Starting phenix.real_space_refine on Thu Feb 5 11:28:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vyq_32211/02_2026/7vyq_32211_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vyq_32211/02_2026/7vyq_32211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vyq_32211/02_2026/7vyq_32211_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vyq_32211/02_2026/7vyq_32211_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vyq_32211/02_2026/7vyq_32211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vyq_32211/02_2026/7vyq_32211.map" } resolution = 3.13 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= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 28 5.16 5 Cl 4 4.86 5 C 5520 2.51 5 N 1420 2.21 5 O 1756 1.98 5 H 8340 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 17080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4212 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 267} Chain: "B" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4212 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 267} Chain: "F" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4212 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 267} Chain: "G" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4212 Classifications: {'peptide': 280} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 267} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'83I': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'83I': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'83I': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'83I': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.19, per 1000 atoms: 0.19 Number of scatterers: 17080 At special positions: 0 Unit cell: (94.581, 87.885, 97.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 28 16.00 P 12 15.00 O 1756 8.00 N 1420 7.00 C 5520 6.00 H 8340 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 487.0 milliseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 50.3% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 removed outlier: 3.925A pdb=" N GLY A 13 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.689A pdb=" N ALA A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 3.854A pdb=" N TYR A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.603A pdb=" N GLU A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.712A pdb=" N ASP A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.644A pdb=" N VAL A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 145 through 163 removed outlier: 4.018A pdb=" N LYS A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 184 through 205 removed outlier: 3.558A pdb=" N LYS A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.602A pdb=" N LYS A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 260 through 263 Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.920A pdb=" N GLY B 13 " --> pdb=" O LYS B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.671A pdb=" N ALA B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 81 removed outlier: 3.830A pdb=" N TYR B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.607A pdb=" N GLU B 99 " --> pdb=" O PRO B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 removed outlier: 3.638A pdb=" N ASP B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.638A pdb=" N VAL B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 145 through 163 removed outlier: 3.977A pdb=" N LYS B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 184 through 206 removed outlier: 3.558A pdb=" N LYS B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 238 removed outlier: 3.590A pdb=" N LYS B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP B 235 " --> pdb=" O MET B 231 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.778A pdb=" N SER B 262 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 12 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.682A pdb=" N ALA F 49 " --> pdb=" O GLY F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 81 removed outlier: 3.857A pdb=" N TYR F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 removed outlier: 3.665A pdb=" N GLU F 99 " --> pdb=" O PRO F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 109 removed outlier: 3.641A pdb=" N ASP F 108 " --> pdb=" O GLN F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 removed outlier: 3.655A pdb=" N VAL F 131 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 144 Processing helix chain 'F' and resid 145 through 163 removed outlier: 4.102A pdb=" N LYS F 157 " --> pdb=" O HIS F 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE F 158 " --> pdb=" O ASN F 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS F 161 " --> pdb=" O