Starting phenix.real_space_refine on Thu Sep 18 08:12:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cb1_45412/09_2025/9cb1_45412.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cb1_45412/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cb1_45412/09_2025/9cb1_45412.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cb1_45412/09_2025/9cb1_45412.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cb1_45412/09_2025/9cb1_45412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cb1_45412/09_2025/9cb1_45412.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.80, per 1000 atoms: 0.32 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: 1.38 Conformation dependent library (CDL) restraints added in 754.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.88 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: 3.21 Time building geometry restraints manager: 1.89 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: 0.01 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: 5.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.620 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.038 0.004 ARG E 103 TYR 0.025 0.005 TYR D 94 PHE 0.010 0.001 PHE G 168 TRP 0.014 0.002 TRP H 43 HIS 0.004 0.001 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00571 (15384) covalent geometry : angle 0.85725 (20862) SS BOND : bond 0.00924 ( 45) SS BOND : angle 1.50183 ( 90) hydrogen bonds : bond 0.22965 ( 703) hydrogen bonds : angle 8.50875 ( 1770) link_BETA1-4 : bond 0.02490 ( 3) link_BETA1-4 : angle 5.06213 ( 9) link_NAG-ASN : bond 0.00599 ( 3) link_NAG-ASN : angle 2.80175 ( 9) *********************** 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 : 0.624 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: 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: 0.8624 (t) REVERT: B 35 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8770 (t) REVERT: C 35 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8793 (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: 0.8039 (p) REVERT: E 87 TYR cc_start: 0.8294 (m-80) cc_final: 0.7839 (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: 0.9316 (mt) REVERT: H 368 HIS cc_start: 0.9344 (t70) cc_final: 0.8947 (t-90) REVERT: I 298 ASN cc_start: 0.8766 (t0) cc_final: 0.8389 (t0) REVERT: I 453 GLN cc_start: 0.9385 (tt0) cc_final: 0.8850 (tm-30) outliers start: 12 outliers final: 1 residues processed: 303 average time/residue: 0.1883 time to fit residues: 75.7325 Evaluate side-chains 125 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN E 27 GLN E 89 GLN F 27 GLN F 89 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 46 ASN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.031447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.023843 restraints weight = 154924.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.024735 restraints weight = 104023.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.025431 restraints weight = 77284.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.025964 restraints weight = 61244.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.026390 restraints weight = 50805.428| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 15435 Z= 0.262 Angle : 0.679 6.756 20970 Z= 0.362 Chirality : 0.044 0.281 2409 Planarity : 0.005 0.063 2664 Dihedral : 4.809 27.633 2256 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.18), residues: 1944 helix: 1.76 (0.27), residues: 360 sheet: -0.32 (0.19), residues: 654 loop : -0.27 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 38 TYR 0.019 0.002 TYR A 32 PHE 0.020 0.002 PHE G 446 TRP 0.021 0.002 TRP A 36 HIS 0.007 0.002 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00533 (15384) covalent geometry : angle 0.67340 (20862) SS BOND : bond 0.00528 ( 45) SS BOND : angle 1.11650 ( 90) hydrogen bonds : bond 0.04734 ( 703) hydrogen bonds : angle 6.58060 ( 1770) link_BETA1-4 : bond 0.00462 ( 3) link_BETA1-4 : angle 2.49186 ( 9) link_NAG-ASN : bond 0.00635 ( 3) link_NAG-ASN : angle 1.93012 ( 9) *********************** 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 128 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.624 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: A 32 TYR cc_start: 0.9533 (m-10) cc_final: 0.9063 (m-80) REVERT: B 32 TYR cc_start: 0.9507 (m-10) cc_final: 0.9136 (m-80) REVERT: C 32 TYR cc_start: 0.9505 (m-10) cc_final: 0.9107 (m-80) REVERT: C 80 MET cc_start: 0.9160 (ttp) cc_final: 