Starting phenix.real_space_refine on Wed Feb 4 15:37:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lkl_63181/02_2026/9lkl_63181.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lkl_63181/02_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_63181/02_2026/9lkl_63181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lkl_63181/02_2026/9lkl_63181.map" model { file = "/net/cci-nas-00/data/ceres_data/9lkl_63181/02_2026/9lkl_63181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lkl_63181/02_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-2.0-5952/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.28 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: 0.94 Conformation dependent library (CDL) restraints added in 662.2 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: 0.55 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: 1.95 Time building geometry restraints manager: 1.33 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 2.510 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: 1.520 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.580 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 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 covalent geometry : bond 0.00720 (11561) covalent geometry : angle 1.00696 (15626) SS BOND : bond 0.00596 ( 20) SS BOND : angle 1.19664 ( 40) hydrogen bonds : bond 0.16778 ( 410) hydrogen bonds : angle 8.01864 ( 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 : 0.421 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: 0.1041 time to fit residues: 56.5994 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 : 0.445 ------------------------------------------------------------------------------- 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: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4312 r_free = 0.4312 target = 0.183407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.146217 restraints weight = 17915.207| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.43 r_work: 0.3646 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 11581 Z= 0.216 Angle : 0.664 10.702 15666 Z= 0.356 Chirality : 0.045 0.276 1650 Planarity : 0.004 0.039 2007 Dihedral : 5.969 56.627 1548 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.47 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: 1.02 (0.49), residues: 103 sheet: -0.20 (0.20), residues: 578 loop : -2.04 (0.20), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 183 TYR 0.020 0.002 TYR H 256 PHE 0.029 0.002 PHE E 48 TRP 0.035 0.003 TRP J 174 HIS 0.007 0.002 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00483 (11561) covalent geometry : angle 0.66029 (15626) SS BOND : bond 0.00538 ( 20) SS BOND : angle 1.47229 ( 40) hydrogen bonds : bond 0.04626 ( 410) hydrogen bonds : angle 6.30526 ( 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 363 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 336 time to evaluate : 0.417 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: 0.8490 (t80) cc_final: 0.8178 (t80) REVERT: A 182 MET cc_start: 0.7874 (ttp) cc_final: 0.7557 (ttm) REVERT: A 194 LEU cc_start: 0.8357 (tp) cc_final: 0.8147 (tt) REVERT: B 196 LYS cc_start: 0.7419 (tmmt) cc_final: 0.6965 (tmmt) REVERT: B 201 ARG cc_start: 0.8469 (mmt90) cc_final: 0.7877 (mmt90) REVERT: B 212 ASN cc_start: 0.8309 (m-40) cc_final: 0.7808 (m-40) REVERT: B 238 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8042 (mttp) REVERT: C 199 GLN cc_start: 0.7227 (tt0) cc_final: 0.6668 (tt0) REVERT: C 248 SER cc_start: 0.8332 (m) cc_final: 0.7942 (p) REVERT: C 256 TYR cc_start: 0.8565 (m-80) cc_final: 0.8051 (m-80) REVERT: D 155 PHE cc_start: 0.7804 (p90) cc_final: 0.7592 (p90) REVERT: D 162 SER cc_start: 0.8623 (p) cc_final: 0.8343 (p) REVERT: D 192 MET cc_start: 0.7292 (ttm) cc_final: 0.6818 (ttm) REVERT: E 109 MET cc_start: 0.7409 (ppp) cc_final: 0.6873 (ppp) REVERT: E 169 HIS cc_start: 0.6364 (OUTLIER) cc_final: 0.5519 (p-80) REVERT: F 147 LYS cc_start: 0.8207 (mttt) cc_final: 0.7627 (mttt) REVERT: F 151 VAL cc_start: 0.8418 (t) cc_final: 0.8178 (m) REVERT: F 154 ASN cc_start: 0.8461 (t0) cc_final: 0.8242 (t0) REVERT: F 190 MET cc_start: 0.7673 (ptm) cc_final: 0.7322 (ptt) REVERT: G 149 ASP cc_start: 0.7901 (t0) cc_final: 0.7598 (t0) REVERT: G 224 LEU cc_start: 0.8050 (mt) cc_final: 0.7819 (mt) REVERT: G 238 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7457 (mtmm) REVERT: G 244 SER cc_start: 0.8712 (m) cc_final: 0.8426 (t) REVERT: H 158 ASN cc_start: 0.7646 (t0) cc_final: 0.7202 (t0) REVERT: H 165 LYS cc_start: 0.6984 (mttt) cc_final: 0.6665 (mttp) REVERT: H 190 MET cc_start: 0.7417 (ttt) cc_final: 0.7152 (ttt) REVERT: H 197 ASN cc_start: 0.8383 (m110) cc_final: 0.8163 (m110) REVERT: H 235 ASP cc_start: 0.8630 (t0) cc_final: 0.8365 (t0) REVERT: H 240 HIS cc_start: 0.8556 (t70) cc_final: 0.8296 (t70) REVERT: I 57 TRP cc_start: 0.7473 (t60) cc_final: 0.7260 (t-100) REVERT: I 58 THR cc_start: 0.8234 (p) cc_final: 0.7229 (p) REVERT: I 66 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7761 (ttmm) REVERT: I 155 PHE cc_start: 0.6484 (p90) cc_final: 0.5989 (p90) REVERT: I 158 LEU cc_start: 0.7758 (mt) cc_final: 0.7444 (mt) REVERT: J 48 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6874 (p90) REVERT: J 153 PHE cc_start: 0.5298 (OUTLIER) cc_final: 0.4281 (t80) outliers start: 27 outliers final: 15 residues processed: 351 average time/residue: 0.0995 time to fit residues: 50.8837 Evaluate side-chains 350 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 330 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 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 48 PHE 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: 3.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 93 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 HIS ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN F 138 ASN G 240 HIS G 245 ASN H 169 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.183763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146369 restraints weight = 17661.957| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.35 r_work: 0.3671 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 11581 Z= 0.173 Angle : 0.589 10.197 15666 Z= 0.318 Chirality : 0.043 0.257 1650 Planarity : 0.003 0.033 2007 Dihedral : 5.554 58.134 1542 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.33 % Allowed : 11.84 % Favored : 84.83 % 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: -1.22 (0.21), residues: 1387 helix: 1.82 (0.52), residues: 103 sheet: 0.05 (0.21), residues: 532 loop : -1.93 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.020 0.002 TYR G 133 PHE 0.020 0.002 PHE E 48 TRP 0.032 0.002 TRP J 174 HIS 0.006 0.001 HIS H 179 Details of bonding type rmsd covalent geometry : bond 0.00386 (11561) covalent geometry : angle 0.58664 (15626) SS BOND : bond 0.00364 ( 20) SS BOND : angle 1.11243 ( 40) hydrogen bonds : bond 0.04032 ( 410) hydrogen bonds : angle 6.02850 ( 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 359 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 318 time to evaluate : 0.471 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: 0.8459 (t80) cc_final: 0.8126 (t80) REVERT: A 182 MET cc_start: 0.7834 (ttp) cc_final: 0.7533 (ttm) REVERT: A 194 LEU cc_start: 0.8299 (tp) cc_final: 0.8096 (tt) REVERT: B 201 ARG cc_start: 0.8324 (mmt90) cc_final: 0.8079 (mmt90) REVERT: B 211 GLN cc_start: 0.8538 (mp10) cc_final: 0.8034 (mp10) REVERT: B 238 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8042 (mttp) REVERT: C 199 GLN cc_start: 0.7352 (tt0) cc_final: 0.6950 (tt0) REVERT: C 201 ARG cc_start: 0.8205 (mmt180) cc_final: 0.7962 (mmt-90) REVERT: C 248 SER cc_start: 0.8338 (m) cc_final: 0.7997 (p) REVERT: C 256 TYR cc_start: 0.8580 (m-80) cc_final: 0.8030 (m-80) REVERT: D 192 MET cc_start: 0.7266 (ttm) cc_final: 0.6725 (ttm) REVERT: E 152 PHE cc_start: 0.6837 (m-80) cc_final: 0.6626 (m-80) REVERT: F 147 LYS cc_start: 0.8345 (mttt) cc_final: 0.7850 (mttt) REVERT: F 151 VAL cc_start: 0.8387 (t) cc_final: 0.8165 (m) REVERT: F 154 ASN cc_start: 0.8479 (t0) cc_final: 0.8266 (t0) REVERT: F 183 ARG cc_start: 0.7563 (ttm170) cc_final: 0.7115 (ttp-170) REVERT: G 224 LEU cc_start: 0.8074 (mt) cc_final: 0.7862 (mt) REVERT: G 238 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7570 (mtmm) REVERT: G 244 SER cc_start: 0.8739 (m) cc_final: 0.8157 (t) REVERT: H 158 ASN cc_start: 0.7624 (t0) cc_final: 0.7323 (t0) REVERT: H 190 MET cc_start: 0.7383 (ttt) cc_final: 0.7150 (ttt) REVERT: H 235 ASP cc_start: 0.8561 (t0) cc_final: 0.8185 (t0) REVERT: I 66 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7748 (ttmm) REVERT: I 70 TYR cc_start: 0.7846 (m-80) cc_final: 0.7215 (m-80) REVERT: I 155 PHE cc_start: 0.6649 (p90) cc_final: 0.6196 (p90) REVERT: I 158 LEU cc_start: 0.7794 (mt) cc_final: 0.7518 (mt) REVERT: J 122 GLN cc_start: 0.7072 (tm-30) cc_final: 0.6738 (tt0) REVERT: J 123 TYR cc_start: 0.6573 (m-80) cc_final: 0.5454 (m-80) REVERT: J 153 PHE cc_start: 0.5122 (OUTLIER) cc_final: 0.4167 (t80) outliers start: 41 outliers final: 24 residues processed: 338 average time/residue: 0.1012 time to fit residues: 49.7479 Evaluate side-chains 341 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 