Starting phenix.real_space_refine on Fri Jun 13 17:24:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cb1_45412/06_2025/9cb1_45412.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cb1_45412/06_2025/9cb1_45412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cb1_45412/06_2025/9cb1_45412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cb1_45412/06_2025/9cb1_45412.map" model { file = "/net/cci-nas-00/data/ceres_data/9cb1_45412/06_2025/9cb1_45412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cb1_45412/06_2025/9cb1_45412.cif" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 9462 2.51 5 N 2589 2.21 5 O 2931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15105 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "B" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "C" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "D" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 841 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 841 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "F" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 841 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3255 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 14, 'TRANS': 414} Chain breaks: 1 Chain: "H" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3255 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 14, 'TRANS': 414} Chain breaks: 1 Chain: "I" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3255 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 14, 'TRANS': 414} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.30, per 1000 atoms: 0.62 Number of scatterers: 15105 At special positions: 0 Unit cell: (136.3, 138.18, 114.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 123 16.00 O 2931 8.00 N 2589 7.00 C 9462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 98 " distance=2.06 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 98 " distance=2.06 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 98 " distance=2.06 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 407 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 182 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS H 249 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 322 " distance=2.03 Simple disulfide: pdb=" SG CYS G 127 " - pdb=" SG CYS G 153 " distance=2.04 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 249 " - pdb=" SG CYS I 84 " distance=2.03 Simple disulfide: pdb=" SG CYS G 283 " - pdb=" SG CYS G 311 " distance=2.03 Simple disulfide: pdb=" SG CYS G 292 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 326 " - pdb=" SG CYS G 335 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 365 " - pdb=" SG CYS G 463 " distance=2.03 Simple disulfide: pdb=" SG CYS G 384 " - pdb=" SG CYS G 390 " distance=2.03 Simple disulfide: pdb=" SG CYS H 28 " - pdb=" SG CYS H 407 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 182 " distance=2.03 Simple disulfide: pdb=" SG CYS H 84 " - pdb=" SG CYS I 249 " distance=2.03 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 322 " distance=2.03 Simple disulfide: pdb=" SG CYS H 127 " - pdb=" SG CYS H 153 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 283 " - pdb=" SG CYS H 311 " distance=2.03 Simple disulfide: pdb=" SG CYS H 292 " - pdb=" SG CYS H 301 " distance=2.03 Simple disulfide: pdb=" SG CYS H 326 " - pdb=" SG CYS H 335 " distance=2.03 Simple disulfide: pdb=" SG CYS H 350 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 365 " - pdb=" SG CYS H 463 " distance=2.03 Simple disulfide: pdb=" SG CYS H 384 " - pdb=" SG CYS H 390 " distance=2.03 Simple disulfide: pdb=" SG CYS I 28 " - pdb=" SG CYS I 407 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 182 " distance=2.03 Simple disulfide: pdb=" SG CYS I 110 " - pdb=" SG CYS I 322 " distance=2.03 Simple disulfide: pdb=" SG CYS I 127 " - pdb=" SG CYS I 153 " distance=2.04 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 283 " - pdb=" SG CYS I 311 " distance=2.03 Simple disulfide: pdb=" SG CYS I 292 " - pdb=" SG CYS I 301 " distance=2.03 Simple disulfide: pdb=" SG CYS I 326 " - pdb=" SG CYS I 335 " distance=2.03 Simple disulfide: pdb=" SG CYS I 350 " - pdb=" SG CYS I 361 " distance=2.03 Simple disulfide: pdb=" SG CYS I 365 " - pdb=" SG CYS I 463 " distance=2.02 Simple disulfide: pdb=" SG CYS I 384 " - pdb=" SG CYS I 390 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG J 1 " - " ASN G 172 " " NAG K 1 " - " ASN H 172 " " NAG L 1 " - " ASN I 172 " Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 2.0 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3630 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 30 sheets defined 26.2% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 28 through 31 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.592A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.548A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.563A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 85 removed outlier: 3.606A pdb=" N SER G 85 " --> pdb=" O LEU G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.533A pdb=" N CYS G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 Processing helix chain 'G' and resid 163 through 172 Processing helix chain 'G' and resid 172 through 177 Processing helix chain 'G' and resid 186 through 210 removed outlier: 3.653A pdb=" N ALA G 190 " --> pdb=" O ASP G 186 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE G 200 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 233 Processing helix chain 'G' and resid 237 through 247 Processing helix chain 'G' and resid 247 through 255 removed outlier: 3.633A pdb=" N ARG G 253 " --> pdb=" O