0.8188 (tmm) REVERT: D 21 ILE cc_start: 0.9696 (mp) cc_final: 0.9478 (tp) REVERT: E 21 ILE cc_start: 0.9745 (mp) cc_final: 0.9544 (tp) REVERT: F 21 ILE cc_start: 0.9786 (mp) cc_final: 0.9570 (tp) REVERT: G 219 LYS cc_start: 0.9474 (tptt) cc_final: 0.9247 (tppt) REVERT: H 219 LYS cc_start: 0.9587 (tmtt) cc_final: 0.9295 (tptt) REVERT: H 302 LEU cc_start: 0.9268 (tp) cc_final: 0.8964 (tp) REVERT: I 219 LYS cc_start: 0.9453 (tptt) cc_final: 0.9220 (tppt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1812 time to fit residues: 31.6068 Evaluate side-chains 75 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 102 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 64 GLN B 43 GLN C 43 GLN C 64 GLN D 89 GLN E 27 GLN E 79 GLN E 89 GLN F 27 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.030766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.023315 restraints weight = 163137.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.024206 restraints weight = 107615.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.024905 restraints weight = 79148.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.025439 restraints weight = 62372.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.025860 restraints weight = 51650.125| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15435 Z= 0.206 Angle : 0.581 6.925 20970 Z= 0.312 Chirality : 0.043 0.213 2409 Planarity : 0.005 0.048 2664 Dihedral : 4.852 25.740 2256 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.19), residues: 1944 helix: 1.95 (0.26), residues: 384 sheet: -0.53 (0.18), residues: 669 loop : 0.05 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 103 TYR 0.024 0.002 TYR G 299 PHE 0.013 0.002 PHE I 446 TRP 0.011 0.002 TRP A 36 HIS 0.006 0.002 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00416 (15384) covalent geometry : angle 0.57673 (20862) SS BOND : bond 0.00438 ( 45) SS BOND : angle 0.95237 ( 90) hydrogen bonds : bond 0.03764 ( 703) hydrogen bonds : angle 6.15557 ( 1770) link_BETA1-4 : bond 0.00280 ( 3) link_BETA1-4 : angle 1.84623 ( 9) link_NAG-ASN : bond 0.00339 ( 3) link_NAG-ASN : angle 1.55642 ( 9) *********************** 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 97 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.637 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: 0.9576 (m-10) cc_final: 0.8944 (m-80) REVERT: B 32 TYR cc_start: 0.9589 (m-10) cc_final: 0.9065 (m-80) REVERT: C 32 TYR cc_start: 0.9542 (m-10) cc_final: 0.9011 (m-80) REVERT: D 21 ILE cc_start: 0.9721 (mp) cc_final: 0.9516 (tp) REVERT: E 92 TYR cc_start: 0.9694 (t80) cc_final: 0.9471 (t80) REVERT: F 21 ILE cc_start: 0.9795 (mp) cc_final: 0.9581 (tp) REVERT: F 92 TYR cc_start: 0.9729 (t80) cc_final: 0.9261 (t80) REVERT: G 234 MET cc_start: 0.9200 (mmm) cc_final: 0.8535 (mmm) REVERT: H 234 MET cc_start: 0.9140 (mmm) cc_final: 0.8313 (mmm) REVERT: H 302 LEU cc_start: 0.9447 (tp) cc_final: 0.9208 (tp) REVERT: I 234 MET cc_start: 0.9116 (mmm) cc_final: 0.8497 (mmm) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1659 time to fit residues: 22.5522 Evaluate side-chains 69 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 153 optimal weight: 0.0030 chunk 91 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- 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 F 27 GLN F 79 GLN F 89 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.030255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.023004 restraints weight = 166975.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.023893 restraints weight = 108995.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.024581 restraints weight = 79957.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.025122 restraints weight = 62799.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.025532 restraints weight = 51831.421| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15435 Z= 0.208 Angle : 0.577 5.585 20970 Z= 0.309 Chirality : 0.043 0.243 2409 Planarity : 0.004 0.048 2664 Dihedral : 4.898 25.545 2256 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.19), residues: 1944 helix: 1.92 (0.27), residues: 384 sheet: -0.50 (0.20), residues: 582 loop : -0.02 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 205 TYR 0.022 0.002 TYR G 299 PHE 0.022 0.002 PHE G 334 TRP 0.011 0.002 TRP D 32 HIS 0.007 0.001 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00417 (15384) covalent geometry : angle 0.57249 (20862) SS BOND : bond 0.00490 ( 45) SS BOND : angle 0.96854 ( 90) hydrogen bonds : bond 0.03482 ( 703) hydrogen bonds : angle 6.09117 ( 1770) link_BETA1-4 : bond 0.00110 ( 3) link_BETA1-4 : angle 1.89517 ( 9) link_NAG-ASN : bond 0.00205 ( 3) link_NAG-ASN : angle 1.64371 ( 9) *********************** 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 93 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.604 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: A 32 TYR cc_start: 0.9593 (m-80) cc_final: 0.8812 (m-80) REVERT: B 32 TYR cc_start: 0.9625 (m-80) cc_final: 0.8950 (m-80) REVERT: C 32 TYR cc_start: 0.9572 (m-80) cc_final: 0.8825 (m-80) REVERT: G 219 LYS cc_start: 0.9383 (tptt) cc_final: 0.9128 (tptp) REVERT: G 234 MET cc_start: 0.8998 (mmm) cc_final: 0.8583 (mmm) REVERT: G 368 HIS cc_start: 0.9382 (t-90) cc_final: 0.9167 (t-90) REVERT: G 457 ASN cc_start: 0.6850 (m110) cc_final: 0.6309 (m110) REVERT: H 219 LYS cc_start: 0.9479 (tmtt) cc_final: 0.9265 (tptt) REVERT: H 234 MET cc_start: 0.8897 (mmm) cc_final: 0.8562 (mmm) REVERT: H 368 HIS cc_start: 0.9413 (t-90) cc_final: 0.9213 (t-90) REVERT: I 234 MET cc_start: 0.8766 (mmm) cc_final: 0.8409 (mmm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1718 time to fit residues: 22.5377 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 : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 78 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 89 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.028553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.021792 restraints weight = 181037.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.022607 restraints weight = 119860.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.023228 restraints weight = 88681.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.023709 restraints weight = 70324.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.024077 restraints weight = 58544.507| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15435 Z= 0.340 Angle : 0.758 8.181 20970 Z= 0.399 Chirality : 0.045 0.246 2409 Planarity : 0.005 0.045 2664 Dihedral : 5.690 35.431 2256 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.19), residues: 1944 helix: 0.65 (0.24), residues: 402 sheet: -0.79 (0.18), residues: 669 loop : -0.24 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 205 TYR 0.029 0.003 TYR I 409 PHE 0.029 0.003 PHE G 334 TRP 0.020 0.003 TRP B 103 HIS 0.011 0.002 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00672 (15384) covalent geometry : angle 0.75277 (20862) SS BOND : bond 0.00447 ( 45) SS BOND : angle 1.02364 ( 90) hydrogen bonds : bond 0.04085 ( 703) hydrogen bonds : angle 6.71035 ( 1770) link_BETA1-4 : bond 0.00508 ( 3) link_BETA1-4 : angle 2.56232 ( 9) link_NAG-ASN : bond 0.00229 ( 3) link_NAG-ASN : angle 2.61642 ( 9) *********************** 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 76 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.606 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: G 234 MET cc_start: 0.8938 (mmm) cc_final: 0.8540 (mmm) REVERT: G 244 MET cc_start: 0.8857 (mtt) cc_final: 0.7989 (mmt) REVERT: G 368 HIS cc_start: 0.9369 (t-90) cc_final: 0.9119 (t-90) REVERT: H 234 MET cc_start: 0.8842 (mmm) cc_final: 0.8583 (mmm) REVERT: H 244 MET cc_start: 0.8859 (mtt) cc_final: 0.8065 (mmt) REVERT: I 234 MET cc_start: 0.8807 (mmm) cc_final: 0.8285 (mmm) REVERT: I 244 MET cc_start: 0.9039 (mtt) cc_final: 0.8590 (mmt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1745 time to fit residues: 18.5516 Evaluate side-chains 47 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 4 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 F 89 GLN F 96 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.029086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.021914 restraints weight = 163935.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.022802 restraints weight = 107598.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.023488 restraints weight = 78877.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.024019 restraints weight = 61969.