314 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 223 HIS 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 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 195 CYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 169 ASN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain I residue 37 VAL 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 153 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 116 optimal weight: 0.0670 chunk 71 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN C 154 ASN D 92 HIS G 223 HIS ** 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 = 0.4336 r_free = 0.4336 target = 0.185063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.147401 restraints weight = 17640.177| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.38 r_work: 0.3694 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11581 Z= 0.125 Angle : 0.581 12.097 15666 Z= 0.307 Chirality : 0.043 0.203 1650 Planarity : 0.003 0.031 2007 Dihedral : 5.343 58.588 1540 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.84 % Allowed : 13.46 % Favored : 83.70 % 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: -1.05 (0.21), residues: 1387 helix: 2.15 (0.53), residues: 103 sheet: 0.12 (0.20), residues: 585 loop : -1.93 (0.20), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.022 0.001 TYR G 133 PHE 0.039 0.002 PHE J 48 TRP 0.042 0.003 TRP J 57 HIS 0.009 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00281 (11561) covalent geometry : angle 0.57964 (15626) SS BOND : bond 0.00332 ( 20) SS BOND : angle 0.90199 ( 40) hydrogen bonds : bond 0.03506 ( 410) hydrogen bonds : angle 5.81800 ( 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 352 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 0.476 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: 0.8382 (t80) cc_final: 0.8097 (t80) REVERT: A 182 MET cc_start: 0.7768 (ttp) cc_final: 0.7465 (ttm) REVERT: B 196 LYS cc_start: 0.7393 (tmmt) cc_final: 0.6784 (tmmt) REVERT: B 201 ARG cc_start: 0.8292 (mmt90) cc_final: 0.7656 (mmt90) REVERT: B 238 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8028 (mttp) REVERT: C 154 ASN cc_start: 0.8400 (t0) cc_final: 0.8123 (t0) REVERT: C 199 GLN cc_start: 0.7240 (tt0) cc_final: 0.6722 (tt0) REVERT: C 201 ARG cc_start: 0.8148 (mmt180) cc_final: 0.7872 (mmt-90) REVERT: C 248 SER cc_start: 0.8287 (m) cc_final: 0.8004 (p) REVERT: C 256 TYR cc_start: 0.8565 (m-80) cc_final: 0.7923 (m-80) REVERT: D 67 TYR cc_start: 0.8145 (m-10) cc_final: 0.7818 (m-10) REVERT: D 93 PHE cc_start: 0.7299 (t80) cc_final: 0.6871 (t80) REVERT: D 192 MET cc_start: 0.7274 (ttm) cc_final: 0.6739 (ttm) REVERT: E 152 PHE cc_start: 0.6912 (m-80) cc_final: 0.6619 (m-80) REVERT: F 147 LYS cc_start: 0.8341 (mttt) cc_final: 0.8063 (mttt) REVERT: F 154 ASN cc_start: 0.8394 (t0) cc_final: 0.8171 (t0) REVERT: F 190 MET cc_start: 0.7802 (ptm) cc_final: 0.7507 (ptm) REVERT: G 224 LEU cc_start: 0.8105 (mt) cc_final: 0.7895 (mt) REVERT: G 238 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7573 (mtmm) REVERT: G 244 SER cc_start: 0.8533 (m) cc_final: 0.7969 (t) REVERT: H 158 ASN cc_start: 0.7578 (t0) cc_final: 0.7330 (t0) REVERT: H 165 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6735 (mttm) REVERT: H 235 ASP cc_start: 0.8583 (t0) cc_final: 0.8158 (t0) REVERT: I 66 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7782 (ttmm) REVERT: I 155 PHE cc_start: 0.6417 (p90) cc_final: 0.5958 (p90) REVERT: J 153 PHE cc_start: 0.4996 (OUTLIER) cc_final: 0.4106 (t80) outliers start: 35 outliers final: 28 residues processed: 331 average time/residue: 0.0924 time to fit residues: 45.0383 Evaluate side-chains 348 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 316 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 199 GLN Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LYS 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 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 153 THR Chi-restraints excluded: chain G residue 182 MET Chi-restraints excluded: chain G residue 195 CYS Chi-restraints excluded: chain G residue 233 LYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 132 PHE Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 195 CYS 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 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: 0.9980 chunk 131 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 HIS 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 = 0.4290 r_free = 0.4290 target = 0.180277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142862 restraints weight = 17615.812| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.44 