LYS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 184 through 205 removed outlier: 3.893A pdb=" N LYS F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F 203 " --> pdb=" O LYS F 199 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU F 204 " --> pdb=" O SER F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 238 removed outlier: 3.593A pdb=" N LYS F 234 " --> pdb=" O ASP F 230 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP F 235 " --> pdb=" O MET F 231 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP F 236 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 249 Processing helix chain 'F' and resid 250 through 257 Processing helix chain 'F' and resid 259 through 263 removed outlier: 3.777A pdb=" N SER F 262 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 removed outlier: 3.911A pdb=" N GLY G 13 " --> pdb=" O LYS G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 45 through 57 removed outlier: 3.681A pdb=" N ALA G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 81 removed outlier: 3.848A pdb=" N TYR G 81 " --> pdb=" O LEU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 removed outlier: 3.604A pdb=" N GLU G 99 " --> pdb=" O PRO G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 109 removed outlier: 3.656A pdb=" N ASP G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 131 removed outlier: 3.645A pdb=" N VAL G 131 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 144 Processing helix chain 'G' and resid 145 through 163 removed outlier: 3.501A pdb=" N ASN G 154 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS G 157 " --> pdb=" O HIS G 153 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE G 158 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS G 161 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 176 Processing helix chain 'G' and resid 184 through 206 removed outlier: 3.560A pdb=" N LYS G 199 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE G 203 " --> pdb=" O LYS G 199 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 204 " --> pdb=" O SER G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 238 removed outlier: 3.590A pdb=" N LYS G 234 " --> pdb=" O ASP G 230 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP G 235 " --> pdb=" O MET G 231 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP G 236 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 238 " --> pdb=" O LYS G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 249 Processing helix chain 'G' and resid 250 through 259 Processing helix chain 'G' and resid 260 through 263 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 89 removed outlier: 3.746A pdb=" N LYS A 86 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS A 35 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ALA A 62 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA A 37 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TRP A 64 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL A 39 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 89 removed outlier: 3.745A pdb=" N LYS B 86 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS B 35 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ALA B 62 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA B 37 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TRP B 64 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL B 39 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 5 removed outlier: 4.482A pdb=" N ILE F 4 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 86 through 89 removed outlier: 3.744A pdb=" N LYS F 86 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS F 35 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ALA F 62 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA F 37 " --> pdb=" O ALA F 62 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TRP F 64 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL F 39 " --> pdb=" O TRP F 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 167 through 169 Processing sheet with id=AA8, first strand: chain 'G' and resid 86 through 89 removed outlier: 3.733A pdb=" N LYS G 86 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS G 35 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA G 62 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA G 37 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N TRP G 64 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL G 39 " --> pdb=" O TRP G 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 167 through 169 314 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8320 1.03 - 1.23: 44 1.23 - 1.42: 3754 1.42 - 1.62: 5134 1.62 - 1.82: 40 Bond restraints: 17292 Sorted by residual: bond pdb=" O2B NAP