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.590A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 66 through 75 removed outlier: 3.678A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.591A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.678A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 92 Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 128 Processing helix chain 'H' and resid 139 through 149 Processing helix chain 'G' and resid 105 through 116 removed outlier: 3.503A pdb=" N ARG G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 144 removed outlier: 3.763A pdb=" N THR G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 178 removed outlier: 4.674A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU G 151 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU G 163 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL G 164 " --> pdb=" O GLU G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 186 through 195 Processing helix chain 'G' and resid 196 through 217 Processing helix chain 'G' and resid 226 through 237 Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 245 through 258 Processing helix chain 'G' and resid 258 through 285 Processing helix chain 'G' and resid 298 through 311 Processing helix chain 'G' and resid 322 through 336 Processing helix chain 'G' and resid 341 through 359 removed outlier: 3.665A pdb=" N GLY G 345 " --> pdb=" O ALA G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 384 removed outlier: 4.223A pdb=" N ALA G 370 " --> pdb=" O ARG G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 396 removed outlier: 3.600A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE G 396 " --> pdb=" O LYS G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 533 Processing helix chain 'G' and resid 537 through 564 removed outlier: 3.632A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL G 554 " --> pdb=" O LEU G 550 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP G 564 " --> pdb=" O GLN G 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 removed outlier: 3.591A pdb=" N LEU F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.678A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'F' and resid 139 through 149 Processing helix chain 'E' and resid 105 through 116 removed outlier: 3.503A pdb=" N ARG E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 144 removed outlier: 3.763A pdb=" N THR E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 178 removed outlier: 4.674A pdb=" N ALA E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU E 151 " --> pdb=" O GLN E 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 163 " --> pdb=" O MET E 159 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 186 through 195 Processing helix chain 'E' and resid 196 through 217 Processing helix chain 'E' and resid 226 through 237 Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 258 through 285 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 322 through 336 Processing helix chain 'E' and resid 341 through 359 removed outlier: 3.664A pdb=" N GLY E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 384 removed outlier: 4.224A pdb=" N ALA E 370 " --> pdb=" O ARG E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 396 removed outlier: 3.600A pdb=" N ILE E 394 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 396 " --> pdb=" O LYS E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 533 Processing helix chain 'E' and resid 537 through 564 removed outlier: 3.633A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 21 Processing helix chain 'D' and resid 29 through 41 removed outlier: 3.590A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.678A pdb=" N ARG D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'C' and resid 105 through 116 removed outlier: 3.503A pdb=" N ARG C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 144 removed outlier: 3.763A pdb=" N THR C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 178 removed outlier: 4.674A pdb=" N ALA C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 186 through 195 Processing helix chain 'C' and resid 196 through 217 Processing helix chain 'C' and resid 226 through 237 Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 245 through 258 Processing helix chain 'C' and resid 258 through 285 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 341 through 359 removed outlier: 3.665A pdb=" N GLY C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 384 removed outlier: 4.223A pdb=" N ALA C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.600A pdb=" N ILE C 394 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 396 " --> pdb=" O LYS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 533 Processing helix chain 'C' and resid 537 through 564 removed outlier: 3.632A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 100 through 102 1108 hydrogen bonds defined for protein. 