r_work: 0.3626 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3482 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= 0.194 Angle : 0.612 16.794 15666 Z= 0.324 Chirality : 0.044 0.206 1650 Planarity : 0.003 0.030 2007 Dihedral : 5.440 55.384 1540 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.41 % Allowed : 14.44 % Favored : 82.16 % 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: -1.01 (0.21), residues: 1387 helix: 2.32 (0.53), residues: 103 sheet: 0.13 (0.20), residues: 593 loop : -1.95 (0.20), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.030 0.002 TYR H 256 PHE 0.050 0.002 PHE J 48 TRP 0.031 0.002 TRP J 174 HIS 0.008 0.001 HIS H 179 Details of bonding type rmsd covalent geometry : bond 0.00431 (11561) covalent geometry : angle 0.61127 (15626) SS BOND : bond 0.00308 ( 20) SS BOND : angle 0.87535 ( 40) hydrogen bonds : bond 0.03833 ( 410) hydrogen bonds : angle 5.80558 ( 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 360 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8387 (t80) cc_final: 0.8131 (t80) REVERT: B 177 THR cc_start: 0.8485 (t) cc_final: 0.8258 (t) REVERT: B 211 GLN cc_start: 0.8535 (mp10) cc_final: 0.8069 (mm-40) REVERT: B 233 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7310 (mmmm) REVERT: B 238 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8082 (mttp) REVERT: B 246 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8341 (mttm) REVERT: C 154 ASN cc_start: 0.8517 (t0) cc_final: 0.8264 (t0) REVERT: C 199 GLN cc_start: 0.7371 (tt0) cc_final: 0.7017 (tt0) REVERT: C 201 ARG cc_start: 0.8307 (mmt180) cc_final: 0.8103 (mmt-90) REVERT: C 248 SER cc_start: 0.8405 (m) cc_final: 0.8073 (p) REVERT: C 256 TYR cc_start: 0.8644 (m-80) cc_final: 0.8022 (m-80) REVERT: D 41 SER cc_start: 0.8091 (t) cc_final: 0.7753 (m) REVERT: D 67 TYR cc_start: 0.8217 (m-10) cc_final: 0.8010 (m-10) REVERT: D 93 PHE cc_start: 0.7471 (t80) cc_final: 0.7013 (t80) REVERT: D 192 MET cc_start: 0.7239 (ttm) cc_final: 0.6636 (ttm) REVERT: F 147 LYS cc_start: 0.8470 (mttt) cc_final: 0.7959 (mttt) REVERT: F 183 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7364 (mtt90) REVERT: F 190 MET cc_start: 0.7791 (ptm) cc_final: 0.7439 (ptm) REVERT: F 195 CYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7272 (p) REVERT: G 199 GLN cc_start: 0.7965 (mp10) cc_final: 0.7532 (mp10) REVERT: G 224 LEU cc_start: 0.8086 (mt) cc_final: 0.7873 (mt) REVERT: G 238 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7733 (mtmm) REVERT: G 244 SER cc_start: 0.8587 (m) cc_final: 0.8022 (t) REVERT: H 146 LEU cc_start: 0.9018 (mt) cc_final: 0.8765 (mp) REVERT: H 235 ASP cc_start: 0.8579 (t0) cc_final: 0.8140 (t0) REVERT: I 66 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7870 (ttmm) REVERT: I 174 TRP cc_start: 0.7470 (OUTLIER) cc_final: 0.6934 (m100) REVERT: J 153 PHE cc_start: 0.5071 (OUTLIER) cc_final: 0.4146 (t80) outliers start: 42 outliers final: 29 residues processed: 338 average time/residue: 0.0983 time to fit residues: 48.6306 Evaluate side-chains 351 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 316 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 238 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 D residue 43 SER Chi-restraints excluded: chain D residue 71 LEU 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 195 CYS 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 233 LYS Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 31 SER 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 48 PHE Chi-restraints excluded: chain J residue 153 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 44 optimal weight: 0.0170 chunk 55 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.177131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139645 restraints weight = 17777.536| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.38 r_work: 0.3564 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.183 11581 Z= 0.349 Angle : 0.715 9.667 15666 Z= 0.388 Chirality : 0.047 0.214 1650 Planarity : 0.004 0.034 2007 Dihedral : 5.965 57.382 1538 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.30 % Allowed : 15.98 % Favored : 79.72 % 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: -1.08 (0.21), residues: 1387 helix: 2.37 (0.54), residues: 103 sheet: 0.21 (0.22), residues: 555 loop : -2.02 (0.19), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 132 TYR 0.032 0.003 TYR G 133 PHE 0.036 0.003 PHE J 48 TRP 0.038 0.003 TRP J 174 HIS 0.013 0.002 HIS H 179 Details of bonding type rmsd covalent geometry : bond 0.00765 (11561) covalent geometry : angle 0.71394 (15626) SS BOND : bond 0.00378 ( 20) SS BOND : angle 0.99307 ( 40) hydrogen bonds : bond 0.04859 ( 410) hydrogen bonds : angle 6.22095 ( 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 390 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 337 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8291 (t80) cc_final: 0.8022 (t80) REVERT: B 150 ASP cc_start: 0.8058 (t0) cc_final: 0.7672 (t0) REVERT: B 196 LYS cc_start: 0.7574 (tmmt) cc_final: 0.7357 (tmmt) REVERT: B 197 ASN cc_start: 0.7771 (m110) cc_final: 0.7525 (m110) REVERT: B 201 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.7586 (mmt90) REVERT: B 208 ASP cc_start: 0.6330 (m-30) cc_final: 0.6128 (m-30) REVERT: B 211 GLN cc_start: 0.8673 (mp10) cc_final: 0.8115 (mm-40) REVERT: B 246 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8113 (mttm) REVERT: C 140 HIS cc_start: 0.7540 (m-70) cc_final: 0.7290 (m90) REVERT: C 201 ARG cc_start: 0.8353 (mmt180) cc_final: 0.8121 (mmt-90) REVERT: C 248 SER cc_start: 0.8457 (m) cc_final: 0.8117 (p) REVERT: C 256 TYR cc_start: 0.8736 (m-80) cc_final: 0.8149 (m-80) REVERT: D 153 PHE cc_start: 0.7474 (t80) cc_final: 0.7213 (t80) REVERT: D 192 MET cc_start: 0.7291 (ttm) cc_final: 0.6724 (ttm) REVERT: F 190 MET cc_start: 0.7831 (ptm) cc_final: 0.7455 (ptm) REVERT: F 195 CYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7470 (p) REVERT: G 190 MET cc_start: 0.7824 (tpp) cc_final: 0.7611 (tpp) REVERT: G 199 GLN cc_start: 0.8044 (mp10) cc_final: 0.7511 (mp10) REVERT: G 224 LEU cc_start: 0.8080 (mt) cc_final: 0.7854 (mt) REVERT: G 238 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7787 (mtmm) REVERT: G 244 SER cc_start: 0.8666 (m) cc_final: 0.8032 (t) REVERT: H 235 ASP cc_start: 0.8664 (t0) cc_final: 0.8266 (t0) REVERT: I 66 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7873 (ttmm) REVERT: I 70 TYR cc_start: 0.7750 (m-10) cc_final: 0.7472 (m-10) REVERT: J 155 PHE cc_start: 0.7686 (p90) cc_final: 0.7481 (p90) outliers start: 53 outliers final: 37 residues processed: 357 average time/residue: 0.0993 time to fit residues: 51.7662 Evaluate side-chains 370 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 331 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 71 LEU 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 195 CYS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 235 ASP 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 173 THR 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 65 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 164 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 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 = 0.4284 r_free = 0.4284 target = 0.180949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143545 restraints weight = 17663.409| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.43 r_work: 0.3615 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11581 Z= 0.149 Angle : 0.613 11.469 15666 Z= 0.326 Chirality : 0.044 0.206 1650 Planarity : 0.003 0.034 2007 Dihedral : 5.546 57.995 1538 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.57 % Allowed : 17.27 % Favored : 79.16 % 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: -0.98 (0.21), residues: 1387 helix: 2.72 (0.53), residues: 103 sheet: 0.14 (0.21), residues: 568 loop : -1.91 (0.20), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.030 0.002 TYR G 133 PHE 0.042 0.002 PHE J 48 TRP 0.030 0.003 TRP J 174 HIS 0.007 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00338 (11561) covalent geometry : angle 0.61267 (15626) SS BOND : bond 0.00302 ( 20) SS BOND : angle 0.83373 ( 40) hydrogen bonds : bond 0.03472 ( 410) hydrogen bonds : angle 5.79511 ( 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 361 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8262 (t80) cc_final: 0.7978 (t80) REVERT: A 182 MET cc_start: 0.7808 (ttp) cc_final: 0.7553 (ttm) REVERT: B 150 ASP cc_start: 0.7934 (t0) cc_final: 0.7499 (t0) REVERT: B 196 LYS cc_start: 0.7393 (tmmt) cc_final: 0.7178 (tmmt) REVERT: B 197 ASN cc_start: 0.7820 (m110) cc_final: 0.7570 (m110) REVERT: B 201 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7510 (mmt90) REVERT: B 208 ASP cc_start: 0.6243 (m-30) cc_final: 0.6034 (m-30) REVERT: B 211 GLN cc_start: 0.8653 (mp10) cc_final: 0.8171 (mm-40) REVERT: B 233 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7273 (mmmm) REVERT: B 246 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8133 (mttm) REVERT: C 140 HIS cc_start: 0.7415 (m-70) cc_final: 0.7174 (m90) REVERT: C 199 GLN cc_start: 0.7486 (tt0) cc_final: 0.7068 (tm-30) REVERT: C 201 ARG cc_start: 0.8351 (mmt180) cc_final: 