G 301 " pdb=" P2B NAP G 301 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" O2B NAP A 301 " pdb=" P2B NAP A 301 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" O2B NAP F 301 " pdb=" P2B NAP F 301 " ideal model delta sigma weight residual 1.736 1.602 0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" O2B NAP B 301 " pdb=" P2B NAP B 301 " ideal model delta sigma weight residual 1.736 1.603 0.133 2.00e-02 2.50e+03 4.46e+01 bond pdb=" O5D NAP B 301 " pdb=" PN NAP B 301 " ideal model delta sigma weight residual 1.649 1.587 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 17287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 30974 2.64 - 5.29: 196 5.29 - 7.93: 14 7.93 - 10.57: 7 10.57 - 13.22: 5 Bond angle restraints: 31196 Sorted by residual: angle pdb=" O2B NAP F 301 " pdb=" P2B NAP F 301 " pdb=" O2X NAP F 301 " ideal model delta sigma weight residual 100.14 113.36 -13.22 3.00e+00 1.11e-01 1.94e+01 angle pdb=" O2B NAP B 301 " pdb=" P2B NAP B 301 " pdb=" O2X NAP B 301 " ideal model delta sigma weight residual 100.14 113.25 -13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" O2B NAP G 301 " pdb=" P2B NAP G 301 " pdb=" O2X NAP G 301 " ideal model delta sigma weight residual 100.14 112.17 -12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O2B NAP A 301 " pdb=" P2B NAP A 301 " pdb=" O2X NAP A 301 " ideal model delta sigma weight residual 100.14 112.15 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C3D NAP F 301 " pdb=" C2D NAP F 301 " pdb=" O2D NAP F 301 " ideal model delta sigma weight residual 116.01 104.56 11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 31191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7222 17.88 - 35.76: 731 35.76 - 53.65: 315 53.65 - 71.53: 105 71.53 - 89.41: 19 Dihedral angle restraints: 8392 sinusoidal: 4608 harmonic: 3784 Sorted by residual: dihedral pdb=" CA ASP F 71 " pdb=" CB ASP F 71 " pdb=" CG ASP F 71 " pdb=" OD1 ASP F 71 " ideal model delta sinusoidal sigma weight residual -30.00 -85.26 55.26 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASP B 71 " pdb=" CB ASP B 71 " pdb=" CG ASP B 71 " pdb=" OD1 ASP B 71 " ideal model delta sinusoidal sigma weight residual -30.00 -85.23 55.23 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASP A 71 " pdb=" CB ASP A 71 " pdb=" CG ASP A 71 " pdb=" OD1 ASP A 71 " ideal model delta sinusoidal sigma weight residual -30.00 -85.22 55.22 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 8389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 918 0.037 - 0.073: 319 0.073 - 0.110: 91 0.110 - 0.147: 26 0.147 - 0.183: 6 Chirality restraints: 1360 Sorted by residual: chirality pdb=" C2D NAP F 301 " pdb=" C1D NAP F 301 " pdb=" C3D NAP F 301 " pdb=" O2D NAP F 301 " both_signs ideal model delta sigma weight residual False -2.55 -2.73 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" C4D NAP A 301 " pdb=" C3D NAP A 301 " pdb=" C5D NAP A 301 " pdb=" O4D NAP A 301 " both_signs ideal model delta sigma weight residual False -2.58 -2.41 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" C4D NAP G 301 " pdb=" C3D NAP G 301 " pdb=" C5D NAP G 301 " pdb=" O4D NAP G 301 " both_signs ideal model delta sigma weight residual False -2.58 -2.41 -0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 1357 not shown) Planarity restraints: 2596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 301 " -0.222 2.00e-02 2.50e+03 1.62e-01 5.28e+02 pdb=" C2N NAP A 301 " 0.287 2.00e-02 2.50e+03 pdb=" C3N NAP A 301 " 0.007 2.00e-02 2.50e+03 pdb=" C4N NAP A 301 " -0.243 2.00e-02 2.50e+03 pdb=" C5N NAP A 301 " 0.091 2.00e-02 2.50e+03 pdb=" C6N NAP A 301 " 0.092 2.00e-02 2.50e+03 pdb=" C7N NAP A 301 " -0.050 2.00e-02 2.50e+03 pdb=" N1N NAP A 301 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAP B 301 " -0.220 2.00e-02 2.50e+03 1.61e-01 5.19e+02 pdb=" C2N NAP B 301 " 0.285 2.00e-02 2.50e+03 pdb=" C3N NAP B 301 " 0.007 2.00e-02 2.50e+03 pdb=" C4N NAP B 301 " -0.239 2.00e-02 2.50e+03 pdb=" C5N NAP B 301 " 0.087 2.00e-02 2.50e+03 pdb=" C6N NAP B 301 " 0.094 2.00e-02 2.50e+03 pdb=" C7N NAP B 301 " -0.050 2.00e-02 2.50e+03 pdb=" N1N NAP B 301 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAP G 301 " 0.218 2.00e-02 2.50e+03 1.60e-01 5.12e+02 pdb=" C2N NAP G 301 " -0.287 2.00e-02 2.50e+03 pdb=" C3N NAP G 301 " -0.009 2.00e-02 2.50e+03 pdb=" C4N NAP G 301 " 0.236 2.00e-02 2.50e+03 pdb=" C5N NAP G 301 " -0.090 2.00e-02 2.50e+03 pdb=" C6N NAP G 301 " -0.085 2.00e-02 2.50e+03 pdb=" C7N NAP G 301 " 0.053 2.00e-02 2.50e+03 pdb=" N1N NAP G 301 " -0.036 2.00e-02 2.50e+03 ... (remaining 2593 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1511 2.22 - 2.82: 36970 2.82 - 3.41: 46584 3.41 - 4.01: 66675 4.01 - 4.60: 101907 Nonbonded interactions: 253647 Sorted by model distance: nonbonded pdb=" OD1 ASN B 146 " pdb=" HE1 TRP F 137 " model vdw 1.625 2.450 nonbonded pdb=" OD1 ASN A 146 " pdb=" HE1 TRP G 137 " model vdw 1.629 2.450 nonbonded pdb="HE22 GLN G 125 " pdb=" OG SER G 136 " model vdw 1.678 2.450 nonbonded pdb="HE22 GLN F 125 " pdb=" OG SER F 136 " model vdw 1.684 2.450 nonbonded pdb="HD22 ASN F 133 " pdb=" OD2 ASP F 135 " model vdw 1.686 2.450 ... (remaining 253642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'G' } 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: 1.060 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: 0.100 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.790 Find NCS groups from input model: 0.250 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 8952 Z= 0.258 Angle : 0.776 13.215 12212 Z= 0.387 Chirality : 0.042 0.183 1360 Planarity : 0.009 0.162 1528 Dihedral : 19.426 89.408 3376 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 22.71 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.84 (0.27), residues: 1112 helix: -0.91 (0.25), residues: 436 sheet: -2.79 (0.39), residues: 180 loop : -0.64 (0.31), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 243 TYR 0.004 0.000 TYR F 65 PHE 0.005 0.000 PHE B 208 TRP 0.005 0.001 TRP G 64 HIS 0.002 0.000 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 8952) covalent geometry : angle 0.77610 (12212) hydrogen bonds : bond 0.24955 ( 314) hydrogen bonds : angle 6.92645 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.376 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2028 time to fit residues: 19.9044 Evaluate side-chains 64 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0020 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.087299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.070262 restraints weight = 34493.182| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 1.97 r_work: 0.2499 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2379 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8952 Z= 0.193 Angle : 0.526 4.260 12212 Z= 0.271 Chirality : 0.044 0.136 1360 Planarity : 0.004 0.050 1528 Dihedral : 12.573 75.282 1480 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.87 % Allowed : 20.74 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.52 (0.26), residues: 1112 helix: -0.27 (0.25), residues: 456 sheet: -1.57 (0.44), residues: 148 loop : -1.44 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 210 TYR 0.010 0.001 TYR F 134 PHE 0.013 0.001 PHE B 208 TRP 0.009 0.001 TRP G 64 HIS 0.005 0.001 HIS G 196 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 8952) covalent geometry : angle 0.52622 (12212) hydrogen bonds : bond 0.04706 ( 314) hydrogen bonds : angle 4.13827 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.484 Fit side-chains REVERT: A 125 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7896 (mt0) REVERT: B 125 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: F 108 ASP cc_start: 0.8088 (m-30) cc_final: 0.7850 (m-30) REVERT: F 125 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: G 125 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7917 (mt0) outliers start: 8 outliers final: 2 residues processed: 68 average time/residue: 0.2052 time to fit residues: 20.1182 Evaluate side-chains 67 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 132 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.085945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.068850 restraints weight = 34759.367| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 1.98 r_work: 0.2474 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2354 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8952 Z= 0.235 Angle : 0.542 4.231 12212 Z= 0.277 Chirality : 0.045 0.136 1360 Planarity : 0.004 0.049 1528 Dihedral : 11.948 68.339 1480 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.20 % Allowed : 20.63 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.60 (0.26), residues: 1112 helix: -0.12 (0.25), residues: 456 sheet: -1.82 (0.41), residues: 156 loop : -1.64 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 210 TYR 0.008 0.001 TYR A 134 PHE 0.014 0.001 PHE F 208 TRP 0.009 0.001 TRP G 64 HIS 0.004 0.001 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 8952) covalent geometry : angle 0.54216 (12212) hydrogen bonds : bond 0.04753 ( 314) hydrogen bonds : angle 3.93009 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: G 125 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7803 (mt0) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.2079 time to fit residues: 20.6107 Evaluate side-chains 69 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 