CYS G 249 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS G 254 " --> pdb=" O MET G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 324 No H-bonds generated for 'chain 'G' and resid 322 through 324' Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 344 through 352 Processing helix chain 'G' and resid 441 through 446 Processing helix chain 'G' and resid 459 through 464 Processing helix chain 'H' and resid 65 through 85 removed outlier: 3.607A pdb=" N THR H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.548A pdb=" N CYS H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 141 Processing helix chain 'H' and resid 163 through 172 Processing helix chain 'H' and resid 172 through 177 Processing helix chain 'H' and resid 186 through 210 removed outlier: 3.715A pdb=" N ALA H 190 " --> pdb=" O ASP H 186 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG H 199 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE H 200 " --> pdb=" O PHE H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 233 Processing helix chain 'H' and resid 237 through 247 Processing helix chain 'H' and resid 247 through 255 removed outlier: 3.857A pdb=" N ARG H 252 " --> pdb=" O ARG H 248 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG H 253 " --> pdb=" O CYS H 249 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS H 254 " --> pdb=" O MET H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 322 through 324 No H-bonds generated for 'chain 'H' and resid 322 through 324' Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 344 through 352 Processing helix chain 'H' and resid 441 through 446 removed outlier: 3.500A pdb=" N SER H 445 " --> pdb=" O PRO H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 451 Processing helix chain 'I' and resid 65 through 85 removed outlier: 3.658A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS I 84 " --> pdb=" O GLU I 80 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER I 85 " --> pdb=" O LEU I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 Processing helix chain 'I' and resid 111 through 129 Processing helix chain 'I' and resid 130 through 141 Processing helix chain 'I' and resid 163 through 172 Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 186 through 210 removed outlier: 3.700A pdb=" N ALA I 190 " --> pdb=" O ASP I 186 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE I 200 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 233 Processing helix chain 'I' and resid 237 through 247 Processing helix chain 'I' and resid 247 through 255 removed outlier: 3.521A pdb=" N ARG I 252 " --> pdb=" O ARG I 248 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG I 253 " --> pdb=" O CYS I 249 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 254 " --> pdb=" O MET I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 322 through 324 No H-bonds generated for 'chain 'I' and resid 322 through 324' Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 344 through 352 Processing helix chain 'I' and resid 442 through 447 removed outlier: 4.210A pdb=" N ASP I 447 " --> pdb=" O SER I 443 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 464 removed outlier: 3.622A pdb=" N CYS I 463 " --> pdb=" O ALA I 459 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.300A pdb=" N GLU A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 58 " --> pdb=" O TRP A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.258A pdb=" N GLU B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.259A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 58 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.752A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.697A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.739A pdb=" N GLU E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.107A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.801A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER F 67 " --> pdb=" O GLU F 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.673A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 278 through 279 removed outlier: 3.605A pdb=" N VAL G 278 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE G 31 " --> pdb=" O LYS G 287 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LYS G 287 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLU G 33 " --> pdb=" O ILE G 285 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE G 285 " --> pdb=" O GLU G 33 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP G 309 " --> pdb=" O TYR G 320 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR G 317 " --> pdb=" O VAL G 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 326 through 329 removed outlier: 7.785A pdb=" N VAL G 333 " --> pdb=" O GLY G 34 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU G 36 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N CYS G 335 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL G 38 " --> pdb=" O CYS G 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 146 through 150 removed outlier: 9.759A pdb=" N TRP G 43 " --> pdb=" O ARG G 156 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N LEU G 158 " --> pdb=" O TRP G 43 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR G 45 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR G 160 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL G 47 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL G 162 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR G 49 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER G 266 " --> pdb=" O VAL G 262 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL G 262 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE G 268 " --> pdb=" O ILE G 260 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE G 256 " --> pdb=" O GLN G 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 291 through 295 removed outlier: 3.663A pdb=" N CYS G 301 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 366 " --> pdb=" O CYS G 301 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 372 through 375 removed outlier: 3.511A pdb=" N MET G 372 " --> pdb=" O ALA G 383 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 398 through 402 removed outlier: 7.341A pdb=" N ILE G 392 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLN G 402 " --> pdb=" O CYS G 390 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N CYS G 390 " --> pdb=" O GLN G 402 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 278 through 279 removed outlier: 3.629A pdb=" N VAL H 278 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE H 31 " --> pdb=" O LYS H 287 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LYS H 287 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU H 33 " --> pdb=" O ILE H 285 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE H 285 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP H 309 " --> pdb=" O TYR H 320 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 326 through 329 removed outlier: 7.750A pdb=" N VAL H 333 " --> pdb=" O GLY H 34 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU H 36 " --> pdb=" O VAL H 333 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS H 335 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL H 38 " --> pdb=" O CYS H 335 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 146 through 150 removed outlier: 9.731A pdb=" N TRP H 43 " --> pdb=" O ARG H 156 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N LEU H 158 " --> pdb=" O TRP H 43 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR H 45 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR H 160 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL H 47 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL H 162 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR H 49 " --> pdb=" O VAL H 162 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER H 266 " --> pdb=" O VAL H 262 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL H 262 " --> pdb=" O SER H 266 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE H 268 " --> pdb=" O ILE H 260 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE H 256 " --> pdb=" O GLN H 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 291 through 295 Processing sheet with id=AC5, first strand: chain 'H' and resid 372 through 375 Processing sheet with id=AC6, first strand: chain 'H' and resid 398 through 402 removed outlier: 7.184A pdb=" N ILE H 392 " --> pdb=" O ILE H 400 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLN H 402 " --> pdb=" O CYS H 390 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N CYS H 390 " --> pdb=" O GLN H 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 278 through 279 removed outlier: 3.600A pdb=" N VAL I 278 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE I 31 " --> pdb=" O LYS I 287 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS I 287 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLU I 33 " --> pdb=" O ILE I 285 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE I 285 " --> pdb=" O GLU I 33 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP I 309 " --> pdb=" O TYR I 320 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR I 317 " --> pdb=" O VAL I 343 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 326 through 329 removed outlier: 7.795A pdb=" N VAL I 333 " --> pdb=" O GLY I 34 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU I 36 " --> pdb=" O VAL I 333 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N CYS I 335 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL I 38 " --> pdb=" O CYS I 335 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 146 through 150 removed outlier: 9.815A pdb=" N TRP I 43 " --> pdb=" O ARG I 156 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N LEU I 158 " --> pdb=" O TRP I 43 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR I 45 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR I 160 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL I 47 " --> pdb=" O THR I 160 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL I 162 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR I 49 " --> pdb=" O VAL I 162 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER I 266 " --> pdb=" O VAL I 262 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL I 262 " --> pdb=" O SER I 266 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE I 268 " --> pdb=" O ILE I 260 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE I 256 " --> pdb=" O GLN I 272 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 291 through 292 removed outlier: 6.374A pdb=" N CYS I 365 " --> pdb=" O PHE I 456 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE I 456 " --> pdb=" O CYS I 365 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 372 through 376 Processing sheet with id=AD3, first strand: chain 'I' and resid 398 through 402 removed outlier: 7.382A pdb=" N ILE I 392 " --> pdb=" O ILE I 400 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLN I 402 " --> pdb=" O CYS I 390 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N CYS I 390 " --> pdb=" O GLN I 402 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 1770 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: 5.71 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4939 1.35 - 1.48: 3564 1.48 - 1.61: 6728 1.61 - 1.74: 0 