Starting phenix.real_space_refine on Fri Jul 3 02:28:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lkl_63181/07_2026/9lkl_63181.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lkl_63181/07_2026/9lkl_63181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lkl_63181/07_2026/9lkl_63181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lkl_63181/07_2026/9lkl_63181.map" model { file = "/net/cci-nas-00/data/ceres_data/9lkl_63181/07_2026/9lkl_63181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lkl_63181/07_2026/9lkl_63181.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 76 5.16 5 C 7218 2.51 5 N 1851 2.21 5 O 2126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11279 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "B" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "C" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "D" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1294 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1294 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "G" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "I" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1287 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1294 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.74, per 1000 atoms: 0.24 Number of scatterers: 11279 At special positions: 0 Unit cell: (100.768, 115.776, 116.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 76 16.00 O 2126 8.00 N 1851 7.00 C 7218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 112 " distance=2.02 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 198 " distance=2.02 Simple disulfide: pdb=" SG CYS D 178 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 55 " distance=2.03 Simple disulfide: pdb=" SG CYS E 80 " - pdb=" SG CYS E 112 " distance=2.03 Simple disulfide: pdb=" SG CYS E 168 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 178 " - pdb=" SG CYS E 189 " distance=2.03 Simple disulfide: pdb=" SG CYS I 30 " - pdb=" SG CYS I 55 " distance=2.03 Simple disulfide: pdb=" SG CYS I 80 " - pdb=" SG CYS I 112 " distance=2.03 Simple disulfide: pdb=" SG CYS I 168 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 172 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 178 " - pdb=" SG CYS I 189 " distance=2.03 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 55 " distance=2.03 Simple disulfide: pdb=" SG CYS J 80 " - pdb=" SG CYS J 112 " distance=2.03 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 196 " distance=2.05 Simple disulfide: pdb=" SG CYS J 172 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 178 " - pdb=" SG CYS J 189 " 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 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 403.8 milliseconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2634 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 27 sheets defined 9.4% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 164 through 181 removed outlier: 4.017A pdb=" N SER D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 removed outlier: 3.528A pdb=" N MET E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 164 through 181 Processing helix chain 'I' and resid 44 through 48 removed outlier: 3.537A pdb=" N PHE I 48 " --> pdb=" O VAL I 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 44 through 48' Processing helix chain 'I' and resid 97 through 105 removed outlier: 3.796A pdb=" N LEU I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 181 Processing helix chain 'J' and resid 43 through 48 Processing helix chain 'J' and resid 97 through 105 Processing helix chain 'J' and resid 164 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 155 removed outlier: 6.830A pdb=" N TYR A 133 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN A 154 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 131 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 173 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 155 removed outlier: 6.830A pdb=" N TYR A 133 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN A 154 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA A 131 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 173 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 181 " --> pdb=" O HIS A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 145 removed outlier: 3.747A pdb=" N GLU A 144 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS A 196 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 155 removed outlier: 4.982A pdb=" N VAL B 151 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY B 135 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 131 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 173 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.701A pdb=" N LYS B 165 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 196 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 199 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.701A pdb=" N LYS B 165 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 153 removed outlier: 6.805A pdb=" N TYR C 133 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 173 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP C 214 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.567A pdb=" N ILE C 232 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 165 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.567A pdb=" N ILE C 232 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE C 231 " --> pdb=" O CYS H 195 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS H 196 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 199 through 205 removed outlier: 5.955A pdb=" N VAL C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS C 196 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS H 165 " --> pdb=" O ASP H 160 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP H 160 " --> pdb=" O LYS H 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 34 removed outlier: 4.023A pdb=" N VAL D 34 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU D 60 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 40 through 43 removed outlier: 3.890A pdb=" N GLY D 40 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 155 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR D 123 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 30 through 34 removed outlier: 6.024A pdb=" N CYS E 30 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR E 58 " --> pdb=" O CYS E 30 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR E 32 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLU E 60 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL E 34 " --> pdb=" O GLU E 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 39 through 42 Processing sheet with id=AB6, first strand: chain 'F' and resid 150 through 155 removed outlier: 6.865A pdb=" N TYR F 133 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN F 154 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA F 131 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR F 173 " --> pdb=" O ILE F 255 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 144 through 145 Processing sheet with id=AB8, first strand: chain 'F' and resid 159 through 160 removed outlier: 3.587A pdb=" N ASP F 160 " --> pdb=" O LYS F 165 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS F 165 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 150 through 155 removed outlier: 4.873A pdb=" N VAL G 151 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY G 135 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR G 153 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA G 131 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR G 173 " --> pdb=" O ILE G 255 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 144 through 145 removed outlier: 3.580A pdb=" N CYS G 195 " --> pdb=" O PHE G 231 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 166 through 168 removed outlier: 3.569A pdb=" N ASP G 228 " --> pdb=" O CYS G 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS G 195 " --> pdb=" O PHE G 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 150 through 153 removed outlier: 6.805A pdb=" N TYR H 133 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR H 173 " --> pdb=" O ILE H 255 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.602A pdb=" N HIS H 140 " --> pdb=" O ALA H 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 33 through 34 removed outlier: 3.605A pdb=" N GLU I 60 " --> pdb=" O VAL I 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 39 through 43 removed outlier: 3.735A pdb=" N GLY I 40 " --> pdb=" O PHE I 155 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE I 155 " --> pdb=" O GLY I 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 31 through 34 removed outlier: 6.016A pdb=" N THR J 32 " --> pdb=" O THR J 58 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLU J 60 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL J 34 " --> pdb=" O GLU J 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 39 through 42 Processing sheet with id=AC9, first strand: chain 'J' and resid 39 through 42 removed outlier: 3.700A pdb=" N ILE J 69 " --> pdb=" O TYR J 123 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR J 123 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU J 71 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU J 121 " --> pdb=" O LEU J 71 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1843 1.31 - 1.44: 3437 1.44 - 1.56: 6181 1.56 - 1.69: 0 1.69 - 1.82: 100 Bond restraints: 11561 Sorted by residual: bond pdb=" C MET I 192 " pdb=" O MET I 192 " ideal model delta sigma weight residual 1.233 1.299 -0.066 1.47e-02 4.63e+03 2.00e+01 bond pdb=" C PRO D 64 " pdb=" O PRO D 64 " ideal model delta sigma weight residual 1.234 1.190 0.044 1.00e-02 1.00e+04 1.93e+01 bond pdb=" C PRO D 62 " pdb=" O PRO D 62 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.29e-02 6.01e+03 1.41e+01 bond pdb=" N TYR I 193 " pdb=" CA TYR I 193 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" C LEU G 234 " pdb=" O LEU G 234 " ideal model delta sigma weight residual 1.235 1.275 -0.040 1.22e-02 6.72e+03 1.07e+01 ... (remaining 11556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 15332 2.96 - 5.92: 280 5.92 - 8.88: 12 8.88 - 11.84: 1 11.84 - 14.80: 1 Bond angle restraints: 15626 Sorted by residual: angle pdb=" C CYS E 168 " pdb=" CA CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sigma weight residual 110.79 95.99 14.80 1.66e+00 3.63e-01 7.95e+01 angle pdb=" CA MET I 192 " pdb=" C MET I 192 " pdb=" O MET I 192 " ideal model delta sigma weight residual 122.03 113.90 8.13 1.25e+00 6.40e-01 4.23e+01 angle pdb=" N ASN B 169 " pdb=" CA ASN B 169 " pdb=" C ASN B 169 " ideal model delta sigma weight residual 114.31 106.58 7.73 1.29e+00 6.01e-01 3.59e+01 angle pdb=" CA GLY F 237 " pdb=" C GLY F 237 " pdb=" O GLY F 237 " ideal model delta sigma weight residual 122.45 118.28 4.17 7.20e-01 1.93e+00 3.35e+01 angle pdb=" CA GLY F 187 " pdb=" C GLY F 187 " pdb=" O GLY F 187 " ideal model delta sigma weight residual 122.52 118.08 4.44 7.90e-01 1.60e+00 3.16e+01 ... (remaining 15621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6242 17.99 - 35.99: 428 35.99 - 53.98: 68 53.98 - 71.97: 16 71.97 - 89.97: 4 Dihedral angle restraints: 6758 sinusoidal: 2637 harmonic: 4121 Sorted by residual: dihedral pdb=" CB CYS I 172 " pdb=" SG CYS I 172 " pdb=" SG CYS I 198 " pdb=" CB CYS I 198 " ideal model delta sinusoidal sigma weight residual -86.00 -170.42 84.42 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" C CYS E 168 " pdb=" N CYS E 168 " pdb=" CA CYS E 168 " pdb=" CB CYS E 168 " ideal model delta harmonic sigma weight residual -122.60 -103.36 -19.24 0 2.50e+00 1.60e-01 5.92e+01 dihedral pdb=" CB CYS I 168 " pdb=" SG CYS I 168 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual -86.00 -138.66 52.66 1 1.00e+01 1.00e-02 3.78e+01 ... (remaining 6755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1391 0.090 - 0.180: 230 0.180 - 0.270: 28 0.270 - 0.360: 0 0.360 - 0.449: 1 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CA CYS E 168 " pdb=" N CYS E 168 " pdb=" C CYS E 168 " pdb=" CB CYS E 168 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" CB ILE G 205 " pdb=" CA ILE G 205 " pdb=" CG1 ILE G 205 " pdb=" CG2 ILE G 205 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ARG I 132 " pdb=" N ARG I 132 " pdb=" C ARG I 132 " pdb=" CB ARG I 132 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1647 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H 138 " -0.080 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO H 139 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO H 139 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO H 139 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 