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.024429 restraints weight = 51107.016| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15435 Z= 0.133 Angle : 0.533 7.272 20970 Z= 0.284 Chirality : 0.043 0.201 2409 Planarity : 0.004 0.048 2664 Dihedral : 5.023 27.925 2256 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.19), residues: 1944 helix: 1.52 (0.25), residues: 405 sheet: -0.36 (0.20), residues: 609 loop : -0.21 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 205 TYR 0.023 0.002 TYR F 92 PHE 0.013 0.001 PHE I 446 TRP 0.017 0.001 TRP F 32 HIS 0.005 0.001 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00282 (15384) covalent geometry : angle 0.52937 (20862) SS BOND : bond 0.00424 ( 45) SS BOND : angle 0.87458 ( 90) hydrogen bonds : bond 0.03108 ( 703) hydrogen bonds : angle 6.15126 ( 1770) link_BETA1-4 : bond 0.00511 ( 3) link_BETA1-4 : angle 1.50830 ( 9) link_NAG-ASN : bond 0.00432 ( 3) link_NAG-ASN : angle 1.50748 ( 9) *********************** 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 78 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.702 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 80 MET cc_start: 0.9304 (mtm) cc_final: 0.8846 (ppp) REVERT: G 234 MET cc_start: 0.9002 (mmm) cc_final: 0.8501 (mmm) REVERT: G 244 MET cc_start: 0.8792 (mtt) cc_final: 0.7853 (mmt) REVERT: G 368 HIS cc_start: 0.9369 (t-90) cc_final: 0.9108 (t-90) REVERT: H 234 MET cc_start: 0.8952 (mmm) cc_final: 0.8625 (mmm) REVERT: I 234 MET cc_start: 0.8861 (mmm) cc_final: 0.8169 (mmm) REVERT: I 244 MET cc_start: 0.8853 (mtt) cc_final: 0.7954 (mmt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1680 time to fit residues: 18.4519 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 : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 96 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN F 37 GLN F 89 GLN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 313 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.028219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.021276 restraints weight = 173576.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.022138 restraints weight = 114172.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.022799 restraints weight = 83847.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.023303 restraints weight = 66001.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.023703 restraints weight = 54627.765| |-----------------------------------------------------------------------------| r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15435 Z= 0.217 Angle : 0.591 7.873 20970 Z= 0.313 Chirality : 0.042 0.206 2409 Planarity : 0.004 0.047 2664 Dihedral : 5.132 28.795 2256 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.19), residues: 1944 helix: 1.48 (0.26), residues: 402 sheet: -0.41 (0.20), residues: 615 loop : -0.16 (0.22), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 205 TYR 0.018 0.002 TYR D 94 PHE 0.030 0.002 PHE I 451 TRP 0.015 0.002 TRP F 32 HIS 0.007 0.002 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00435 (15384) covalent geometry : angle 0.58696 (20862) SS BOND : bond 0.00388 ( 45) SS BOND : angle 0.90405 ( 90) hydrogen bonds : bond 0.03285 ( 703) hydrogen bonds : angle 6.21353 ( 1770) link_BETA1-4 : bond 0.00315 ( 3) link_BETA1-4 : angle 1.82970 ( 9) link_NAG-ASN : bond 0.00333 ( 3) link_NAG-ASN : angle 1.77482 ( 9) *********************** 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 73 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.604 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: 0.9269 (mtm) cc_final: 0.8880 (ppp) REVERT: F 19 VAL cc_start: 0.9860 (t) cc_final: 0.9640 (t) REVERT: G 234 MET cc_start: 0.9022 (mmm) cc_final: 0.8430 (mmm) REVERT: G 244 MET cc_start: 0.8760 (mtt) cc_final: 0.7813 (mmt) REVERT: G 368 HIS cc_start: 0.9381 (t-90) cc_final: 0.9060 (t-90) REVERT: H 234 MET cc_start: 0.9021 (mmm) cc_final: 0.8668 (mmm) REVERT: H 244 MET cc_start: 0.8846 (mmt) cc_final: 0.8464 (mmt) REVERT: I 234 MET cc_start: 0.8852 (mmm) cc_final: 0.8182 (mmm) REVERT: I 244 MET cc_start: 0.8963 (mtt) cc_final: 0.8472 (mmt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1687 time to fit residues: 17.4103 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 : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 136 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN F 89 GLN ** 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** H 313 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.027471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.020807 restraints weight = 183369.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.021640 restraints weight = 120529.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.022279 restraints weight = 88573.