3300 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: 2.90 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4244 1.33 - 1.45: 2976 1.45 - 1.57: 8916 1.57 - 1.69: 8 1.69 - 1.81: 136 Bond restraints: 16280 Sorted by residual: bond pdb=" C31 PC1 G 701 " pdb=" O31 PC1 G 701 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C31 PC1 A 705 " pdb=" O31 PC1 A 705 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C31 PC1 C 701 " pdb=" O31 PC1 C 701 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C31 PC1 E 701 " pdb=" O31 PC1 E 701 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C21 PC1 A 705 " pdb=" O21 PC1 A 705 " ideal model delta sigma weight residual 1.331 1.445 -0.114 2.00e-02 2.50e+03 3.28e+01 ... (remaining 16275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 21530 1.72 - 3.45: 316 3.45 - 5.17: 86 5.17 - 6.90: 16 6.90 - 8.62: 12 Bond angle restraints: 21960 Sorted by residual: angle pdb=" CA GLU F 8 " pdb=" CB GLU F 8 " pdb=" CG GLU F 8 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA GLU B 8 " pdb=" CB GLU B 8 " pdb=" CG GLU B 8 " ideal model delta sigma weight residual 114.10 120.91 -6.81 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA GLU H 8 " pdb=" CB GLU H 8 " pdb=" CG GLU H 8 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA GLU D 8 " pdb=" CB GLU D 8 " pdb=" CG GLU D 8 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" C2 PC1 E 701 " pdb=" O21 PC1 E 701 " pdb=" C21 PC1 E 701 " ideal model delta sigma weight residual 119.24 110.62 8.62 3.00e+00 1.11e-01 8.26e+00 ... (remaining 21955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 8600 16.53 - 33.05: 801 33.05 - 49.58: 187 49.58 - 66.11: 32 66.11 - 82.63: 12 Dihedral angle restraints: 9632 sinusoidal: 3944 harmonic: 5688 Sorted by residual: dihedral pdb=" CB MET B 110 " pdb=" CG MET B 110 " pdb=" SD MET B 110 " pdb=" CE MET B 110 " ideal model delta sinusoidal sigma weight residual 60.00 107.98 -47.98 3 1.50e+01 4.44e-03 8.57e+00 dihedral pdb=" CB MET H 110 " pdb=" CG MET H 110 " pdb=" SD MET H 110 " pdb=" CE MET H 110 " ideal model delta sinusoidal sigma weight residual 60.00 107.96 -47.96 3 1.50e+01 4.44e-03 8.57e+00 dihedral pdb=" CB MET F 110 " pdb=" CG MET F 110 " pdb=" SD MET F 110 " pdb=" CE MET F 110 " ideal model delta sinusoidal sigma weight residual 60.00 107.95 -47.95 3 1.50e+01 4.44e-03 8.57e+00 ... (remaining 9629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1518 0.033 - 0.065: 736 0.065 - 0.098: 133 0.098 - 0.131: 45 0.131 - 0.164: 4 Chirality restraints: 2436 Sorted by residual: chirality pdb=" C2 PC1 E 701 " pdb=" C1 PC1 E 701 " pdb=" C3 PC1 E 701 " pdb=" O21 PC1 E 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.65 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" C2 PC1 G 701 " pdb=" C1 PC1 G 701 " pdb=" C3 PC1 G 701 " pdb=" O21 PC1 G 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.65 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" C2 PC1 C 701 " pdb=" C1 PC1 C 701 " pdb=" C3 PC1 C 701 " pdb=" O21 PC1 C 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.65 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 2433 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 164 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" C VAL E 164 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL E 164 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL E 165 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 164 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C VAL C 164 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL C 164 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 165 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 164 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C VAL G 164 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL G 164 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL G 165 " 0.008 2.00e-02 2.50e+03 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 5164 2.82 - 3.40: 18053 3.40 - 3.98: 30674 3.98 - 4.56: 44557 4.56 - 5.14: 62569 Nonbonded interactions: 161017 Sorted by model distance: nonbonded pdb=" O LEU E 175 " pdb=" NH1 ARG E 190 " model vdw 2.245 3.120 nonbonded pdb=" O LEU A 175 " pdb=" NH1 ARG A 190 " model vdw 2.245 3.120 nonbonded pdb=" O LEU G 175 " pdb=" NH1 ARG G 190 " model vdw 2.245 3.120 nonbonded pdb=" O LEU C 175 " pdb=" NH1 ARG C 190 " model vdw 2.245 3.120 nonbonded pdb=" NZ LYS C 362 " pdb=" O GLN C 531 " model vdw 2.333 3.120 ... (remaining 161012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 104 through 564) selection = (chain 'C' and resid 104 through 564) selection = (chain 'E' and resid 104 through 564) selection = (chain 'G' and resid 104 through 564) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 5.