127 " -0.057 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO B 128 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 195 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C LYS J 195 " 0.055 2.00e-02 2.50e+03 pdb=" O LYS J 195 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS J 196 " -0.019 2.00e-02 2.50e+03 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 696 2.73 - 3.28: 11190 3.28 - 3.82: 17868 3.82 - 4.36: 22528 4.36 - 4.90: 38118 Nonbonded interactions: 90400 Sorted by model distance: nonbonded pdb=" OD2 ASP A 214 " pdb="CA CA A 301 " model vdw 2.192 3.250 nonbonded pdb=" OD2 ASP I 124 " pdb=" NZ LYS I 160 " model vdw 2.217 3.120 nonbonded pdb=" NE2 HIS B 223 " pdb=" OD2 ASP B 258 " model vdw 2.312 3.120 nonbonded pdb=" O VAL E 170 " pdb=" OG1 THR E 173 " model vdw 2.318 3.040 nonbonded pdb=" OH TYR E 88 " pdb=" OE1 GLN E 129 " model vdw 2.330 3.040 ... (remaining 90395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 127 through 301) selection = chain 'C' selection = chain 'F' selection = (chain 'G' and resid 127 through 301) selection = chain 'H' } ncs_group { reference = (chain 'D' and (resid 28 through 135 or resid 148 through 199)) selection = (chain 'E' and (resid 28 through 135 or resid 148 through 199)) selection = chain 'I' selection = (chain 'J' and (resid 28 through 135 or resid 148 through 199)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.720 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 : 0.007 0.066 11581 Z= 0.514 Angle : 1.007 14.800 15666 Z= 0.695 Chirality : 0.065 0.449 1650 Planarity : 0.005 0.121 2007 Dihedral : 11.882 89.966 4064 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.56 % Favored : 93.22 % Rotamer: Outliers : 1.30 % Allowed : 2.60 % Favored : 96.11 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.20), residues: 1387 helix: -0.91 (0.42), residues: 103 sheet: -0.59 (0.22), residues: 515 loop : -2.42 (0.19), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 201 TYR 0.015 0.001 TYR G 159 PHE 0.021 0.001 PHE I 90 TRP 0.051 0.002 TRP E 174 HIS 0.005 0.001 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.51 (11561) covalent geometry : angle 1.00696 / 0.70 (15626) SS BOND : bond 0.00596 / 0.36 ( 20) SS BOND : angle 1.19664 / 0.82 ( 40) hydrogen bonds : bond 0.16778 / 11.77 ( 410) hydrogen bonds : angle 8.01864 / 5.49 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 367 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8075 (ttmt) REVERT: A 154 ASN cc_start: 0.7907 (t0) cc_final: 0.7685 (t0) REVERT: A 166 PHE cc_start: 0.8335 (t80) cc_final: 0.8030 (t80) REVERT: A 194 LEU cc_start: 0.8345 (tp) cc_final: 0.8019 (tt) REVERT: A 213 TYR cc_start: 0.8072 (m-80) cc_final: 0.7703 (m-80) REVERT: B 212 ASN cc_start: 0.7664 (m-40) cc_final: 0.7321 (m-40) REVERT: B 238 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7583 (mttp) REVERT: C 199 GLN cc_start: 0.6656 (tt0) cc_final: 0.6187 (tt0) REVERT: C 231 PHE cc_start: 0.7920 (p90) cc_final: 0.7607 (p90) REVERT: C 248 SER cc_start: 0.8239 (m) cc_final: 0.7861 (p) REVERT: C 255 ILE cc_start: 0.8566 (mt) cc_final: 0.8363 (mt) REVERT: C 256 TYR cc_start: 0.8203 (m-80) cc_final: 0.7762 (m-80) REVERT: D 48 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6951 (p90) REVERT: D 92 HIS cc_start: 0.6259 (OUTLIER) cc_final: 0.5985 (t-90) REVERT: D 155 PHE cc_start: 0.7196 (p90) cc_final: 0.6871 (p90) REVERT: D 162 SER cc_start: 0.8426 (p) cc_final: 0.7960 (p) REVERT: D 192 MET cc_start: 0.7522 (ttm) cc_final: 0.6973 (ttm) REVERT: E 109 MET cc_start: 0.7123 (ppp) cc_final: 0.6303 (mmp) REVERT: E 152 PHE cc_start: 0.6913 (m-80) cc_final: 0.6468 (m-80) REVERT: F 147 LYS cc_start: 0.7732 (mttt) cc_final: 0.7462 (mttt) REVERT: F 151 VAL cc_start: 0.8326 (t) cc_final: 0.8081 (m) REVERT: F 154 ASN cc_start: 0.7991 (t0) cc_final: 0.7743 (t0) REVERT: F 174 TYR cc_start: 0.7047 (m-80) cc_final: 0.6844 (m-80) REVERT: F 182 MET cc_start: 0.6329 (ttp) cc_final: 0.5753 (ttp) REVERT: F 214 ASP cc_start: 0.6338 (t0) cc_final: 0.5949 (t0) REVERT: F 230 VAL cc_start: 0.8737 (m) cc_final: 0.8362 (p) REVERT: G 233 LYS cc_start: 0.8066 (tttm) cc_final: 0.7851 (tttm) REVERT: G 238 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6696 (mtmm) REVERT: G 244 SER cc_start: 0.8395 (m) cc_final: 0.8079 (t) REVERT: H 146 LEU cc_start: 0.8723 (mt) cc_final: 0.8523 (mt) REVERT: H 165 LYS cc_start: 0.6426 (mttt) cc_final: 0.6222 (mttp) REVERT: H 169 ASN cc_start: 0.6945 (m-40) cc_final: 0.6630 (m-40) REVERT: H 212 ASN cc_start: 0.7774 (m-40) cc_final: 0.7559 (m-40) REVERT: H 222 LEU cc_start: 0.6666 (mt) cc_final: 0.6392 (mt) REVERT: H 235 ASP cc_start: 0.8133 (t0) cc_final: 0.7919 (t0) REVERT: I 57 TRP cc_start: 0.7631 (t60) cc_final: 0.6762 (t-100) REVERT: I 58 THR cc_start: 0.7031 (p) cc_final: 0.6300 (p) REVERT: I 66 LYS cc_start: 0.7622 (ttmm) cc_final: 0.7318 (ttmm) REVERT: I 158 LEU cc_start: 0.7390 (mt) cc_final: 0.7090 (mt) REVERT: J 48 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6989 (p90) REVERT: J 109 MET cc_start: 0.4277 (ttp) cc_final: 0.4070 (ttp) outliers start: 16 outliers final: 6 residues processed: 378 average time/residue: 0.1020 time to fit residues: 55.8403 Evaluate side-chains 358 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 347 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain G residue 199 GLN Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain I residue 174 TRP Chi-restraints excluded: chain J residue 48 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.0060 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 211 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN D 122 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS F 197 ASN F 211 GLN F 245 ASN G 199 GLN H 140 HIS H 157 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.182940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.146327 restraints weight = 18018.281| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.42 r_work: 0.3636 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 11581 Z= 0.215 Angle : 0.663 10.665 15666 Z= 0.356 Chirality : 0.045 0.233 1650 Planarity : 0.004 0.040 2007 Dihedral : 5.969 56.748 1548 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.19 % Allowed : 10.06 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.21), residues: 1387 helix: 1.01 (0.49), residues: 103 sheet: -0.20 (0.20), residues: 578 