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.022771 restraints weight = 69678.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.023145 restraints weight = 57511.794| |-----------------------------------------------------------------------------| r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15435 Z= 0.305 Angle : 0.713 8.257 20970 Z= 0.376 Chirality : 0.044 0.199 2409 Planarity : 0.005 0.048 2664 Dihedral : 5.652 34.066 2256 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.19), residues: 1944 helix: 0.86 (0.25), residues: 402 sheet: -0.74 (0.19), residues: 627 loop : -0.33 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 103 TYR 0.026 0.003 TYR I 409 PHE 0.037 0.003 PHE G 334 TRP 0.021 0.003 TRP F 32 HIS 0.010 0.002 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00598 (15384) covalent geometry : angle 0.70906 (20862) SS BOND : bond 0.00409 ( 45) SS BOND : angle 0.97912 ( 90) hydrogen bonds : bond 0.03781 ( 703) hydrogen bonds : angle 6.60160 ( 1770) link_BETA1-4 : bond 0.00203 ( 3) link_BETA1-4 : angle 2.34150 ( 9) link_NAG-ASN : bond 0.00291 ( 3) link_NAG-ASN : angle 2.36934 ( 9) *********************** 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 69 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.642 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: 0.8427 (pmm) cc_final: 0.7610 (pmm) REVERT: E 4 MET cc_start: 0.7856 (pmm) cc_final: 0.7156 (pmm) REVERT: G 234 MET cc_start: 0.8978 (mmm) cc_final: 0.8422 (mmm) REVERT: G 244 MET cc_start: 0.8858 (mtt) cc_final: 0.7894 (mmt) REVERT: G 368 HIS cc_start: 0.9307 (t-90) cc_final: 0.8994 (t-90) REVERT: H 205 ARG cc_start: 0.9482 (ptp90) cc_final: 0.9262 (ptp-170) REVERT: H 222 MET cc_start: 0.9532 (tpt) cc_final: 0.8446 (tpp) REVERT: H 234 MET cc_start: 0.8982 (mmm) cc_final: 0.8662 (mmm) REVERT: I 234 MET cc_start: 0.8877 (mmm) cc_final: 0.8143 (mmm) REVERT: I 244 MET cc_start: 0.9044 (mtt) cc_final: 0.8535 (mmt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1623 time to fit residues: 16.1021 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 : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 173 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN F 37 GLN F 89 GLN ** G 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 462 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.027867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.021318 restraints weight = 183339.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.022110 restraints weight = 121192.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.022711 restraints weight = 89622.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.023179 restraints weight = 70974.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.023545 restraints weight = 58935.766| |-----------------------------------------------------------------------------| r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15435 Z= 0.206 Angle : 0.598 8.838 20970 Z= 0.320 Chirality : 0.043 0.183 2409 Planarity : 0.005 0.049 2664 Dihedral : 5.418 31.346 2256 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.19), residues: 1944 helix: 1.19 (0.26), residues: 402 sheet: -0.66 (0.19), residues: 627 loop : -0.30 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 205 TYR 0.019 0.002 TYR E 94 PHE 0.029 0.002 PHE I 451 TRP 0.020 0.002 TRP F 32 HIS 0.008 0.002 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00414 (15384) covalent geometry : angle 0.59399 (20862) SS BOND : bond 0.00380 ( 45) SS BOND : angle 0.89845 ( 90) hydrogen bonds : bond 0.03309 ( 703) hydrogen bonds : angle 6.38957 ( 1770) link_BETA1-4 : bond 0.00503 ( 3) link_BETA1-4 : angle 1.82854 ( 9) link_NAG-ASN : bond 0.00330 ( 3) link_NAG-ASN : angle 1.96966 ( 9) *********************** 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 65 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.608 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: 0.9315 (mtm) cc_final: 0.9072 (ppp) REVERT: B 80 MET cc_start: 0.9336 (mtm) cc_final: 0.9090 (mtm) REVERT: D 4 MET cc_start: 0.8354 (pmm) cc_final: 0.7483 (pmm) REVERT: E 4 MET cc_start: 0.7896 (pmm) cc_final: 0.7214 (pmm) REVERT: G 234 MET cc_start: 0.9024 (mmm) cc_final: 0.8454 (mmm) REVERT: G 244 MET cc_start: 0.8805 (mtt) cc_final: 0.7809 (mmt) REVERT: H 234 MET cc_start: 0.9004 (mmm) cc_final: 0.8598 (mmm) REVERT: I 222 MET cc_start: 0.9610 (tpp) cc_final: 0.9405 (tpp) REVERT: I 234 MET cc_start: 0.8914 (mmm) cc_final: 0.8131 (mmm) REVERT: I 244 MET cc_start: 0.9003 (mtt) cc_final: 0.8114 (mmt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1539 time to fit residues: 14.5374 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 : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 171 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN F 89 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.027863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.020972 restraints weight = 175604.