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.670 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.005 0.122 16280 Z= 0.217 Angle : 0.620 8.621 21960 Z= 0.333 Chirality : 0.038 0.164 2436 Planarity : 0.003 0.034 2748 Dihedral : 13.725 82.633 5968 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.48 % Allowed : 3.39 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.16), residues: 1940 helix: -1.22 (0.11), residues: 1500 sheet: None (None), residues: 0 loop : -0.96 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 507 TYR 0.013 0.001 TYR F 139 PHE 0.010 0.001 PHE C 332 TRP 0.014 0.002 TRP E 305 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00471 (16280) covalent geometry : angle 0.61964 (21960) hydrogen bonds : bond 0.14388 ( 1108) hydrogen bonds : angle 6.54378 ( 3300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 358 time to evaluate : 0.621 Fit side-chains REVERT: A 249 ARG cc_start: 0.7452 (ttm110) cc_final: 0.7219 (ttp-110) REVERT: A 293 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7527 (ptt180) REVERT: A 366 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.7055 (mmp-170) REVERT: A 393 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7541 (mmtt) REVERT: G 249 ARG cc_start: 0.7458 (ttm110) cc_final: 0.7223 (ttp-110) REVERT: G 293 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7515 (ptt180) REVERT: G 366 ARG cc_start: 0.7396 (mmt-90) cc_final: 0.7060 (mmp-170) REVERT: G 393 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7533 (mmtt) REVERT: E 249 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7250 (ttp-110) REVERT: E 293 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7534 (ptt180) REVERT: E 393 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7573 (mmtt) REVERT: C 249 ARG cc_start: 0.7456 (ttm110) cc_final: 0.7227 (ttp-110) REVERT: C 293 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7543 (ptt180) REVERT: C 366 ARG cc_start: 0.7392 (mmt-90) cc_final: 0.7058 (mmp-170) REVERT: C 393 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7532 (mmtt) outliers start: 8 outliers final: 0 residues processed: 363 average time/residue: 0.9101 time to fit residues: 354.4602 Evaluate side-chains 276 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN A 386 ASN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN B 54 ASN B 108 HIS H 54 ASN H 108 HIS H 112 ASN G 365 ASN G 386 ASN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN F 54 ASN F 108 HIS F 112 ASN E 365 ASN E 386 ASN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN D 54 ASN D 108 HIS D 112 ASN C 365 ASN C 386 ASN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.185136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134029 restraints weight = 15887.611| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.77 r_work: 0.3312 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16280 Z= 0.153 Angle : 0.515 5.450 21960 Z= 0.281 Chirality : 0.039 0.121 2436 Planarity : 0.003 0.040 2748 Dihedral : 8.886 89.163 2344 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 2.60 % Allowed : 10.29 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 1940 helix: 0.43 (0.12), residues: 1516 sheet: None (None), residues: 0 loop : 0.05 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 555 TYR 0.010 0.001 TYR H 139 PHE 0.011 0.001 PHE E 332 TRP 0.013 0.002 TRP E 305 HIS 0.003 0.001 HIS G 240 Details of bonding type rmsd covalent geometry : bond 0.00345 (16280) covalent geometry : angle 0.51526 (21960) hydrogen bonds : bond 0.04908 ( 1108) hydrogen bonds : angle 4.41856 ( 3300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 0.652 Fit side-chains REVERT: A 249 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7143 (ttp-110) REVERT: A 293 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7321 (ptt180) REVERT: A 365 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7675 (m-40) REVERT: A 366 ARG cc_start: 0.7688 (mmt-90) cc_final: 0.7114 (mmp-170) REVERT: B 23 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7139 (p0) REVERT: B 25 ASP cc_start: 0.7652 (m-30) cc_final: 0.7384 (m-30) REVERT: B 83 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7476 (mt-10) REVERT: H 23 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7204 (p0) REVERT: H 25 ASP cc_start: 0.7643 (m-30) cc_final: 0.7406 (m-30) REVERT: H 83 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7465 (mt-10) REVERT: G 249 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7146 (ttp-110) REVERT: G 293 ARG cc_start: 0.8355 (mtt90) cc_final: 0.7325 (ptt180) REVERT: G 365 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7669 (m-40) REVERT: G 366 ARG cc_start: 0.7697 (mmt-90) cc_final: 0.7127 (mmp-170) REVERT: F 25 ASP cc_start: 0.7650 (m-30) cc_final: 0.7397 (m-30) REVERT: F 83 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7441 (mt-10) REVERT: E 249 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7161 (ttp-110) REVERT: E 293 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7329 (ptt180) REVERT: D 23 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7154 (p0) REVERT: D 25 ASP cc_start: 0.7642 (m-30) cc_final: 0.7404 (m-30) REVERT: D 83 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7469 (mt-10) REVERT: C 249 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7147 (ttp-110) REVERT: C 293 ARG cc_start: 0.8359 (mtt90) cc_final: 0.7332 (ptt180) REVERT: C 365 