0.8138 (mmt-90) REVERT: C 248 SER cc_start: 0.8402 (m) cc_final: 0.8080 (p) REVERT: C 256 TYR cc_start: 0.8612 (m-80) cc_final: 0.7985 (m-80) REVERT: D 153 PHE cc_start: 0.7449 (t80) cc_final: 0.7139 (t80) REVERT: D 192 MET cc_start: 0.7237 (ttm) cc_final: 0.6665 (ttm) REVERT: F 195 CYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7082 (p) REVERT: F 196 LYS cc_start: 0.7830 (pttt) cc_final: 0.7606 (pttt) REVERT: G 160 ASP cc_start: 0.8005 (t70) cc_final: 0.7508 (p0) REVERT: G 199 GLN cc_start: 0.8024 (mp10) cc_final: 0.7514 (mp10) REVERT: G 238 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7736 (mtmm) REVERT: G 244 SER cc_start: 0.8577 (m) cc_final: 0.8058 (t) REVERT: H 165 LYS cc_start: 0.7344 (mtpp) cc_final: 0.6534 (mtpp) REVERT: H 200 VAL cc_start: 0.9009 (t) cc_final: 0.8788 (p) REVERT: H 235 ASP cc_start: 0.8615 (t0) cc_final: 0.8206 (t0) REVERT: I 66 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7827 (ttmm) REVERT: I 155 PHE cc_start: 0.6917 (p90) cc_final: 0.6479 (p90) REVERT: J 155 PHE cc_start: 0.7652 (p90) cc_final: 0.7384 (p90) outliers start: 44 outliers final: 33 residues processed: 331 average time/residue: 0.1038 time to fit residues: 50.1312 Evaluate side-chains 349 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 313 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 203 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 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 71 LEU 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 E residue 109 MET 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 F residue 235 ASP 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 173 THR Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 175 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 11 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 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 = 0.4271 r_free = 0.4271 target = 0.179821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143242 restraints weight = 17600.650| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.37 r_work: 0.3602 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 11581 Z= 0.211 Angle : 0.638 12.238 15666 Z= 0.340 Chirality : 0.044 0.207 1650 Planarity : 0.004 0.034 2007 Dihedral : 5.450 57.751 1534 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.89 % Allowed : 17.76 % Favored : 78.35 % 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: -0.95 (0.21), residues: 1387 helix: 2.91 (0.52), residues: 103 sheet: 0.21 (0.21), residues: 570 loop : -1.97 (0.20), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 201 TYR 0.032 0.002 TYR H 256 PHE 0.045 0.002 PHE J 48 TRP 0.033 0.003 TRP D 174 HIS 0.009 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00473 (11561) covalent geometry : angle 0.63787 (15626) SS BOND : bond 0.00280 ( 20) SS BOND : angle 0.80727 ( 40) hydrogen bonds : bond 0.03838 ( 410) hydrogen bonds : angle 5.80532 ( 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 376 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 328 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8248 (t80) cc_final: 0.8030 (t80) REVERT: B 150 ASP cc_start: 0.7980 (t0) cc_final: 0.7545 (t0) REVERT: B 197 ASN cc_start: 0.7826 (m110) cc_final: 0.7568 (m110) REVERT: B 201 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.8127 (mmm-85) REVERT: B 211 GLN cc_start: 0.8646 (mp10) cc_final: 0.8125 (mm-40) REVERT: B 246 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8109 (mttm) REVERT: C 199 GLN cc_start: 0.7450 (tt0) cc_final: 0.7105 (tm-30) REVERT: C 225 ASP cc_start: 0.7640 (m-30) cc_final: 0.7070 (m-30) REVERT: C 248 SER cc_start: 0.8320 (m) cc_final: 0.7979 (p) REVERT: C 256 TYR cc_start: 0.8656 (m-80) cc_final: 0.7961 (m-80) REVERT: D 153 PHE cc_start: 0.7438 (t80) cc_final: 0.7118 (t80) REVERT: D 192 MET cc_start: 0.7311 (ttm) cc_final: 0.6721 (ttm) REVERT: F 195 CYS cc_start: 0.7815 (OUTLIER) cc_final: 0.6998 (p) REVERT: F 196 LYS cc_start: 0.7823 (pttt) cc_final: 0.7590 (pttt) REVERT: G 160 ASP cc_start: 0.7987 (t70) cc_final: 0.7460 (p0) REVERT: G 199 GLN cc_start: 0.8027 (mp10) cc_final: 0.7526 (mp10) REVERT: G 244 SER cc_start: 0.8559 (m) cc_final: 0.8103 (t) REVERT: H 165 LYS cc_start: 0.7427 (mtpp) cc_final: 0.6653 (mtpp) REVERT: H 190 MET cc_start: 0.7504 (tmm) cc_final: 0.7020 (tmm) REVERT: H 235 ASP cc_start: 0.8643 (t0) cc_final: 0.8226 (t0) REVERT: I 66 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7808 (ttmm) REVERT: I 155 PHE cc_start: 0.6912 (p90) cc_final: 0.6462 (p90) REVERT: I 159 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7812 (t0) REVERT: J 155 PHE