1.74 - 1.87: 153 Bond restraints: 15384 Sorted by residual: bond pdb=" N VAL H 363 " pdb=" CA VAL H 363 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.17e+01 bond pdb=" N VAL H 458 " pdb=" CA VAL H 458 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.17e+01 bond pdb=" N ILE H 279 " pdb=" CA ILE H 279 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N ILE I 279 " pdb=" CA ILE I 279 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.15e+01 bond pdb=" N ILE G 279 " pdb=" CA ILE G 279 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.12e+01 ... (remaining 15379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 20281 2.33 - 4.66: 560 4.66 - 6.99: 18 6.99 - 9.33: 0 9.33 - 11.66: 3 Bond angle restraints: 20862 Sorted by residual: angle pdb=" C6 NAG J 2 " pdb=" C5 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 108.73 120.39 -11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C6 NAG L 2 " pdb=" C5 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 108.73 120.36 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C6 NAG K 2 " pdb=" C5 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 108.73 120.33 -11.60 3.00e+00 1.11e-01 1.49e+01 angle pdb=" N LEU H 460 " pdb=" CA LEU H 460 " pdb=" C LEU H 460 " ideal model delta sigma weight residual 113.97 109.13 4.84 1.28e+00 6.10e-01 1.43e+01 angle pdb=" CA ASP I 280 " pdb=" C ASP I 280 " pdb=" O ASP I 280 " ideal model delta sigma weight residual 122.14 117.62 4.52 1.24e+00 6.50e-01 1.33e+01 ... (remaining 20857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 8842 14.96 - 29.91: 447 29.91 - 44.87: 102 44.87 - 59.82: 50 59.82 - 74.78: 21 Dihedral angle restraints: 9462 sinusoidal: 3798 harmonic: 5664 Sorted by residual: dihedral pdb=" CB CYS I 140 " pdb=" SG CYS I 140 " pdb=" SG CYS I 147 " pdb=" CB CYS I 147 " ideal model delta sinusoidal sigma weight residual 93.00 146.72 -53.72 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CB CYS G 140 " pdb=" SG CYS G 140 " pdb=" SG CYS G 147 " pdb=" CB CYS G 147 " ideal model delta sinusoidal sigma weight residual 93.00 144.63 -51.63 1 1.00e+01 1.00e-02 3.64e+01 dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 147 " pdb=" CB CYS H 147 " ideal model delta sinusoidal sigma weight residual 93.00 143.61 -50.61 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 9459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2156 0.093 - 0.186: 232 0.186 - 0.279: 11 0.279 - 0.372: 3 0.372 - 0.465: 7 Chirality restraints: 2409 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.73e+02 chirality pdb=" C5 NAG J 2 " pdb=" C4 NAG J 2 " pdb=" C6 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.41 -1.94 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C5 NAG K 2 " pdb=" C4 NAG K 2 " pdb=" C6 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.41 -1.95 -0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 2406 not shown) Planarity restraints: 2667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.103 2.00e-02 2.50e+03 8.59e-02 9.23e+01 pdb=" C7 NAG L 1 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.141 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 103 " 0.343 9.50e-02 1.11e+02 1.55e-01 1.92e+01 pdb=" NE ARG E 103 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG E 103 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG E 103 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG E 103 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.66e+01 pdb=" C7 NAG J 2 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.008 2.00e-02 2.50e+03 ... (remaining 2664 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2976 2.78 - 3.31: 13998 3.31 - 3.84: 25262 3.84 - 4.37: 29875 4.37 - 4.90: 51299 Nonbonded interactions: 123410 Sorted by model distance: nonbonded pdb=" OE2 GLU H 21 " pdb=" OH TYR H 409 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU I 21 " pdb=" OH TYR I 409 " model vdw 2.258 3.040 nonbonded pdb=" NH2 ARG C 94 " pdb=" OD2 ASP C 101 " model vdw 2.268 3.120 nonbonded pdb=" O VAL H 388 " pdb=" NZ LYS H 405 " model vdw 2.270 3.120 nonbonded pdb=" OE2 GLU G 21 " pdb=" OH TYR G 409 " model vdw 2.275 3.040 ... (remaining 123405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.006 0.060 15435 Z= 0.388 Angle : 0.869 12.169 20970 Z= 0.555 Chirality : 0.060 0.465 2409 Planarity : 0.010 0.155 2664 Dihedral : 10.320 70.837 5697 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.50 % Favored : 96.35 % Rotamer: Outliers : 0.72 % Allowed : 1.67 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 1944 helix: 0.28 (0.25), residues: 375 sheet: -0.12 (0.20), residues: 612 loop : -0.67 (0.17), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 43 HIS 0.004 0.001 HIS I 435 PHE 0.010 0.001 PHE G 168 TYR 0.025 0.005 TYR D 94 ARG 0.038 0.004 ARG E 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 3) link_NAG-ASN : angle 2.80175 ( 9) link_BETA1-4 : bond 0.02490 ( 3) link_BETA1-4 : angle 5.06213 ( 9) hydrogen bonds : bond 0.22965 ( 703) hydrogen bonds : angle 8.50875 ( 1770) SS BOND : bond 0.00924 ( 45) SS BOND : angle 1.50183 ( 90) covalent geometry : bond 0.00571 (15384) covalent geometry : angle 0.85725 (20862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 294 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8621 (t) REVERT: B 35 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8765 (t) REVERT: C 35 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8795 (t) REVERT: C 80 MET cc_start: 0.8764 (ttp) cc_final: 0.8425 (tmm) REVERT: D 97 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8042 (p) REVERT: E 87 TYR cc_start: 0.8294 (m-80) cc_final: 0.7840 (m-80) REVERT: E 97 