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7667 (m-40) REVERT: C 366 ARG cc_start: 0.7686 (mmt-90) cc_final: 0.7119 (mmp-170) REVERT: C 555 ARG cc_start: 0.7416 (mmt90) cc_final: 0.6931 (mtt180) outliers start: 43 outliers final: 12 residues processed: 297 average time/residue: 0.8813 time to fit residues: 281.5716 Evaluate side-chains 273 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain G residue 365 ASN Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain C residue 365 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 510 HIS ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.183982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131389 restraints weight = 16080.744| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.78 r_work: 0.3287 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16280 Z= 0.166 Angle : 0.508 5.398 21960 Z= 0.275 Chirality : 0.039 0.125 2436 Planarity : 0.003 0.039 2748 Dihedral : 8.797 89.256 2344 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.51 % Allowed : 10.65 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.18), residues: 1940 helix: 0.92 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : 0.19 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 38 TYR 0.011 0.002 TYR H 139 PHE 0.013 0.002 PHE E 332 TRP 0.014 0.002 TRP E 305 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00385 (16280) covalent geometry : angle 0.50754 (21960) hydrogen bonds : bond 0.04878 ( 1108) hydrogen bonds : angle 4.25667 ( 3300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 0.722 Fit side-chains REVERT: A 249 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7201 (ttp-110) REVERT: A 293 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7338 (ptt180) REVERT: A 363 HIS cc_start: 0.7334 (m170) cc_final: 0.6992 (t70) REVERT: B 23 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7193 (p0) REVERT: B 25 ASP cc_start: 0.7693 (m-30) cc_final: 0.7346 (m-30) REVERT: B 140 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6060 (mp0) REVERT: H 23 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7198 (p0) REVERT: H 25 ASP cc_start: 0.7690 (m-30) cc_final: 0.7363 (m-30) REVERT: H 140 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: G 249 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7198 (ttp-110) REVERT: G 293 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7332 (ptt180) REVERT: G 363 HIS cc_start: 0.7323 (m170) cc_final: 0.6989 (t70) REVERT: G 555 ARG cc_start: 0.7427 (mmt90) cc_final: 0.6881 (mtt180) REVERT: F 140 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: E 249 ARG cc_start: 0.7830 (ttm110) cc_final: 0.7503 (ttp-110) REVERT: E 293 ARG cc_start: 0.8385 (mtt90) cc_final: 0.7341 (ptt180) REVERT: E 363 HIS cc_start: 0.7354 (m170) cc_final: 0.7145 (t70) REVERT: D 23 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7208 (p0) REVERT: D 25 ASP cc_start: 0.7686 (m-30) cc_final: 0.7350 (m-30) REVERT: D 110 MET cc_start: 0.8315 (mmp) cc_final: 0.7882 (mmt) REVERT: D 140 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: C 249 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7194 (ttp-110) REVERT: C 293 ARG cc_start: 0.8389 (mtt90) cc_final: 0.7352 (ptt180) REVERT: C 363 HIS cc_start: 0.7323 (m170) cc_final: 0.7003 (t70) REVERT: C 555 ARG cc_start: 0.7449 (mmt90) cc_final: 0.6900 (mtt180) outliers start: 58 outliers final: 16 residues processed: 302 average time/residue: 0.8551 time to fit residues: 277.8704 Evaluate side-chains 272 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 510 HIS ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 HIS ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 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 = 0.4094 r_free = 0.4094 target = 0.184431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132967 restraints weight = 15961.751| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.73 r_work: 0.3284 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16280 Z= 0.153 Angle : 0.488 5.407 21960 Z= 0.265 Chirality : 0.039 0.124 2436 Planarity : 0.003 0.037 2748 Dihedral : 8.642 89.309 2344 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 3.21 % Allowed : 13.62 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.18), residues: 1940 helix: 1.20 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : 0.31 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 38 TYR 0.011 0.001 TYR B 139 PHE 0.012 0.002 PHE A 332 TRP 0.013 0.001 TRP A 305 HIS 0.003 0.001 HIS G 509 Details of bonding type rmsd covalent geometry : bond 0.00352 (16280) covalent geometry : angle 0.48850 (21960) hydrogen bonds : bond 0.04606 ( 1108) hydrogen bonds : angle 4.11969 ( 3300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 261 time to evaluate : 0.620 Fit side-chains REVERT: A 249 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7129 (ttp-110) REVERT: A 293 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7325 (ptt180) REVERT: A 363 HIS cc_start: 0.7296 (m170) cc_final: 0.7038 (t70) REVERT: A 555 ARG cc_start: 0.7578 (mtt90) cc_final: 0.7282 (mtt180) REVERT: B 23 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7085 (p0) REVERT: B 25 ASP cc_start: 0.7658 (m-30) cc_final: 0.7214 (m-30) REVERT: B 140 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: H 23 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7115 (p0) REVERT: H 25 ASP cc_start: 0.7663 (m-30) cc_final: 0.7241 (m-30) REVERT: H 140 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5908 (mp0) REVERT: G 249 ARG cc_start: 0.7758 (ttm110) cc_final: 0.7128 (ttp-110) REVERT: G 293 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7318 (ptt180) REVERT: G 363 HIS cc_start: 0.7300 (m170) cc_final: 0.7045 (t70) REVERT: F 140 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.5965 (mp0) REVERT: E 249 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7131 (ttp-110) REVERT: E 293 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7313 (ptt180) REVERT: E 363 HIS cc_start: 0.7318 (m170) cc_final: 0.7067 (t70) REVERT: D 23 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7111 (p0) REVERT: D 25 ASP cc_start: 0.7660 (m-30) cc_final: 0.7234 (m-30) REVERT: D 140 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5976 (mp0) REVERT: C 249 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7127 (ttp-110) REVERT: C 293 ARG cc_start: 0.8353 (mtt90) cc_final: 0.7336 (ptt180) REVERT: C 363 HIS cc_start: 0.7315 (m170) cc_final: 0.7052 (t70) outliers start: 53 outliers final: 14 residues processed: 289 average time/residue: 0.8634 time to fit residues: 268.4667 Evaluate side-chains 262 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 21 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 154 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 156 optimal weight: 0.0980 chunk 152 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 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 = 0.4125 r_free = 0.4125 target = 0.187664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137135 restraints weight = 15906.297| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.71 r_work: 0.3363 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16280 Z= 0.103 Angle : 0.438 6.151 21960 Z= 0.237 Chirality : 0.036 0.120 2436 Planarity : 0.003 0.037 2748 Dihedral : 8.163 86.950 2344 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.21 % Allowed : 14.71 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.19), residues: 1940 helix: 1.57 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.67 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.008 0.001 TYR C 315 PHE 0.011 0.001 PHE E 332 TRP 0.010 0.001 TRP A 323 HIS 0.003 0.001 HIS E 509 Details of bonding type rmsd covalent geometry : bond 0.00212 (16280) covalent geometry : angle 0.43822 (21960) hydrogen bonds : bond 0.03902 ( 1108) hydrogen bonds : angle 3.88044 ( 3300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 257 time to evaluate : 0.645 Fit side-chains REVERT: A 159 MET cc_start: 0.6585 (mmp) cc_final: 0.5859 (mtp) REVERT: A 293 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7285 (ptt180) REVERT: A 363 HIS cc_start: 0.7300 (m170) cc_final: 0.7036 (t70) REVERT: A 555 ARG cc_start: 0.7550 (mtt90) cc_final: 0.7286 (mtt180) REVERT: B 37 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7514 (mtt) REVERT: H 37 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7491 (mtt) REVERT: G 159 MET cc_start: 0.6556 (mmp) cc_final: 0.5844 (mtp) REVERT: G 293 ARG cc_start: 0.8326 (mtt90) cc_final: 0.7276 (ptt180) REVERT: G 363 HIS cc_start: 0.7246 (m170) cc_final: 0.7014 (t70) REVERT: F 73 MET cc_start: 0.7883 (mmm) cc_final: 0.7461 (mmp) REVERT: E 159 MET cc_start: 0.6608 (mmp) cc_final: 0.5898 (mtp) REVERT: E 293 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7320 (ptt180) REVERT: E 363 HIS cc_start: 0.7320 (m170) cc_final: 0.7086 (t70) REVERT: D 73 MET cc_start: 0.7860 (mmm) cc_final: 0.7419 (mmp) REVERT: C 159 MET cc_start: 0.6560 (mmp) cc_final: 0.5836 (mtp) REVERT: C 293 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7290 (ptt180) REVERT: C 363 HIS cc_start: 0.7278 (m170) cc_final: 0.7048 (t70) REVERT: C 555 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7290 (mtt180) outliers start: 53 outliers final: 8 residues processed: 282 average time/residue: 0.7589 time to fit residues: 232.3502 Evaluate side-chains 247 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 237 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 160 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 530 GLN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 544 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 = 0.4109 r_free = 0.4109 target = 0.186105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139778 restraints weight = 15964.779| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.37 r_work: 0.3329 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16280 Z= 0.127 Angle : 0.460 5.326 21960 Z= 0.248 Chirality : 0.038 0.123 2436 Planarity : 0.003 0.036 2748 Dihedral : 8.129 85.583 2344 