cc_start: 0.7679 (p90) cc_final: 0.7417 (p90) outliers start: 48 outliers final: 37 residues processed: 347 average time/residue: 0.0974 time to fit residues: 49.3727 Evaluate side-chains 365 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 199 GLN Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 160 LYS 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 177 THR Chi-restraints excluded: chain F residue 195 CYS Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 235 ASP 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 H residue 170 ILE Chi-restraints excluded: chain H residue 173 THR 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 65 THR Chi-restraints excluded: chain I residue 159 ASN Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 153 PHE 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: 0.8980 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN C 199 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 ASN ** 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 = 0.4267 r_free = 0.4267 target = 0.178664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142531 restraints weight = 17376.800| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.25 r_work: 0.3603 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 11581 Z= 0.232 Angle : 0.662 12.168 15666 Z= 0.353 Chirality : 0.045 0.208 1650 Planarity : 0.004 0.034 2007 Dihedral : 5.434 54.283 1530 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.65 % Allowed : 18.73 % Favored : 77.62 % 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: -1.01 (0.21), residues: 1387 helix: 2.94 (0.52), residues: 103 sheet: 0.11 (0.22), residues: 549 loop : -1.92 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.031 0.002 TYR H 256 PHE 0.047 0.002 PHE J 48 TRP 0.032 0.002 TRP J 174 HIS 0.009 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00515 (11561) covalent geometry : angle 0.66191 (15626) SS BOND : bond 0.00288 ( 20) SS BOND : angle 0.79938 ( 40) hydrogen bonds : bond 0.03882 ( 410) hydrogen bonds : angle 5.84186 ( 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 373 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 328 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8232 (t80) cc_final: 0.8013 (t80) REVERT: B 150 ASP cc_start: 0.8047 (t0) cc_final: 0.7626 (t0) REVERT: B 246 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8097 (mttm) REVERT: C 199 GLN cc_start: 0.7384 (tt0) cc_final: 0.7176 (tm-30) REVERT: C 248 SER cc_start: 0.8246 (m) cc_final: 0.7965 (p) REVERT: C 256 TYR cc_start: 0.8659 (m-80) cc_final: 0.8011 (m-80) REVERT: D 153 PHE cc_start: 0.7435 (t80) cc_final: 0.7108 (t80) REVERT: D 192 MET cc_start: 0.7272 (ttm) cc_final: 0.6706 (ttm) REVERT: F 147 LYS cc_start: 0.8442 (mttt) cc_final: 0.8190 (mttp) REVERT: F 195 CYS cc_start: 0.7787 (OUTLIER) cc_final: 0.6960 (p) REVERT: F 196 LYS cc_start: 0.7949 (pttt) cc_final: 0.7717 (pttt) REVERT: G 160 ASP cc_start: 0.7951 (t70) cc_final: 0.7494 (p0) REVERT: G 183 ARG cc_start: 0.6958 (ttp-170) cc_final: 0.6365 (ttp-170) REVERT: G 199 GLN cc_start: 0.8043 (mp10) cc_final: 0.7565 (mp10) REVERT: G 244 SER cc_start: 0.8554 (m) cc_final: 0.8012 (t) REVERT: H 165 LYS cc_start: 0.7425 (mtpp) cc_final: 0.6659 (mtpp) REVERT: H 190 MET cc_start: 0.7640 (tmm) cc_final: 0.7191 (tmm) REVERT: H 235 ASP cc_start: 0.8613 (t0) cc_final: 0.8245 (t0) REVERT: I 66 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7864 (ttmm) REVERT: I 70 TYR cc_start: 0.7799 (m-80) cc_final: 0.7437 (m-80) REVERT: I 155 PHE cc_start: 0.6906 (p90) cc_final: 0.6570 (p90) REVERT: J 155 PHE cc_start: 0.7827 (p90) cc_final: 0.7404 (p90) outliers start: 45 outliers final: 32 residues processed: 345 average time/residue: 0.0944 time to fit residues: 47.5540 Evaluate side-chains 360 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 327 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 199 GLN Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 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 71 LEU Chi-restraints excluded: chain D residue 160 LYS 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 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 H residue 170 ILE Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 43 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 0.0000 chunk 109 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN C 245 ASN G 245 ASN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4291 r_free = 0.4291 target = 0.180850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145290 restraints weight = 17528.292| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.25 