loop : -2.03 (0.20), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 183 TYR 0.019 0.002 TYR J 42 PHE 0.027 0.002 PHE E 48 TRP 0.037 0.003 TRP J 174 HIS 0.007 0.002 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (11561) covalent geometry : angle 0.65870 / 0.35 (15626) SS BOND : bond 0.00479 / 0.36 ( 20) SS BOND : angle 1.55985 / 0.93 ( 40) hydrogen bonds : bond 0.04671 / 3.19 ( 410) hydrogen bonds : angle 6.29814 / 4.40 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 337 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8434 (t80) cc_final: 0.8120 (t80) REVERT: A 182 MET cc_start: 0.7839 (ttp) cc_final: 0.7536 (ttm) REVERT: A 194 LEU cc_start: 0.8375 (tp) cc_final: 0.8167 (tt) REVERT: A 213 TYR cc_start: 0.8165 (m-80) cc_final: 0.7794 (m-80) REVERT: B 196 LYS cc_start: 0.7437 (tmmt) cc_final: 0.6999 (tmmt) REVERT: B 201 ARG cc_start: 0.8438 (mmt90) cc_final: 0.7884 (mmt90) REVERT: B 212 ASN cc_start: 0.8333 (m-40) cc_final: 0.7854 (m-40) REVERT: B 238 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8044 (mmtp) REVERT: C 199 GLN cc_start: 0.7211 (tt0) cc_final: 0.6683 (tt0) REVERT: C 248 SER cc_start: 0.8328 (m) cc_final: 0.7965 (p) REVERT: C 256 TYR cc_start: 0.8593 (m-80) cc_final: 0.8056 (m-80) REVERT: D 162 SER cc_start: 0.8626 (p) cc_final: 0.8367 (p) REVERT: D 192 MET cc_start: 0.7234 (ttm) cc_final: 0.6788 (ttm) REVERT: E 109 MET cc_start: 0.7401 (ppp) cc_final: 0.6868 (ppp) REVERT: E 169 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.5532 (p-80) REVERT: F 147 LYS cc_start: 0.8225 (mttt) cc_final: 0.7666 (mttt) REVERT: F 151 VAL cc_start: 0.8432 (t) cc_final: 0.8178 (m) REVERT: F 154 ASN cc_start: 0.8462 (t0) cc_final: 0.8242 (t0) REVERT: F 183 ARG cc_start: 0.7471 (ttm170) cc_final: 0.7189 (ttm170) REVERT: F 190 MET cc_start: 0.7615 (ptm) cc_final: 0.7279 (ptt) REVERT: G 149 ASP cc_start: 0.7891 (t0) cc_final: 0.7593 (t0) REVERT: G 150 ASP cc_start: 0.7426 (t0) cc_final: 0.6751 (t0) REVERT: G 205 ILE cc_start: 0.7952 (tt) cc_final: 0.7747 (tt) REVERT: G 224 LEU cc_start: 0.8061 (mt) cc_final: 0.7840 (mt) REVERT: G 238 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7509 (mtmm) REVERT: G 244 SER cc_start: 0.8708 (m) cc_final: 0.8406 (t) REVERT: H 158 ASN cc_start: 0.7639 (t0) cc_final: 0.7210 (t0) REVERT: H 165 LYS cc_start: 0.6982 (mttt) cc_final: 0.6672 (mttp) REVERT: H 173 THR cc_start: 0.7573 (m) cc_final: 0.7313 (m) REVERT: H 190 MET cc_start: 0.7376 (ttt) cc_final: 0.7121 (ttt) REVERT: H 197 ASN cc_start: 0.8399 (m110) cc_final: 0.8187 (m110) REVERT: H 235 ASP cc_start: 0.8587 (t0) cc_final: 0.8318 (t0) REVERT: H 240 HIS cc_start: 0.8564 (t70) cc_final: 0.8318 (t70) REVERT: I 58 THR cc_start: 0.8244 (p) cc_final: 0.7235 (p) REVERT: I 66 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7788 (ttmm) REVERT: I 155 PHE cc_start: 0.6514 (p90) cc_final: 0.5980 (p90) REVERT: I 158 LEU cc_start: 0.7771 (mt) cc_final: 0.7459 (mt) REVERT: J 153 PHE cc_start: 0.5286 (OUTLIER) cc_final: 0.4232 (t80) outliers start: 27 outliers final: 17 residues processed: 351 average time/residue: 0.1002 time to fit residues: 51.4381 Evaluate side-chains 350 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 329 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 174 TRP Chi-restraints excluded: chain J residue 153 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 46 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 93 optimal weight: 0.0030 chunk 92 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN B 138 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 HIS D 92 HIS E 89 GLN F 138 ASN G 223 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.186096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.148667 restraints weight = 18118.445| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.50 r_work: 0.3671 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11581 Z= 0.111 Angle : 0.570 11.544 15666 Z= 0.307 Chirality : 0.043 0.196 1650 Planarity : 0.003 0.031 2007 Dihedral : 5.295 57.759 1540 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.76 % Allowed : 12.33 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.21), residues: 1387 helix: 1.89 (0.52), residues: 103 sheet: 0.02 (0.22), residues: 518 loop : -1.85 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 132 TYR 0.020 0.001 TYR G 133 PHE 0.026 0.001 PHE J 48 TRP 0.031 0.003 TRP I 174 HIS 0.006 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11561) covalent geometry : angle 0.56884 / 0.31 (15626) SS BOND : bond 0.00338 / 0.22 ( 20) SS BOND : angle 0.98595 / 0.58 ( 40) hydrogen bonds : bond 0.03744 / 2.47 ( 410) hydrogen bonds : angle 5.93360 / 4.14 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 327 time to evaluate : 0.374 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 166 PHE cc_start: 0.8492 (t80) cc_final: 0.8199 (t80) REVERT: A 182 MET cc_start: 0.7830 (ttp) cc_final: 0.7538 (ttm) REVERT: A 213 TYR cc_start: 0.8158 (m-80) cc_final: 0.7794 (m-80) REVERT: B 196 LYS cc_start: 0.7467 (tmmt) cc_final: 0.7105 (tmmt) REVERT: B 201 ARG cc_start: 0.8366 (mmt90) cc_final: 0.8010 (mmt90) REVERT: B 238 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8008 (mttp) REVERT: C 154 ASN cc_start: 0.8439 (t0) cc_final: 0.8005 (t0) REVERT: C 199 GLN cc_start: 0.7437 (tt0) cc_final: 0.6986 (tt0) REVERT: C 201 ARG cc_start: 0.8129 (mmt180) cc_final: 0.7871 (mmt-90) REVERT: C 248 SER cc_start: 0.8350 (m) cc_final: 0.7993 (p) REVERT: C 256 TYR cc_start: 0.8514 (m-80) cc_final: 0.7913 (m-80) REVERT: D 192 MET cc_start: 0.7268 (ttm) cc_final: 0.6691 (ttm) REVERT: E 109 MET cc_start: 0.7408 (ppp) cc_final: 0.6847 (ppp) REVERT: F 147 LYS cc_start: 0.8203 (mttt) cc_final: 0.7762 (mttt) REVERT: F 154 ASN cc_start: 0.8388 (t0) cc_final: 0.8179 (t0) REVERT: F 183 ARG cc_start: 0.7505 (ttm170) cc_final: 0.7100 (ttp-170) REVERT: F 190 MET cc_start: 0.7639 (ptm) cc_final: 0.7382 (ptm) REVERT: F 230 VAL cc_start: 0.8936 (t) cc_final: 0.8584 (p) REVERT: G 224 LEU cc_start: 0.8054 (mt) cc_final: 0.7827 (mt) REVERT: G 238 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7456 (mtmm) REVERT: G 244 SER cc_start: 0.8647 (m) cc_final: 0.8081 (t) REVERT: H 158 ASN cc_start: 0.7663 (t0) cc_final: 0.7333 (t0) REVERT: H 165 LYS cc_start: 0.6846 (mttt) cc_final: 0.6608 (mttm) REVERT: H 190 MET cc_start: 0.7356 (ttt) cc_final: 0.7120 (ttt) REVERT: H 235 ASP cc_start: 0.8564 (t0) cc_final: 0.8181 (t0) REVERT: I 57 TRP cc_start: 0.7422 (t-100) cc_final: 0.6790 (t-100) REVERT: I 66 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7712 (ttmm) REVERT: I 155 PHE cc_start: 0.6273 (p90) cc_final: 0.5768 (p90) REVERT: I 158 LEU cc_start: 0.7653 (mt) cc_final: 0.7368 (mt) REVERT: J 47 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7227 (ppp) REVERT: J 122 GLN cc_start: 0.6948 (tm-30) cc_final: 0.6670 (tt0) REVERT: J 123 TYR cc_start: 0.6772 (m-80) cc_final: 0.5652 (m-80) REVERT: J 153 PHE cc_start: 0.5110 (OUTLIER) cc_final: 0.4196 (t80) outliers start: 34 outliers final: 22 residues processed: 341 average time/residue: 0.0937 time to fit residues: 46.2847 Evaluate side-chains 348 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 322 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 223 HIS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 166 PHE Chi-restraints excluded: chain I residue 174 TRP Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 153 PHE Chi-restraints excluded: chain J residue 170 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 130 optimal weight: 40.0000 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 HIS ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 HIS G 245 ASN ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.183299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145958 restraints weight = 17624.548| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.35 r_work: 0.3672 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 11581 Z= 0.186 Angle : 0.591 11.032 15666 Z= 0.319 Chirality : 0.044 0.228 1650 Planarity : 0.004 0.030 2007 Dihedral : 5.399 58.764 1540 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.33 % Allowed : 13.22 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1387 helix: 2.12 (0.53), residues: 103 sheet: 0.17 (0.20), residues: 597 loop : -2.00 (0.20), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 201 TYR 0.027 0.002 TYR H 256 PHE 0.028 0.002 PHE E 48 TRP 0.031 0.002 TRP J 174 HIS 0.018 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (11561) covalent geometry : angle 0.58994 / 0.32 (15626) SS BOND : bond 0.00284 / 0.20 ( 20) SS BOND : angle 0.94975 / 0.54 ( 40) hydrogen bonds : bond 0.03965 / 2.61 ( 410) hydrogen bonds : angle 5.89293 / 4.11 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 315 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8414 (t80) cc_final: 0.8171 (t80) REVERT: B 196 LYS cc_start: 0.7421 (tmmt) cc_final: 0.7205 (tmmt) REVERT: B 238 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8094 (mttp) REVERT: C 154 ASN cc_start: 0.8489 (t0) cc_final: 0.8142 (t0) REVERT: C 199 GLN cc_start: 0.7221 (tt0) cc_final: 0.6708 (tt0) REVERT: C 201 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7933 (mmt-90) REVERT: C 248 SER cc_start: 0.8311 (m) cc_final: 0.8044 (p) REVERT: C 256 TYR cc_start: 0.8628 (m-80) cc_final: 0.8015 (m-80) REVERT: D 93 PHE cc_start: 0.7343 (t80) cc_final: 0.6880 (t80) REVERT: D 192 MET cc_start: 0.7192 (ttm) cc_final: 0.6676 (ttm) REVERT: F 147 LYS cc_start: 0.8368 (mttt) cc_final: 0.7870 (mttt) REVERT: F 196 LYS cc_start: 0.7969 (pttt) cc_final: 0.7725 (pttt) REVERT: G 224 LEU cc_start: 0.8064 (mt) cc_final: 0.7836 (mt) REVERT: G 238 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7674 (mtmm) REVERT: G 244 SER cc_start: 0.8728 (m) cc_final: 0.8124 (t) REVERT: H 158 ASN cc_start: 0.7707 (t0) cc_final: 0.7390 (t0) REVERT: H 165 LYS cc_start: 0.7109 (mttt) cc_final: 0.6825 (mttm) REVERT: H 235 ASP cc_start: 0.8595 (t0) cc_final: 0.8196 (t0) REVERT: I 66 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7826 (ttmm) REVERT: I 155 PHE cc_start: 0.6727 (p90) cc_final: 0.6192 (p90) REVERT: I 158 LEU cc_start: 0.7737 (mt) cc_final: 0.7479 (mt) REVERT: J 47 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7342 (ppp) REVERT: J 153 PHE cc_start: 0.5069 (OUTLIER) cc_final: 0.4145 (t80) outliers start: 41 outliers final: 29 residues processed: 336 average time/residue: 0.0872 time to fit residues: 42.9035 Evaluate side-chains 344 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 166 PHE Chi-restraints excluded: chain I residue 174 TRP Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 48 PHE Chi-restraints excluded: chain J residue 153 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 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 = 0.4272 r_free = 0.4272 target = 0.178043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141145 restraints weight = 17749.337| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.30 r_work: 0.3594 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 11581 Z= 0.223 Angle : 0.629 14.655 15666 Z= 0.336 Chirality : 0.044 0.231 1650 Planarity : 0.004 0.030 2007 Dihedral : 5.516 53.728 1540 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.81 % Allowed : 14.19 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1387 helix: 2.36 (0.53), residues: 103 sheet: 0.15 (0.21), residues: 561 loop : -1.95 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.028 0.002 TYR G 133 PHE 0.025 0.002 PHE J 48 TRP 0.035 0.003 TRP J 174 HIS 0.009 0.001 HIS H 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (11561) covalent geometry : angle 0.62839 / 0.34 (15626) SS BOND : bond 0.00338 / 0.21 ( 20) SS BOND : angle 0.88685 / 0.51 ( 40) hydrogen bonds : bond 0.04093 / 2.65 ( 410) hydrogen bonds : angle 5.91157 / 4.14 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8381 (t80) cc_final: 0.8084 (t80) REVERT: B 177 THR cc_start: 0.8504 (t) cc_final: 0.8272 (t) REVERT: B 211 GLN cc_start: 0.8498 (mp10) cc_final: 0.8078 (mm-40) REVERT: C 154 ASN cc_start: 0.8528 (t0) cc_final: 0.8214 (t0) REVERT: C 199 GLN cc_start: 0.7371 (tt0) cc_final: 0.7113 (tt0) REVERT: C 248 SER cc_start: 0.8389 (m) cc_final: 0.8103 (p) REVERT: C 256 TYR cc_start: 0.8653 (m-80) cc_final: 0.8030 (m-80) REVERT: D 41 SER cc_start: 0.8136 (t) cc_final: 0.7824 (m) REVERT: D 93 PHE cc_start: 0.7445 (t80) cc_final: 0.7010 (t80) REVERT: D 192 MET cc_start: 0.7209 (ttm) cc_final: 0.6597 (ttm) REVERT: F 147 LYS cc_start: 0.8460 (mttt) cc_final: 0.7956 (mttt) REVERT: F 183 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7373 (mtt90) REVERT: F 190 MET cc_start: 0.7807 (ptm) cc_final: 0.7377 (ptm) REVERT: F 196 LYS cc_start: 0.7972 (pttt) cc_final: 0.7682 (pttt) REVERT: G 238 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7746 (mtmm) REVERT: G 244 SER cc_start: 0.8696 (m) cc_final: 0.8386 (t) REVERT: H 235 ASP cc_start: 0.8609 (t0) cc_final: 0.8191 (t0) REVERT: I 66 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7894 (ttmm) REVERT: I 155 PHE cc_start: 0.6969 (p90) cc_final: 0.6381 (p90) REVERT: I 158 LEU cc_start: 0.7954 (mt) cc_final: 0.7627 (mt) REVERT: I 174 TRP cc_start: 0.7506 (OUTLIER) cc_final: 0.7011 (m100) REVERT: J 47 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7045 (ppp) REVERT: J 153 PHE cc_start: 0.5049 (OUTLIER) cc_final: 0.4095 (t80) outliers start: 47 outliers final: 30 residues processed: 338 average time/residue: 0.0888 time to fit residues: 44.0535 Evaluate side-chains 347 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 166 PHE Chi-restraints excluded: chain I residue 174 TRP Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain J residue 48 PHE Chi-restraints excluded: chain J residue 153 PHE Chi-restraints excluded: chain J residue 191 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 122 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN G 245 ASN ** H 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.176130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140042 restraints weight = 17725.057| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.27 r_work: 0.3569 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.194 11581 Z= 0.382 Angle : 0.737 12.933 15666 Z= 0.401 Chirality : 0.048 0.247 1650 Planarity : 0.005 0.039 2007 Dihedral : 6.014 58.386 1534 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.46 % Allowed : 16.30 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.21), residues: 1387 helix: 2.31 (0.54), residues: 103 sheet: 0.10 (0.21), residues: 579 loop : -2.09 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 183 TYR 0.031 0.003 TYR G 133 PHE 0.031 0.003 PHE B 176 TRP 0.032 0.003 TRP J 174 HIS 0.013 0.002 HIS H 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00838 / 0.38 (11561) covalent geometry : angle 0.73646 / 0.40 (15626) SS BOND : bond 0.00393 / 0.26 ( 20) SS BOND : angle 1.00808 / 0.58 ( 40) hydrogen bonds : bond 0.05188 / 3.36 ( 410) hydrogen bonds : angle 6.33594 / 4.45 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 337 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8294 (t80) cc_final: 0.8077 (t80) REVERT: B 170 ILE cc_start: 0.6864 (mp) cc_final: 0.6614 (mt) REVERT: B 177 THR cc_start: 0.8600 (t) cc_final: 0.8371 (t) REVERT: B 196 LYS cc_start: 0.7542 (tmmt) cc_final: 0.7314 (tmmt) REVERT: B 201 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.7716 (mmt90) REVERT: B 211 GLN cc_start: 0.8598 (mp10) cc_final: 0.8014 (mm-40) REVERT: C 248 SER cc_start: 0.8386 (m) cc_final: 0.8050 (p) REVERT: C 256 TYR cc_start: 0.8743 (m-80) cc_final: 0.8231 (m-80) REVERT: D 109 MET cc_start: 0.6868 (mmt) cc_final: 0.6526 (mmp) REVERT: D 153 PHE cc_start: 0.7502 (t80) cc_final: 0.7212 (t80) REVERT: D 192 MET cc_start: 0.7260 (ttm) cc_final: 0.6716 (ttm) REVERT: F 147 LYS cc_start: 0.8578 (mttt) cc_final: 0.8371 (mttt) REVERT: F 190 MET cc_start: 0.7794 (ptm) cc_final: 0.7423 (ptm) REVERT: F 194 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8483 (tp) REVERT: F 195 CYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7289 (p) REVERT: G 190 MET cc_start: 0.7892 (tpp) cc_final: 0.7572 (tpp) REVERT: G 199 GLN cc_start: 0.8044 (mp10) cc_final: 0.7523 (mp10) REVERT: G 200 VAL cc_start: 0.8486 (t) cc_final: 0.8280 (m) REVERT: G 238 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7703 (mtmm) REVERT: G 244 SER cc_start: 0.8820 (m) cc_final: 0.8304 (t) REVERT: H 158 ASN cc_start: 0.7840 (t0) cc_final: 0.7618 (t0) REVERT: H 165 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6623 (mtpp) REVERT: H 235 ASP cc_start: 0.8643 (t0) cc_final: 0.8251 (t0) REVERT: I 66 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7911 (ttmm) REVERT: I 122 GLN cc_start: 0.5427 (tt0) cc_final: 0.5069 (tt0) REVERT: I 155 PHE cc_start: 0.7054 (p90) cc_final: 0.6595 (p90) REVERT: I 158 LEU cc_start: 0.8139 (mt) cc_final: 0.7828 (mt) REVERT: J 122 GLN cc_start: 0.7604 (tm-30) cc_final: 0.6823 (tt0) REVERT: J 123 TYR cc_start: 0.6980 (m-80) cc_final: 0.5834 (m-80) REVERT: J 153 PHE cc_start: 0.5210 (OUTLIER) cc_final: 0.4214 (t80) REVERT: J 155 PHE cc_start: 0.7653 (p90) cc_final: 0.7427 (p90) outliers start: 55 outliers final: 35 residues processed: 362 average time/residue: 0.0912 time to fit residues: 48.2652 Evaluate side-chains 373 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 333 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 153 PHE Chi-restraints excluded: chain J residue 191 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN C 154 ASN G 243 ASN G 245 ASN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.180231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142510 restraints weight = 17664.027| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.50 r_work: 0.3614 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11581 Z= 0.157 Angle : 0.619 13.399 15666 Z= 0.330 Chirality : 0.044 0.198 1650 Planarity : 0.004 0.036 2007 Dihedral : 5.339 59.569 1532 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.49 % Allowed : 18.33 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1387 helix: 2.59 (0.53), residues: 103 sheet: 0.14 (0.21), residues: 574 loop : -1.93 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.030 0.002 TYR H 256 PHE 0.035 0.002 PHE J 120 TRP 0.040 0.003 TRP J 174 HIS 0.006 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (11561) covalent geometry : angle 0.61865 / 0.33 (15626) SS BOND : bond 0.00312 / 0.21 ( 20) SS BOND : angle 0.83767 / 0.49 ( 40) hydrogen bonds : bond 0.03537 / 2.28 ( 410) hydrogen bonds : angle 5.90191 / 4.12 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8243 (t80) cc_final: 0.8025 (t80) REVERT: A 182 MET cc_start: 0.7819 (ttp) cc_final: 0.7545 (ttm) REVERT: B 177 THR cc_start: 0.8513 (t) cc_final: 0.8262 (t) REVERT: B 196 LYS cc_start: 0.7409 (tmmt) cc_final: 0.7146 (tmmt) REVERT: B 197 ASN cc_start: 0.7804 (m110) cc_final: 0.7272 (m110) REVERT: B 201 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7537 (mmt90) REVERT: B 211 GLN cc_start: 0.8584 (mp10) cc_final: 0.8213 (mm-40) REVERT: C 199 GLN cc_start: 0.7371 (tt0) cc_final: 0.7021 (tm-30) REVERT: C 248 SER cc_start: 0.8336 (m) cc_final: 0.8035 (p) REVERT: C 256 TYR cc_start: 0.8614 (m-80) cc_final: 0.7989 (m-80) REVERT: D 153 PHE cc_start: 0.7415 (t80) cc_final: 0.7132 (t80) REVERT: D 192 MET cc_start: 0.7292 (ttm) cc_final: 0.6704 (ttm) REVERT: F 190 MET cc_start: 0.7629 (ptm) cc_final: 0.7333 (ptm) REVERT: F 195 CYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7052 (p) REVERT: G 160 ASP cc_start: 0.8007 (t70) cc_final: 0.7505 (p0) REVERT: G 199 GLN cc_start: 0.8043 (mp10) cc_final: 0.7548 (mp10) REVERT: G 238 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7644 (mtmm) REVERT: G 244 SER cc_start: 0.8615 (m) cc_final: 0.8099 (t) REVERT: H 165 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6596 (mtpp) REVERT: H 200 VAL cc_start: 0.9010 (t) cc_final: 0.8802 (p) REVERT: H 235 ASP cc_start: 0.8559 (t0) cc_final: 0.8155 (t0) REVERT: I 66 LYS cc_start: 0.8326 (ttmm) cc_final: 0.7937 (ttmm) REVERT: I 155 PHE cc_start: 0.6617 (p90) cc_final: 0.5968 (p90) REVERT: I 158 LEU cc_start: 0.7826 (mt) cc_final: 0.7511 (mt) REVERT: J 122 GLN cc_start: 0.7397 (tm-30) cc_final: 0.6713 (tt0) REVERT: J 123 TYR cc_start: 0.6983 (m-80) cc_final: 0.5856 (m-80) REVERT: J 155 PHE cc_start: 0.7734 (p90) cc_final: 0.7498 (p90) outliers start: 43 outliers final: 28 residues processed: 343 average time/residue: 0.0870 time to fit residues: 44.3485 Evaluate side-chains 354 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 323 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 166 PHE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 34 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 11 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.177562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140471 restraints weight = 17655.938| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.34 r_work: 0.3590 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 11581 Z= 0.235 Angle : 0.658 12.921 15666 Z= 0.353 Chirality : 0.045 0.205 1650 Planarity : 0.004 0.035 2007 Dihedral : 5.391 55.869 1530 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.57 % Allowed : 18.57 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.21), residues: 1387 helix: 2.68 (0.53), residues: 103 sheet: 0.23 (0.21), residues: 572 loop : -1.98 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 132 TYR 0.031 0.002 TYR H 256 PHE 0.039 0.002 PHE J 48 TRP 0.041 0.003 TRP D 174 HIS 0.009 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (11561) covalent geometry : angle 0.65812 / 0.35 (15626) SS BOND : bond 0.00287 / 0.18 ( 20) SS BOND : angle 0.78433 / 0.46 ( 40) hydrogen bonds : bond 0.04090 / 2.62 ( 410) hydrogen bonds : angle 5.94098 / 4.14 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8203 (t80) cc_final: 0.7993 (t80) REVERT: B 177 THR cc_start: 0.8538 (t) cc_final: 0.8270 (t) REVERT: B 196 LYS cc_start: 0.7456 (tmmt) cc_final: 0.7211 (tmmt) REVERT: B 197 ASN cc_start: 0.7847 (m110) cc_final: 0.7282 (m110) REVERT: B 201 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.8151 (mmm-85) REVERT: B 212 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8156 (t0) REVERT: C 199 GLN cc_start: 0.7356 (tt0) cc_final: 0.6965 (tm-30) REVERT: C 248 SER cc_start: 0.8360 (m) cc_final: 0.8075 (p) REVERT: C 256 TYR cc_start: 0.8678 (m-80) cc_final: 0.8067 (m-80) REVERT: D 153 PHE cc_start: 0.7385 (t80) cc_final: 0.7105 (t80) REVERT: D 192 MET cc_start: 0.7264 (ttm) cc_final: 0.6705 (ttm) REVERT: F 147 LYS cc_start: 0.8534 (mttt) cc_final: 0.8289 (mttt) REVERT: F 195 CYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7015 (p) REVERT: G 199 GLN cc_start: 0.8063 (mp10) cc_final: 0.7583 (mp10) REVERT: G 233 LYS cc_start: 0.8678 (tttm) cc_final: 0.8453 (tttm) REVERT: G 235 ASP cc_start: 0.7604 (m-30) cc_final: 0.7273 (m-30) REVERT: G 244 SER cc_start: 0.8673 (m) cc_final: 0.8147 (t) REVERT: H 165 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6627 (mtpp) REVERT: H 235 ASP cc_start: 0.8620 (t0) cc_final: 0.8209 (t0) REVERT: I 66 LYS cc_start: 0.8251 (ttmm) cc_final: 0.7881 (ttmm) REVERT: I 155 PHE cc_start: 0.6849 (p90) cc_final: 0.6262 (p90) REVERT: I 158 LEU cc_start: 0.7973 (mt) cc_final: 0.7661 (mt) REVERT: J 122 GLN cc_start: 0.7435 (tm-30) cc_final: 0.6758 (tt0) REVERT: J 123 TYR cc_start: 0.6918 (m-80) cc_final: 0.5826 (m-80) REVERT: J 155 PHE cc_start: 0.7896 (p90) cc_final: 0.7433 (p90) outliers start: 44 outliers final: 32 residues processed: 345 average time/residue: 0.0896 time to fit residues: 45.6839 Evaluate side-chains 361 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 326 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 196 LYS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 174 TRP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 191 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 100 optimal weight: 0.3980 chunk 80 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.0040 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 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 = 0.4285 r_free = 0.4285 target = 0.180242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142622 restraints weight = 17395.567| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.41 r_work: 0.3609 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 11581 Z= 0.151 Angle : 0.627 11.701 15666 Z= 0.336 Chirality : 0.043 0.197 1650 Planarity : 0.003 0.036 2007 Dihedral : 5.260 53.167 1530 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.41 % Allowed : 19.71 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.22), residues: 1387 helix: 2.76 (0.52), residues: 103 sheet: 0.23 (0.22), residues: 561 loop : -1.88 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 132 TYR 0.031 0.001 TYR G 133 PHE 0.035 0.002 PHE J 48 TRP 0.034 0.003 TRP D 174 HIS 0.009 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (11561) covalent geometry : angle 0.62670 / 0.34 (15626) SS BOND : bond 0.00250 / 0.16 ( 20) SS BOND : angle 0.72071 / 0.43 ( 40) hydrogen bonds : bond 0.03401 / 2.17 ( 410) hydrogen bonds : angle 5.76271 / 3.99 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 319 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8209 (t80) cc_final: 0.7944 (t80) REVERT: B 177 THR cc_start: 0.8518 (t) cc_final: 0.8249 (t) REVERT: B 196 LYS cc_start: 0.7386 (tmmt) cc_final: 0.7108 (tmmt) REVERT: B 197 ASN cc_start: 0.7821 (m110) cc_final: 0.7278 (m110) REVERT: B 201 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7581 (mmt90) REVERT: B 212 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8156 (t0) REVERT: C 196 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7585 (tttt) REVERT: C 199 GLN cc_start: 0.7406 (tt0) cc_final: 0.7125 (tm-30) REVERT: C 248 SER cc_start: 0.8306 (m) cc_final: 0.8026 (p) REVERT: C 256 TYR cc_start: 0.8576 (m-80) cc_final: 0.7905 (m-80) REVERT: D 153 PHE cc_start: 0.7418 (t80) cc_final: 0.7124 (t80) REVERT: D 192 MET cc_start: 0.7294 (ttm) cc_final: 0.6676 (ttm) REVERT: F 147 LYS cc_start: 0.8471 (mttt) cc_final: 0.8199 (mttt) REVERT: F 195 CYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6903 (p) REVERT: G 160 ASP cc_start: 0.7944 (t70) cc_final: 0.7480 (p0) REVERT: G 183 ARG cc_start: 0.6892 (ttp-170) cc_final: 0.6263 (ttp-170) REVERT: G 199 GLN cc_start: 0.7996 (mp10) cc_final: 0.7493 (mp10) REVERT: G 233 LYS cc_start: 0.8709 (tttm) cc_final: 0.8450 (tttm) REVERT: G 235 ASP cc_start: 0.7550 (m-30) cc_final: 0.7259 (m-30) REVERT: H 165 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6644 (mtpp) REVERT: H 235 ASP cc_start: 0.8537 (t0) cc_final: 0.8128 (t0) REVERT: I 66 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7867 (ttmm) REVERT: I 155 PHE cc_start: 0.6566 (p90) cc_final: 0.5957 (p90) REVERT: I 158 LEU cc_start: 0.7892 (mt) cc_final: 0.7550 (mt) REVERT: J 88 TYR cc_start: 0.7442 (p90) cc_final: 0.7104 (p90) REVERT: J 122 GLN cc_start: 0.7430 (tm-30) cc_final: 0.6721 (tt0) REVERT: J 123 TYR cc_start: 0.6987 (m-80) cc_final: 0.5822 (m-80) REVERT: J 155 PHE cc_start: 0.7798 (p90) cc_final: 0.7338 (p90) outliers start: 42 outliers final: 31 residues processed: 337 average time/residue: 0.0868 time to fit residues: 43.4843 Evaluate side-chains 355 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 320 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 174 TRP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 0.0570 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.180034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143756 restraints weight = 17410.396| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.27 r_work: 0.3638 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11581 Z= 0.148 Angle : 0.623 11.899 15666 Z= 0.332 Chirality : 0.043 0.192 1650 Planarity : 0.003 0.036 2007 Dihedral : 5.167 53.193 1530 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.84 % Allowed : 20.68 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.22), residues: 1387 helix: 2.89 (0.52), residues: 103 sheet: 0.23 (0.21), residues: 588 loop : -1.89 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 132 TYR 0.028 0.001 TYR H 256 PHE 0.031 0.002 PHE J 48 TRP 0.037 0.003 TRP D 174 HIS 0.009 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11561) covalent geometry : angle 0.62318 / 0.33 (15626) SS BOND : bond 0.00238 / 0.15 ( 20) SS BOND : angle 0.71184 / 0.44 ( 40) hydrogen bonds : bond 0.03340 / 2.13 ( 410) hydrogen bonds : angle 5.67684 / 3.93 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 318 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8177 (t80) cc_final: 0.7938 (t80) REVERT: B 177 THR cc_start: 0.8464 (t) cc_final: 0.8185 (t) REVERT: B 188 THR cc_start: 0.7315 (m) cc_final: 0.6993 (t) REVERT: B 212 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.8173 (t0) REVERT: B 233 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7287 (mmmm) REVERT: C 196 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7554 (tttt) REVERT: C 199 GLN cc_start: 0.7369 (tt0) cc_final: 0.7150 (tm-30) REVERT: C 248 SER cc_start: 0.8306 (m) cc_final: 0.8014 (t) REVERT: C 256 TYR cc_start: 0.8573 (m-80) cc_final: 0.7899 (m-80) REVERT: D 153 PHE cc_start: 0.7363 (t80) cc_final: 0.7026 (t80) REVERT: D 192 MET cc_start: 0.7264 (ttm) cc_final: 0.6681 (ttm) REVERT: F 147 LYS cc_start: 0.8463 (mttt) cc_final: 0.8197 (mttt) REVERT: F 195 CYS cc_start: 0.7666 (OUTLIER) cc_final: 0.6848 (p) REVERT: G 160 ASP cc_start: 0.7964 (t70) cc_final: 0.7635 (p0) REVERT: G 183 ARG cc_start: 0.6853 (ttp-170) cc_final: 0.6232 (ttp-170) REVERT: G 199 GLN cc_start: 0.7939 (mp10) cc_final: 0.7459 (mp10) REVERT: G 233 LYS cc_start: 0.8668 (tttm) cc_final: 0.8418 (tttm) REVERT: G 235 ASP cc_start: 0.7537 (m-30) cc_final: 0.7247 (m-30) REVERT: H 165 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6597 (mtpp) REVERT: H 235 ASP cc_start: 0.8547 (t0) cc_final: 0.8145 (t0) REVERT: I 66 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7864 (ttmm) REVERT: I 155 PHE cc_start: 0.6463 (p90) cc_final: 0.5863 (p90) REVERT: I 158 LEU cc_start: 0.7899 (mt) cc_final: 0.7579 (mt) REVERT: J 88 TYR cc_start: 0.7440 (p90) cc_final: 0.7091 (p90) REVERT: J 122 GLN cc_start: 0.7369 (tm-30) cc_final: 0.6681 (tt0) REVERT: J 123 TYR cc_start: 0.6907 (m-80) cc_final: 0.5503 (m-80) REVERT: J 155 PHE cc_start: 0.7793 (p90) cc_final: 0.7342 (p90) outliers start: 35 outliers final: 28 residues processed: 334 average time/residue: 0.0846 time to fit residues: 41.9824 Evaluate side-chains 352 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 319 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 174 TRP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 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 = 0.4296 r_free = 0.4296 target = 0.180572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143815 restraints weight = 17692.657| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.40 r_work: 0.3622 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11581 Z= 0.139 Angle : 0.625 12.182 15666 Z= 0.329 Chirality : 0.043 0.195 1650 Planarity : 0.003 0.036 2007 Dihedral : 5.097 56.118 1530 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.92 % Allowed : 20.60 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.22), residues: 1387 helix: 2.91 (0.52), residues: 103 sheet: 0.18 (0.21), residues: 591 loop : -1.85 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 132 TYR 0.027 0.001 TYR H 256 PHE 0.029 0.002 PHE J 48 TRP 0.037 0.003 TRP D 174 HIS 0.008 0.001 HIS C 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11561) covalent geometry : angle 0.62435 / 0.33 (15626) SS BOND : bond 0.00213 / 0.14 ( 20) SS BOND : angle 0.69856 / 0.43 ( 40) hydrogen bonds : bond 0.03252 / 2.08 ( 410) hydrogen bonds : angle 5.57532 / 3.86 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2624.53 seconds wall clock time: 45 minutes 54.15 seconds (2754.15 seconds total)