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.60 % Allowed : 16.40 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.19), residues: 1940 helix: 1.61 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.69 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 38 TYR 0.009 0.001 TYR F 139 PHE 0.012 0.001 PHE A 332 TRP 0.011 0.001 TRP C 305 HIS 0.002 0.001 HIS G 509 Details of bonding type rmsd covalent geometry : bond 0.00286 (16280) covalent geometry : angle 0.46002 (21960) hydrogen bonds : bond 0.04150 ( 1108) hydrogen bonds : angle 3.90783 ( 3300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.655 Fit side-chains REVERT: A 159 MET cc_start: 0.6715 (mmp) cc_final: 0.5946 (mtp) REVERT: A 249 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7544 (ttp-110) REVERT: A 293 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7361 (ptt90) REVERT: A 555 ARG cc_start: 0.7578 (mtt90) cc_final: 0.7279 (mtt180) REVERT: B 73 MET cc_start: 0.7967 (mmm) cc_final: 0.7607 (mmp) REVERT: G 159 MET cc_start: 0.6692 (mmp) cc_final: 0.5937 (mtp) REVERT: G 249 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7551 (ttp-110) REVERT: G 293 ARG cc_start: 0.8342 (mtt90) cc_final: 0.7354 (ptt90) REVERT: F 73 MET cc_start: 0.8011 (mmm) cc_final: 0.7696 (mmp) REVERT: E 159 MET cc_start: 0.6712 (mmp) cc_final: 0.5983 (mtp) REVERT: E 249 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7548 (ttp-110) REVERT: E 293 ARG cc_start: 0.8362 (mtt90) cc_final: 0.7387 (ptt180) REVERT: D 73 MET cc_start: 0.7996 (mmm) cc_final: 0.7516 (mmp) REVERT: C 159 MET cc_start: 0.6671 (mmp) cc_final: 0.5924 (mtp) REVERT: C 249 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7552 (ttp-110) REVERT: C 293 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7374 (ptt90) REVERT: C 555 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7346 (mtt180) outliers start: 43 outliers final: 11 residues processed: 264 average time/residue: 0.8165 time to fit residues: 232.5596 Evaluate side-chains 253 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 242 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 0.4980 chunk 110 optimal weight: 0.3980 chunk 124 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.186808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141022 restraints weight = 15897.877| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.46 r_work: 0.3351 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16280 Z= 0.112 Angle : 0.452 5.881 21960 Z= 0.242 Chirality : 0.037 0.126 2436 Planarity : 0.003 0.035 2748 Dihedral : 7.993 84.516 2344 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.54 % Allowed : 17.13 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.19), residues: 1940 helix: 1.70 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.72 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 38 TYR 0.009 0.001 TYR F 139 PHE 0.012 0.001 PHE G 332 TRP 0.009 0.001 TRP C 323 HIS 0.003 0.001 HIS G 509 Details of bonding type rmsd covalent geometry : bond 0.00243 (16280) covalent geometry : angle 0.45243 (21960) hydrogen bonds : bond 0.03976 ( 1108) hydrogen bonds : angle 3.84314 ( 3300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.580 Fit side-chains REVERT: A 159 MET cc_start: 0.6609 (mmp) cc_final: 0.5846 (mtp) REVERT: A 293 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7316 (ptt180) REVERT: A 555 ARG cc_start: 0.7583 (mtt90) cc_final: 0.7252 (mtt180) REVERT: B 73 MET cc_start: 0.7980 (mmm) cc_final: 0.7623 (mmp) REVERT: H 73 MET cc_start: 0.7966 (mmm) cc_final: 0.7613 (mmp) REVERT: G 159 MET cc_start: 0.6601 (mmp) cc_final: 0.5830 (mtp) REVERT: G 293 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7299 (ptt180) REVERT: G 555 ARG cc_start: 0.7421 (mtt90) cc_final: 0.7206 (mtt180) REVERT: F 73 MET cc_start: 0.7995 (mmm) cc_final: 0.7563 (mmp) REVERT: E 159 MET cc_start: 0.6600 (mmp) cc_final: 0.5849 (mtp) REVERT: E 249 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7537 (ttp-110) REVERT: E 293 ARG cc_start: 0.8365 (mtt90) cc_final: 0.7330 (ptt180) REVERT: E 555 ARG cc_start: 0.7519 (mtt90) cc_final: 0.7294 (mtt180) REVERT: D 37 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7543 (mtt) REVERT: D 73 MET cc_start: 0.7971 (mmm) cc_final: 0.7724 (mmp) REVERT: C 159 MET cc_start: 0.6606 (mmp) cc_final: 0.5825 (mtp) REVERT: C 249 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7412 (ttp-110) REVERT: C 293 ARG cc_start: 0.8350 (mtt90) cc_final: 0.7320 (ptt180) REVERT: C 555 ARG cc_start: 0.7633 (mtt90) cc_final: 0.7312 (mtt180) outliers start: 42 outliers final: 6 residues processed: 284 average time/residue: 0.7913 time to fit residues: 243.5554 Evaluate side-chains 257 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 250 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 68 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 22 optimal weight: 0.0980 chunk 160 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 530 GLN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 544 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 = 0.4092 r_free = 0.4092 target = 0.184554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132820 restraints weight = 15949.696| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.69 r_work: 0.3315 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16280 Z= 0.170 Angle : 0.516 5.611 21960 Z= 0.274 Chirality : 0.040 0.138 2436 Planarity : 0.003 0.034 2748 Dihedral : 8.119 83.110 2344 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.00 % Allowed : 18.40 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.19), residues: 1940 helix: 1.52 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.74 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 38 TYR 0.012 0.002 TYR F 139 PHE 0.014 0.002 PHE C 332 TRP 0.014 0.002 TRP C 305 HIS 0.003 0.001 HIS G 126 Details of bonding type rmsd covalent geometry : bond 0.00403 (16280) covalent geometry : angle 0.51570 (21960) hydrogen bonds : bond 0.04518 ( 1108) hydrogen bonds : angle 4.00272 ( 3300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.670 Fit side-chains REVERT: A 159 MET cc_start: 0.6503 (mmp) cc_final: 0.5798 (mtp) REVERT: A 249 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7551 (ttp-110) REVERT: A 293 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7277 (ptt180) REVERT: A 555 ARG cc_start: 0.7571 (mtt90) cc_final: 0.7211 (mtt180) REVERT: H 73 MET cc_start: 0.7950 (mmm) cc_final: 0.7592 (mmp) REVERT: G 159 MET cc_start: 0.6494 (mmp) cc_final: 0.5792 (mtp) REVERT: G 249 ARG cc_start: 0.7771 (ttm110) cc_final: 0.7545 (ttp-110) REVERT: G 293 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7275 (ptt180) REVERT: G 555 ARG cc_start: 0.7424 (mtt90) cc_final: 0.7186 (mtt180) REVERT: E 159 MET cc_start: 0.6551 (mmp) cc_final: 0.5804 (mtp) REVERT: E 249 ARG cc_start: 0.7773 (ttm110) cc_final: 0.7551 (ttp-110) REVERT: E 293 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7330 (ptt180) REVERT: E 555 ARG cc_start: 0.7498 (mtt90) cc_final: 0.7277 (mtt180) REVERT: D 73 MET cc_start: 0.7948 (mmm) cc_final: 0.7507 (mmp) REVERT: C 159 MET cc_start: 0.6498 (mmp) cc_final: 0.5794 (mtp) REVERT: C 249 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7555 (ttp-110) REVERT: C 293 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7290 (ptt180) REVERT: C 555 ARG cc_start: 0.7604 (mtt90) cc_final: 0.7246 (mtt180) outliers start: 33 outliers final: 8 residues processed: 269 average time/residue: 0.8520 time to fit residues: 247.2786 Evaluate side-chains 267 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 259 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 110 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 544 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 = 0.4102 r_free = 0.4102 target = 0.185450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139699 restraints weight = 15864.828| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.39 r_work: 0.3321 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16280 Z= 0.136 Angle : 0.490 6.509 21960 Z= 0.260 Chirality : 0.039 0.145 2436 Planarity : 0.003 0.033 2748 Dihedral : 7.940 80.812 2344 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.21 % Allowed : 19.67 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.19), residues: 1940 helix: 1.58 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : 0.92 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 38 TYR 0.010 0.001 TYR H 139 PHE 0.013 0.001 PHE E 332 TRP 0.011 0.001 TRP E 305 HIS 0.002 0.001 HIS A 509 Details of bonding type rmsd covalent geometry : bond 0.00308 (16280) covalent geometry : angle 0.49024 (21960) hydrogen bonds : bond 0.04234 ( 1108) hydrogen bonds : angle 3.94704 ( 3300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.650 Fit side-chains REVERT: A 159 MET cc_start: 0.6564 (mmp) cc_final: 0.5894 (mtp) REVERT: A 249 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7568 (ttp-110) REVERT: A 293 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7375 (ptt90) REVERT: A 555 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7308 (mtt180) REVERT: B 37 MET cc_start: 0.7833 (mtt) cc_final: 0.7564 (mtt) REVERT: B 73 MET cc_start: 0.7991 (mmm) cc_final: 0.7786 (mmp) REVERT: H 37 MET cc_start: 0.7822 (mtt) cc_final: 0.7527 (mtt) REVERT: H 73 MET cc_start: 0.7990 (mmm) cc_final: 0.7709 (mmp) REVERT: G 159 MET cc_start: 0.6535 (mmp) cc_final: 0.5873 (mtp) REVERT: G 249 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7566 (ttp-110) REVERT: G 293 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7363 (ptt90) REVERT: G 555 ARG cc_start: 0.7450 (mtt90) cc_final: 0.7229 (mtt180) REVERT: F 37 MET cc_start: 0.7812 (mtt) cc_final: 0.7517 (mtt) REVERT: F 73 MET cc_start: 0.7998 (mmm) cc_final: 0.7777 (mmp) REVERT: E 159 MET cc_start: 0.6593 (mmp) cc_final: 0.5879 (mtp) REVERT: E 185 VAL cc_start: 0.8937 (t) cc_final: 0.8699 (m) REVERT: E 249 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7582 (ttp-110) REVERT: E 293 ARG cc_start: 0.8382 (mtt90) cc_final: 0.7391 (ptt90) REVERT: E 555 ARG cc_start: 0.7520 (mtt90) cc_final: 0.7319 (mtt180) REVERT: D 37 MET cc_start: 0.7826 (mtt) cc_final: 0.7563 (mtt) REVERT: D 73 MET cc_start: 0.7992 (mmm) cc_final: 0.7651 (mmp) REVERT: C 159 MET cc_start: 0.6550 (mmp) cc_final: 0.5875 (mtp) REVERT: C 249 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7584 (ttp-110) REVERT: C 293 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7372 (ptt90) outliers start: 20 outliers final: 9 residues processed: 254 average time/residue: 0.8285 time to fit residues: 227.2218 Evaluate side-chains 252 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 243 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 156 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 63 optimal weight: 0.0020 chunk 124 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 overall best weight: 0.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.188895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138079 restraints weight = 16002.945| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.68 r_work: 0.3380 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16280 Z= 0.101 Angle : 0.456 6.873 21960 Z= 0.241 Chirality : 0.037 0.153 2436 Planarity : 0.003 0.034 2748 Dihedral : 7.560 76.743 2344 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.91 % Allowed : 20.04 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.19), residues: 1940 helix: 1.77 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : 1.10 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 38 TYR 0.006 0.001 TYR A 315 PHE 0.011 0.001 PHE E 332 TRP 0.010 0.001 TRP C 323 HIS 0.002 0.001 HIS E 509 Details of bonding type rmsd covalent geometry : bond 0.00203 (16280) covalent geometry : angle 0.45612 (21960) hydrogen bonds : bond 0.03706 ( 1108) hydrogen bonds : angle 3.81257 ( 3300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 265 time to evaluate : 0.743 Fit side-chains REVERT: A 159 MET cc_start: 0.6489 (mmp) cc_final: 0.5833 (mtp) REVERT: A 185 VAL cc_start: 0.8806 (t) cc_final: 0.8576 (m) REVERT: A 293 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7309 (ptt180) REVERT: A 366 ARG cc_start: 0.7808 (mmt180) cc_final: 0.7532 (mmp-170) REVERT: A 555 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7351 (mtt180) REVERT: B 37 MET cc_start: 0.7761 (mtt) cc_final: 0.7475 (mtt) REVERT: B 73 MET cc_start: 0.7923 (mmm) cc_final: 0.7691 (mmp) REVERT: H 12 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6676 (pt0) REVERT: H 37 MET cc_start: 0.7780 (mtt) cc_final: 0.7487 (mtt) REVERT: H 73 MET cc_start: 0.7911 (mmm) cc_final: 0.7690 (mmp) REVERT: G 159 MET cc_start: 0.6498 (mmp) cc_final: 0.5831 (mtp) REVERT: G 185 VAL cc_start: 0.8808 (t) cc_final: 0.8573 (m) REVERT: G 293 ARG cc_start: 0.8337 (mtt90) cc_final: 0.7311 (ptt180) REVERT: G 366 ARG cc_start: 0.7801 (mmt180) cc_final: 0.7531 (mmp-170) REVERT: F 12 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6747 (pt0) REVERT: F 37 MET cc_start: 0.7737 (mtt) cc_final: 0.7423 (mtt) REVERT: E 159 MET cc_start: 0.6604 (mmp) cc_final: 0.5862 (mtp) REVERT: E 185 VAL cc_start: 0.8827 (t) cc_final: 0.8591 (m) REVERT: E 293 ARG cc_start: 0.8372 (mtt90) cc_final: 0.7385 (ptt180) REVERT: E 366 ARG cc_start: 0.7792 (mmt180) cc_final: 0.7519 (mmp-170) REVERT: D 37 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7499 (mtt) REVERT: C 159 MET cc_start: 0.6492 (mmp) cc_final: 0.5825 (mtp) REVERT: C 185 VAL cc_start: 0.8801 (t) cc_final: 0.8572 (m) REVERT: C 293 ARG cc_start: 0.8350 (mtt90) cc_final: 0.7314 (ptt180) REVERT: C 366 ARG cc_start: 0.7820 (mmt180) cc_final: 0.7544 (mmp-170) outliers start: 15 outliers final: 5 residues processed: 272 average time/residue: 0.8336 time to fit residues: 245.1150 Evaluate side-chains 241 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 235 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN H 54 ASN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 530 GLN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.186305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.134813 restraints weight = 16033.389| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.74 r_work: 0.3301 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16280 Z= 0.133 Angle : 0.499 10.314 21960 Z= 0.261 Chirality : 0.039 0.139 2436 Planarity : 0.003 0.033 2748 Dihedral : 7.569 74.404 2344 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.79 % Allowed : 20.34 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.19), residues: 1940 helix: 1.65 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : 1.07 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 38 TYR 0.010 0.001 TYR B 139 PHE 0.012 0.001 PHE C 332 TRP 0.011 0.001 TRP A 305 HIS 0.002 0.001 HIS E 509 Details of bonding type rmsd covalent geometry : bond 0.00303 (16280) covalent geometry : angle 0.49891 (21960) hydrogen bonds : bond 0.04090 ( 1108) hydrogen bonds : angle 3.91219 ( 3300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8776.43 seconds wall clock time: 149 minutes 36.32 seconds (8976.32 seconds total)