r_work: 0.3628 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11581 Z= 0.156 Angle : 0.657 12.440 15666 Z= 0.344 Chirality : 0.044 0.208 1650 Planarity : 0.003 0.036 2007 Dihedral : 5.314 56.313 1530 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.92 % Allowed : 19.63 % Favored : 77.45 % 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: -1.00 (0.22), residues: 1387 helix: 3.14 (0.53), residues: 103 sheet: 0.03 (0.22), residues: 544 loop : -1.84 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 132 TYR 0.030 0.002 TYR H 256 PHE 0.049 0.002 PHE J 48 TRP 0.032 0.002 TRP D 174 HIS 0.011 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00356 (11561) covalent geometry : angle 0.65665 (15626) SS BOND : bond 0.00246 ( 20) SS BOND : angle 0.78645 ( 40) hydrogen bonds : bond 0.03413 ( 410) hydrogen bonds : angle 5.70374 ( 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 356 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8175 (t80) cc_final: 0.7965 (t80) REVERT: B 150 ASP cc_start: 0.7941 (t0) cc_final: 0.7568 (t0) REVERT: B 201 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7753 (mmt90) REVERT: B 233 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7469 (mmmm) REVERT: B 246 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8187 (mttm) REVERT: C 248 SER cc_start: 0.8184 (m) cc_final: 0.7914 (p) REVERT: C 256 TYR cc_start: 0.8589 (m-80) cc_final: 0.7841 (m-80) REVERT: D 153 PHE cc_start: 0.7362 (t80) cc_final: 0.7045 (t80) REVERT: D 192 MET cc_start: 0.7312 (ttm) cc_final: 0.6713 (ttm) REVERT: F 195 CYS cc_start: 0.7695 (OUTLIER) cc_final: 0.6885 (p) REVERT: F 196 LYS cc_start: 0.7903 (pttt) cc_final: 0.7661 (pttt) REVERT: G 160 ASP cc_start: 0.7987 (t70) cc_final: 0.7654 (p0) REVERT: G 183 ARG cc_start: 0.6880 (ttp-170) cc_final: 0.6221 (ttp-170) REVERT: G 199 GLN cc_start: 0.7970 (mp10) cc_final: 0.7484 (mp10) REVERT: G 244 SER cc_start: 0.8520 (m) cc_final: 0.8286 (t) REVERT: H 165 LYS cc_start: 0.7289 (mtpp) cc_final: 0.6537 (mtpp) REVERT: H 190 MET cc_start: 0.7719 (tmm) cc_final: 0.7304 (tmm) REVERT: H 200 VAL cc_start: 0.9036 (t) cc_final: 0.8827 (p) REVERT: H 235 ASP cc_start: 0.8556 (t0) cc_final: 0.8152 (t0) REVERT: H 238 LYS cc_start: 0.7724 (mttt) cc_final: 0.7397 (ttmm) REVERT: I 66 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7725 (ttmm) REVERT: I 70 TYR cc_start: 0.7795 (m-80) cc_final: 0.7411 (m-10) REVERT: I 155 PHE cc_start: 0.6804 (p90) cc_final: 0.6472 (p90) REVERT: J 88 TYR cc_start: 0.7449 (p90) cc_final: 0.7085 (p90) REVERT: J 155 PHE cc_start: 0.7725 (p90) cc_final: 0.7319 (p90) outliers start: 36 outliers final: 30 residues processed: 333 average time/residue: 0.0840 time to fit residues: 41.1814 Evaluate side-chains 352 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 320 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 195 CYS Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 160 LYS 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 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 H residue 170 ILE Chi-restraints excluded: chain H residue 195 CYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 43 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 0.1980 chunk 11 optimal weight: 0.0170 chunk 112 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.0470 chunk 68 optimal weight: 10.0000 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** 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 = 0.4305 r_free = 0.4305 target = 0.181949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145611 restraints weight = 17750.950| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 3.39 r_work: 0.3634 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11581 Z= 0.128 Angle : 0.635 11.790 15666 Z= 0.335 Chirality : 0.044 0.208 1650 Planarity : 0.003 0.037 2007 Dihedral : 5.194 58.140 1530 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.16 % Allowed : 19.46 % Favored : 77.37 % 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: -0.96 (0.22), residues: 1387 helix: 3.17 (0.53), residues: 103 sheet: 0.04 (0.21), residues: 576 loop : -1.88 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.029 0.001 TYR H 256 PHE 0.041 0.002 PHE J 48 TRP 0.037 0.003 TRP D 174 HIS 0.011 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00293 (11561) covalent geometry : angle 0.63447 (15626) SS BOND : bond 0.00231 ( 20) SS BOND : angle 0.77261 ( 40) hydrogen bonds : bond 0.03183 ( 410) hydrogen bonds : angle 5.64147 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2828.77 seconds wall clock time: 49 minutes 25.04 seconds (2965.04 seconds total)