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8538 (p) REVERT: F 97 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.7876 (p) REVERT: G 81 LEU cc_start: 0.9526 (tp) cc_final: 0.9313 (mt) REVERT: H 368 HIS cc_start: 0.9344 (t70) cc_final: 0.8945 (t-90) REVERT: I 298 ASN cc_start: 0.8766 (t0) cc_final: 0.8390 (t0) REVERT: I 453 GLN cc_start: 0.9385 (tt0) cc_final: 0.8851 (tm-30) outliers start: 12 outliers final: 1 residues processed: 303 average time/residue: 0.3890 time to fit residues: 157.1672 Evaluate side-chains 121 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 GLN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN E 27 GLN F 27 GLN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 435 HIS H 46 ASN H 298 ASN ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 435 HIS ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 455 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.031907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.024248 restraints weight = 152658.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.025175 restraints weight = 101907.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.025887 restraints weight = 75322.019| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 15435 Z= 0.214 Angle : 0.630 5.510 20970 Z= 0.338 Chirality : 0.044 0.278 2409 Planarity : 0.005 0.050 2664 Dihedral : 4.699 27.188 2256 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 1944 helix: 1.87 (0.27), residues: 360 sheet: -0.28 (0.19), residues: 651 loop : -0.24 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 36 HIS 0.006 0.002 HIS I 435 PHE 0.019 0.002 PHE G 446 TYR 0.020 0.002 TYR A 32 ARG 0.009 0.001 ARG C 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 3) link_NAG-ASN : angle 1.76131 ( 9) link_BETA1-4 : bond 0.00198 ( 3) link_BETA1-4 : angle 2.32033 ( 9) hydrogen bonds : bond 0.04578 ( 703) hydrogen bonds : angle 6.47868 ( 1770) SS BOND : bond 0.00520 ( 45) SS BOND : angle 1.08821 ( 90) covalent geometry : bond 0.00448 (15384) covalent geometry : angle 0.62427 (20862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.9532 (m-10) cc_final: 0.9115 (m-80) REVERT: B 32 TYR cc_start: 0.9462 (m-10) cc_final: 0.9085 (m-80) REVERT: C 32 TYR cc_start: 0.9484 (m-10) cc_final: 0.9144 (m-80) REVERT: C 80 MET cc_start: 0.9196 (ttp) cc_final: 0.8239 (tmm) REVERT: D 21 ILE cc_start: 0.9699 (mp) cc_final: 0.9478 (tp) REVERT: D 29 ILE cc_start: 0.9752 (mt) cc_final: 0.9511 (tt) REVERT: E 21 ILE cc_start: 0.9767 (mp) cc_final: 0.9546 (tp) REVERT: E 29 ILE cc_start: 0.9749 (mt) cc_final: 0.9505 (tt) REVERT: F 21 ILE cc_start: 0.9799 (mp) cc_final: 0.9564 (tp) REVERT: G 219 LYS cc_start: 0.9487 (tptt) cc_final: 0.9266 (tppt) REVERT: H 219 LYS cc_start: 0.9592 (tmtt) cc_final: 0.9307 (tptt) REVERT: H 302 LEU cc_start: 0.9235 (tp) cc_final: 0.8935 (tp) REVERT: I 219 LYS cc_start: 0.9454 (tptt) cc_final: 0.9238 (tppt) REVERT: I 453 GLN cc_start: 0.9450 (tt0) cc_final: 0.8939 (tm-30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.4063 time to fit residues: 73.6976 Evaluate side-chains 82 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 25 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN B 64 GLN C 43 GLN D 89 GLN E 27 GLN E 79 GLN E 89 GLN E 96 GLN F 27 GLN G 46 ASN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.031105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.023638 restraints weight = 161618.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.024517 restraints weight = 107597.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.025201 restraints weight = 79877.765| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15435 Z= 0.193 Angle : 0.566 8.189 20970 Z= 0.303 Chirality : 0.043 0.215 2409 Planarity : 0.004 0.046 2664 Dihedral : 4.649 25.935 2256 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1944 helix: 1.91 (0.26), residues: 384 sheet: -0.46 (0.18), residues: 687 loop : 0.09 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 36 HIS 0.005 0.001 HIS I 435 PHE 0.012 0.002 PHE I 446 TYR 0.019 0.002 TYR G 299 ARG 0.010 0.001 ARG D 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 3) link_NAG-ASN : angle 1.43881 ( 9) link_BETA1-4 : bond 0.00254 ( 3) link_BETA1-4 : angle 1.84886 ( 9) hydrogen bonds : bond 0.03714 ( 703) hydrogen bonds : angle 6.01977 ( 1770) SS BOND : bond 0.00415 ( 45) SS BOND : angle 0.86017 ( 90) covalent geometry : bond 0.00391 (15384) covalent geometry : angle 0.56286 (20862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.9536 (m-10) cc_final: 0.9003 (m-80) REVERT: B 32 TYR cc_start: 0.9554 (m-10) cc_final: 0.9134 (m-80) REVERT: C 32 TYR cc_start: 0.9512 (m-10) cc_final: 0.9037 (m-80) REVERT: D 21 ILE cc_start: 0.9710 (mp) cc_final: 0.9495 (tp) REVERT: D 29 ILE cc_start: 0.9764 (mt) cc_final: 0.9518 (tt) REVERT: F 21 ILE cc_start: 0.9787 (mp) cc_final: 0.9573 (tp) REVERT: G 234 MET cc_start: 0.9114 (mmm) cc_final: 0.8358 (mmm) REVERT: H 219 LYS cc_start: 0.9517 (tmtt) cc_final: 0.9290 (tptt) REVERT: H 234 MET cc_start: 0.9095 (mmm) cc_final: 0.8275 (mmm) REVERT: H 302 LEU cc_start: 0.9404 (tp) cc_final: 0.9158 (tp) REVERT: I 234 MET cc_start: 0.9071 (mmm) cc_final: 0.8454 (mmm) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3470 time to fit residues: 49.1015 Evaluate side-chains 71 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 113 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN D 89 GLN E 89 GLN E 96 GLN F 27 GLN F 79 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 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 = 0.2762 r_free = 0.2762 target = 0.029581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.022643 restraints weight = 172195.