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.021829 restraints weight = 115706.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.022480 restraints weight = 85243.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.022987 restraints weight = 67085.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.023375 restraints weight = 55356.787| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15435 Z= 0.180 Angle : 0.569 7.759 20970 Z= 0.303 Chirality : 0.043 0.181 2409 Planarity : 0.004 0.049 2664 Dihedral : 5.234 28.240 2256 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.19), residues: 1944 helix: 1.39 (0.26), residues: 402 sheet: -0.58 (0.19), residues: 627 loop : -0.26 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 205 TYR 0.021 0.002 TYR H 23 PHE 0.028 0.002 PHE I 451 TRP 0.018 0.002 TRP F 32 HIS 0.007 0.001 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00364 (15384) covalent geometry : angle 0.56557 (20862) SS BOND : bond 0.00378 ( 45) SS BOND : angle 0.86502 ( 90) hydrogen bonds : bond 0.03149 ( 703) hydrogen bonds : angle 6.24444 ( 1770) link_BETA1-4 : bond 0.00498 ( 3) link_BETA1-4 : angle 1.64419 ( 9) link_NAG-ASN : bond 0.00342 ( 3) link_NAG-ASN : angle 1.79223 ( 9) ********************** 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 65 residues out of total 1674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.578 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: B 80 MET cc_start: 0.9447 (mtm) cc_final: 0.9208 (mtm) REVERT: D 4 MET cc_start: 0.8004 (pmm) cc_final: 0.7111 (pmm) REVERT: E 4 MET cc_start: 0.7665 (pmm) cc_final: 0.7117 (pmm) REVERT: G 234 MET cc_start: 0.9053 (mmm) cc_final: 0.8458 (mmm) REVERT: G 244 MET cc_start: 0.8762 (mtt) cc_final: 0.7736 (mmt) REVERT: G 368 HIS cc_start: 0.9289 (t-90) cc_final: 0.9021 (t-90) REVERT: H 234 MET cc_start: 0.9032 (mmm) cc_final: 0.8622 (mmm) REVERT: I 234 MET cc_start: 0.8945 (mmm) cc_final: 0.8130 (mmm) REVERT: I 244 MET cc_start: 0.9000 (mtt) cc_final: 0.8096 (mmt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1453 time to fit residues: 14.2082 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 : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 130 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN D 89 GLN D 96 GLN E 89 GLN F 89 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.027650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.020949 restraints weight = 173431.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.021778 restraints weight = 115293.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.022407 restraints weight = 85253.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.022897 restraints weight = 67303.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.023275 restraints weight = 55733.492| |-----------------------------------------------------------------------------| r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15435 Z= 0.186 Angle : 0.571 7.291 20970 Z= 0.303 Chirality : 0.042 0.161 2409 Planarity : 0.004 0.049 2664 Dihedral : 5.195 27.794 2256 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.06 % Allowed : 0.54 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.19), residues: 1944 helix: 1.34 (0.26), residues: 402 sheet: -0.52 (0.19), residues: 627 loop : -0.23 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 205 TYR 0.016 0.002 TYR E 94 PHE 0.027 0.002 PHE I 451 TRP 0.018 0.002 TRP F 32 HIS 0.007 0.001 HIS I 435 Details of bonding type rmsd covalent geometry : bond 0.00375 (15384) covalent geometry : angle 0.56771 (20862) SS BOND : bond 0.00373 ( 45) SS BOND : angle 0.85946 ( 90) hydrogen bonds : bond 0.03136 ( 703) hydrogen bonds : angle 6.18099 ( 1770) link_BETA1-4 : bond 0.00487 ( 3) link_BETA1-4 : angle 1.71427 ( 9) link_NAG-ASN : bond 0.00336 ( 3) link_NAG-ASN : angle 1.84798 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2387.62 seconds wall clock time: 42 minutes 49.65 seconds (2569.65 seconds total)