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.023505 restraints weight = 112429.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.024167 restraints weight = 82358.889| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15435 Z= 0.279 Angle : 0.675 6.353 20970 Z= 0.354 Chirality : 0.044 0.256 2409 Planarity : 0.005 0.047 2664 Dihedral : 5.171 29.497 2256 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 1944 helix: 1.41 (0.26), residues: 402 sheet: -0.58 (0.19), residues: 582 loop : -0.03 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 103 HIS 0.009 0.002 HIS I 435 PHE 0.028 0.002 PHE G 334 TYR 0.023 0.003 TYR C 32 ARG 0.005 0.001 ARG I 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 3) link_NAG-ASN : angle 2.06065 ( 9) link_BETA1-4 : bond 0.00336 ( 3) link_BETA1-4 : angle 2.23781 ( 9) hydrogen bonds : bond 0.03798 ( 703) hydrogen bonds : angle 6.31114 ( 1770) SS BOND : bond 0.00438 ( 45) SS BOND : angle 1.07059 ( 90) covalent geometry : bond 0.00553 (15384) covalent geometry : angle 0.67001 (20862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.9590 (m-80) cc_final: 0.8729 (m-80) REVERT: B 32 TYR cc_start: 0.9587 (m-80) cc_final: 0.8798 (m-80) REVERT: C 32 TYR cc_start: 0.9600 (m-80) cc_final: 0.9239 (m-80) REVERT: G 219 LYS cc_start: 0.9356 (tptt) cc_final: 0.9096 (tptp) REVERT: G 234 MET cc_start: 0.9064 (mmm) cc_final: 0.8678 (mmm) REVERT: G 457 ASN cc_start: 0.7002 (m110) cc_final: 0.6437 (m110) REVERT: H 234 MET cc_start: 0.8954 (mmm) cc_final: 0.8616 (mmm) REVERT: H 244 MET cc_start: 0.8998 (mtt) cc_final: 0.8198 (mmt) REVERT: I 219 LYS cc_start: 0.9369 (tptt) cc_final: 0.9154 (tptp) REVERT: I 234 MET cc_start: 0.8878 (mmm) cc_final: 0.8498 (mmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3732 time to fit residues: 46.5385 Evaluate side-chains 61 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 81 optimal weight: 0.1980 chunk 68 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 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 = 0.2751 r_free = 0.2751 target = 0.028911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.022096 restraints weight = 178186.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.022943 restraints weight = 116100.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.023595 restraints weight = 85136.398| |-----------------------------------------------------------------------------| r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15435 Z= 0.289 Angle : 0.668 7.233 20970 Z= 0.356 Chirality : 0.044 0.240 2409 Planarity : 0.005 0.053 2664 Dihedral : 5.417 32.987 2256 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 1944 helix: 1.03 (0.25), residues: 402 sheet: -0.62 (0.18), residues: 648 loop : -0.14 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 32 HIS 0.009 0.002 HIS I 435 PHE 0.021 0.002 PHE H 200 TYR 0.024 0.003 TYR C 32 ARG 0.009 0.001 ARG H 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 3) link_NAG-ASN : angle 2.04088 ( 9) link_BETA1-4 : bond 0.00242 ( 3) link_BETA1-4 : angle 2.07739 ( 9) hydrogen bonds : bond 0.03745 ( 703) hydrogen bonds : angle 6.44157 ( 1770) SS BOND : bond 0.00455 ( 45) SS BOND : angle 0.95092 ( 90) covalent geometry : bond 0.00569 (15384) covalent geometry : angle 0.66409 (20862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 234 MET cc_start: 0.8940 (mmm) cc_final: 0.8592 (mmm) REVERT: H 234 MET cc_start: 0.8883 (mmm) cc_final: 0.8519 (mmm) REVERT: I 205 ARG cc_start: 0.9532 (ptp-110) cc_final: 0.9239 (ptp-110) REVERT: I 234 MET cc_start: 0.8836 (mmm) cc_final: 0.8371 (mmm) REVERT: I 244 MET cc_start: 0.8957 (mtt) cc_final: 0.8511 (mmm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3557 time to fit residues: 42.1770 Evaluate side-chains 50 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 11 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 122 optimal weight: 0.1980 chunk 162 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 141 optimal weight: 0.0670 chunk 43 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 96 GLN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 313 ASN ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 435 HIS ** 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 = 0.2773 r_free = 0.2773 target = 0.028317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.021543 restraints weight = 176108.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.022362 restraints weight = 115924.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.022997 restraints weight = 85585.995| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15435 Z= 0.164 Angle : 0.546 8.473 20970 Z= 0.293 Chirality : 0.043 0.188 2409 Planarity : 0.004 0.047 2664 Dihedral : 5.059 29.088 2256 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1944 helix: 1.48 (0.26), residues: 405 sheet: -0.32 (0.19), residues: 591 loop : -0.16 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 32 HIS 0.006 0.001 HIS I 435 PHE 0.014 0.002 PHE G 334 TYR 0.021 0.002 TYR E 94 ARG 0.009 0.000 ARG H 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 3) link_NAG-ASN : angle 1.61856 ( 9) link_BETA1-4 : bond 0.00271 ( 3) link_BETA1-4 : angle 1.67867 ( 9) hydrogen bonds : bond 0.03178 ( 703) hydrogen bonds : angle 6.18844 ( 1770) SS BOND : bond 0.00395 ( 45) SS BOND : angle 0.90578 ( 90) covalent geometry : bond 0.00332 (15384) covalent geometry : angle 0.54223 (20862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9265 (mtm) cc_final: 0.8842 (ppp) REVERT: D 29 ILE cc_start: 0.9774 (pt) cc_final: 0.9556 (mt) REVERT: G 234 MET cc_start: 0.8980 (mmm) cc_final: 0.8554 (mmm) REVERT: G 368 HIS cc_start: 0.9372 (t-90) cc_final: 0.9164 (t-90) REVERT: H 234 MET cc_start: 0.8949 (mmm) cc_final: 0.8553 (mmm) REVERT: H 244 MET cc_start: 0.8771 (mtt) cc_final: 0.8018 (mmt) REVERT: I 234 MET cc_start: 0.8862 (mmm) cc_final: 0.8209 (mmm) REVERT: I 244 MET cc_start: 0.8832 (mtt) cc_final: 0.7965 (mmt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3903 time to fit residues: 44.0314 Evaluate side-chains 52 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 92 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 187 optimal weight: 0.0470 chunk 136 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 overall best weight: 6.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 313 ASN ** I 435 HIS ** 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 = 0.2718 r_free = 0.2718 target = 0.027348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.020812 restraints weight = 187079.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.021630 restraints weight = 122496.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.022257 restraints weight = 89933.952| |-----------------------------------------------------------------------------| r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 15435 Z= 0.347 Angle : 0.745 8.394 20970 Z= 0.393 Chirality : 0.045 0.234 2409 Planarity : 0.005 0.047 2664 Dihedral : 5.655 34.948 2256 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 1944 helix: 0.74 (0.24), residues: 402 sheet: -0.71 (0.19), residues: 624 loop : -0.26 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 32 HIS 0.012 0.002 HIS I 435 PHE 0.018 0.003 PHE I 48 TYR 0.027 0.003 TYR G 409 ARG 0.010 0.001 ARG D 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 3) link_NAG-ASN : angle 2.53491 ( 9) link_BETA1-4 : bond 0.00520 ( 3) link_BETA1-4 : angle 2.45949 ( 9) hydrogen bonds : bond 0.03956 ( 703) hydrogen bonds : angle 6.73028 ( 1770) SS BOND : bond 0.00432 ( 45) SS BOND : angle 1.01922 ( 90) covalent geometry : bond 0.00675 (15384) covalent geometry : angle 0.74045 (20862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 MET cc_start: 0.8474 (pmm) cc_final: 0.7644 (pmm) REVERT: F 4 MET cc_start: 0.8630 (pmm) cc_final: 0.7806 (pmm) REVERT: G 234 MET cc_start: 0.8943 (mmm) cc_final: 0.8499 (mmm) REVERT: G 244 MET cc_start: 0.8873 (mmt) cc_final: 0.8657 (mmt) REVERT: G 368 HIS cc_start: 0.9363 (t-90) cc_final: 0.9138 (t-90) REVERT: H 234 MET cc_start: 0.8981 (mmm) cc_final: 0.8668 (mmm) REVERT: H 244 MET cc_start: 0.8994 (mtt) cc_final: 0.8303 (mmt) REVERT: I 234 MET cc_start: 0.8921 (mmm) cc_final: 0.8243 (mmm) REVERT: I 302 LEU cc_start: 0.9668 (tp) cc_final: 0.9439 (tp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3232 time to fit residues: 31.2040 Evaluate side-chains 46 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 89 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN E 89 GLN F 37 GLN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 435 HIS ** 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 = 0.2755 r_free = 0.2755 target = 0.028341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.021332 restraints weight = 170747.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.022191 restraints weight = 111202.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.022861 restraints weight = 81750.546| |-----------------------------------------------------------------------------| r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15435 Z= 0.136 Angle : 0.536 5.545 20970 Z= 0.287 Chirality : 0.043 0.215 2409 Planarity : 0.004 0.049 2664 Dihedral : 5.133 29.000 2256 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1944 helix: 1.53 (0.26), residues: 402 sheet: -0.53 (0.19), residues: 627 loop : -0.15 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 32 HIS 0.005 0.001 HIS I 435 PHE 0.032 0.002 PHE H 446 TYR 0.021 0.002 TYR E 94 ARG 0.008 0.000 ARG H 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 3) link_NAG-ASN : angle 1.66769 ( 9) link_BETA1-4 : bond 0.00402 ( 3) link_BETA1-4 : angle 1.60395 ( 9) hydrogen bonds : bond 0.03061 ( 703) hydrogen bonds : angle 6.19413 ( 1770) SS BOND : bond 0.00391 ( 45) SS BOND : angle 0.85960 ( 90) covalent geometry : bond 0.00281 (15384) covalent geometry : angle 0.53208 (20862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9376 (mtm) cc_final: 0.9099 (ppp) REVERT: D 4 MET cc_start: 0.8365 (pmm) cc_final: 0.7487 (pmm) REVERT: F 4 MET cc_start: 0.8580 (pmm) cc_final: 0.7717 (pmm) REVERT: G 234 MET cc_start: 0.8934 (mmm) cc_final: 0.8519 (mmm) REVERT: G 244 MET cc_start: 0.8686 (mmt) cc_final: 0.8435 (mmt) REVERT: G 368 HIS cc_start: 0.9381 (t-90) cc_final: 0.9160 (t-90) REVERT: H 234 MET cc_start: 0.9008 (mmm) cc_final: 0.8586 (mmm) REVERT: H 244 MET cc_start: 0.8846 (mtt) cc_final: 0.8084 (mmt) REVERT: I 234 MET cc_start: 0.8875 (mmm) cc_final: 0.8170 (mmm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3292 time to fit residues: 34.5197 Evaluate side-chains 51 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 48 optimal weight: 0.0270 chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 GLN G 210 ASN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 210 ASN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 435 HIS ** 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 = 0.2748 r_free = 0.2748 target = 0.028190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.021254 restraints weight = 171621.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.022112 restraints weight = 113256.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.022766 restraints weight = 83272.205| |-----------------------------------------------------------------------------| r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15435 Z= 0.160 Angle : 0.544 9.207 20970 Z= 0.290 Chirality : 0.042 0.159 2409 Planarity : 0.004 0.051 2664 Dihedral : 5.035 27.115 2256 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 1944 helix: 1.54 (0.26), residues: 402 sheet: -0.42 (0.19), residues: 627 loop : -0.15 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 32 HIS 0.006 0.001 HIS I 435 PHE 0.017 0.002 PHE G 334 TYR 0.020 0.002 TYR E 94 ARG 0.014 0.001 ARG H 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 3) link_NAG-ASN : angle 1.63547 ( 9) link_BETA1-4 : bond 0.00466 ( 3) link_BETA1-4 : angle 1.63001 ( 9) hydrogen bonds : bond 0.03045 ( 703) hydrogen bonds : angle 6.08075 ( 1770) SS BOND : bond 0.00383 ( 45) SS BOND : angle 0.85839 ( 90) covalent geometry : bond 0.00325 (15384) covalent geometry : angle 0.54023 (20862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 MET cc_start: 0.9391 (mtm) cc_final: 0.9128 (mtm) REVERT: D 4 MET cc_start: 0.8218 (pmm) cc_final: 0.7302 (pmm) REVERT: F 4 MET cc_start: 0.8572 (pmm) cc_final: 0.7712 (pmm) REVERT: G 234 MET cc_start: 0.8952 (mmm) cc_final: 0.8531 (mmm) REVERT: G 244 MET cc_start: 0.8714 (mmt) cc_final: 0.8464 (mmt) REVERT: G 368 HIS cc_start: 0.9370 (t-90) cc_final: 0.9070 (t-90) REVERT: H 234 MET cc_start: 0.9020 (mmm) cc_final: 0.8603 (mmm) REVERT: H 244 MET cc_start: 0.8788 (mtt) cc_final: 0.8008 (mmt) REVERT: I 234 MET cc_start: 0.8887 (mmm) cc_final: 0.8250 (mmm) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3327 time to fit residues: 33.4232 Evaluate side-chains 48 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 173 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 84 optimal weight: 0.0970 chunk 26 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 ASN ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.028626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.021496 restraints weight = 169129.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.022362 restraints weight = 111175.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.023031 restraints weight = 81942.353| |-----------------------------------------------------------------------------| r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15435 Z= 0.115 Angle : 0.511 8.061 20970 Z= 0.273 Chirality : 0.043 0.188 2409 Planarity : 0.004 0.049 2664 Dihedral : 4.793 25.166 2256 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 1944 helix: 1.70 (0.26), residues: 402 sheet: -0.19 (0.20), residues: 621 loop : -0.11 (0.22), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 32 HIS 0.006 0.001 HIS H 435 PHE 0.012 0.001 PHE I 334 TYR 0.017 0.002 TYR E 94 ARG 0.011 0.001 ARG H 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 3) link_NAG-ASN : angle 1.36239 ( 9) link_BETA1-4 : bond 0.00462 ( 3) link_BETA1-4 : angle 1.38509 ( 9) hydrogen bonds : bond 0.02862 ( 703) hydrogen bonds : angle 5.82075 ( 1770) SS BOND : bond 0.00378 ( 45) SS BOND : angle 0.84666 ( 90) covalent geometry : bond 0.00245 (15384) covalent geometry : angle 0.50806 (20862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.9286 (mtm) cc_final: 0.9026 (ppp) REVERT: B 80 MET cc_start: 0.9424 (mtm) cc_final: 0.9164 (mtm) REVERT: D 4 MET cc_start: 0.8020 (pmm) cc_final: 0.7098 (pmm) REVERT: F 4 MET cc_start: 0.8480 (pmm) cc_final: 0.7591 (pmm) REVERT: F 21 ILE cc_start: 0.9805 (mp) cc_final: 0.9575 (tp) REVERT: G 234 MET cc_start: 0.8965 (mmm) cc_final: 0.8528 (mmm) REVERT: G 244 MET cc_start: 0.8683 (mmt) cc_final: 0.8423 (mmt) REVERT: G 368 HIS cc_start: 0.9373 (t-90) cc_final: 0.9074 (t-90) REVERT: H 234 MET cc_start: 0.9025 (mmm) cc_final: 0.8582 (mmm) REVERT: H 244 MET cc_start: 0.8737 (mtt) cc_final: 0.7933 (mmt) REVERT: H 250 MET cc_start: 0.9190 (tmm) cc_final: 0.8849 (tpp) REVERT: I 219 LYS cc_start: 0.9334 (tptp) cc_final: 0.9103 (tppt) REVERT: I 234 MET cc_start: 0.8915 (mmm) cc_final: 0.8074 (mmm) REVERT: I 244 MET cc_start: 0.8959 (mmt) cc_final: 0.8066 (mmt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3392 time to fit residues: 35.5500 Evaluate side-chains 50 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 3 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 435 HIS ** 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 = 0.2766 r_free = 0.2766 target = 0.028805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.021683 restraints weight = 169065.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.022545 restraints weight = 110811.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.023212 restraints weight = 81645.191| |-----------------------------------------------------------------------------| r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15435 Z= 0.115 Angle : 0.499 7.429 20970 Z= 0.265 Chirality : 0.042 0.152 2409 Planarity : 0.004 0.052 2664 Dihedral : 4.602 25.142 2256 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1944 helix: 1.83 (0.26), residues: 402 sheet: -0.05 (0.20), residues: 624 loop : -0.07 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 32 HIS 0.004 0.001 HIS I 435 PHE 0.011 0.001 PHE I 334 TYR 0.023 0.002 TYR H 23 ARG 0.011 0.000 ARG H 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 3) link_NAG-ASN : angle 1.38073 ( 9) link_BETA1-4 : bond 0.00510 ( 3) link_BETA1-4 : angle 1.40964 ( 9) hydrogen bonds : bond 0.02756 ( 703) hydrogen bonds : angle 5.67725 ( 1770) SS BOND : bond 0.00384 ( 45) SS BOND : angle 0.82942 ( 90) covalent geometry : bond 0.00245 (15384) covalent geometry : angle 0.49527 (20862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4498.90 seconds wall clock time: 81 minutes 27.21 seconds (4887.21 seconds total)