132 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 2 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.089741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.072482 restraints weight = 34084.641| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 1.99 r_work: 0.2525 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8952 Z= 0.096 Angle : 0.459 4.210 12212 Z= 0.230 Chirality : 0.042 0.126 1360 Planarity : 0.004 0.049 1528 Dihedral : 11.023 70.375 1480 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.76 % Allowed : 19.32 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.13 (0.26), residues: 1112 helix: 0.39 (0.26), residues: 456 sheet: -1.79 (0.41), residues: 148 loop : -1.43 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 243 TYR 0.009 0.001 TYR A 149 PHE 0.009 0.001 PHE G 208 TRP 0.005 0.001 TRP G 123 HIS 0.004 0.001 HIS G 196 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8952) covalent geometry : angle 0.45900 (12212) hydrogen bonds : bond 0.03286 ( 314) hydrogen bonds : angle 3.60684 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.471 Fit side-chains REVERT: A 108 ASP cc_start: 0.8029 (m-30) cc_final: 0.7546 (m-30) REVERT: A 125 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: B 108 ASP cc_start: 0.7963 (m-30) cc_final: 0.7396 (m-30) REVERT: B 125 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: F 108 ASP cc_start: 0.7996 (m-30) cc_final: 0.7439 (m-30) REVERT: F 125 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: G 125 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7918 (mt0) outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 0.2384 time to fit residues: 20.5922 Evaluate side-chains 63 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 132 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 107 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.088130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.070886 restraints weight = 34312.039| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 2.00 r_work: 0.2503 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8952 Z= 0.155 Angle : 0.486 4.103 12212 Z= 0.245 Chirality : 0.043 0.125 1360 Planarity : 0.004 0.047 1528 Dihedral : 10.980 69.480 1480 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.98 % Allowed : 19.54 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.09 (0.26), residues: 1112 helix: 0.48 (0.26), residues: 456 sheet: -1.78 (0.42), residues: 148 loop : -1.47 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 210 TYR 0.008 0.001 TYR F 149 PHE 0.011 0.001 PHE A 208 TRP 0.007 0.001 TRP G 64 HIS 0.004 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8952) covalent geometry : angle 0.48593 (12212) hydrogen bonds : bond 0.03667 ( 314) hydrogen bonds : angle 3.61520 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8029 (m-30) cc_final: 0.7485 (m-30) REVERT: B 108 ASP cc_start: 0.7974 (m-30) cc_final: 0.7340 (m-30) REVERT: B 125 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7761 (mt0) REVERT: F 108 ASP cc_start: 0.8014 (m-30) cc_final: 0.7389 (m-30) REVERT: G 125 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7886 (mt0) outliers start: 9 outliers final: 6 residues processed: 61 average time/residue: 0.2265 time to fit residues: 19.6470 Evaluate side-chains 62 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 132 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.088559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.071362 restraints weight = 33961.881| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 1.98 r_work: 0.2509 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2388 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8952 Z= 0.141 Angle : 0.476 4.103 12212 Z= 0.239 Chirality : 0.043 0.126 1360 Planarity : 0.004 0.048 1528 Dihedral : 10.846 69.972 1480 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.75 % Allowed : 19.32 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.26), residues: 1112 helix: 0.60 (0.26), residues: 456 sheet: -1.77 (0.42), residues: 148 loop : -1.42 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 243 TYR 0.008 0.001 TYR B 149 PHE 0.010 0.001 PHE G 208 TRP 0.006 0.001 TRP A 64 HIS 0.004 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8952) covalent geometry : angle 0.47579 (12212) hydrogen bonds : bond 0.03493 ( 314) hydrogen bonds : angle 3.56191 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8055 (m-30) cc_final: 0.7451 (m-30) REVERT: B 108 ASP cc_start: 0.7979 (m-30) cc_final: 0.7325 (m-30) REVERT: B 125 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: B 132 ASP cc_start: 0.7705 (p0) cc_final: 0.7498 (p0) REVERT: F 108 ASP cc_start: 0.8028 (m-30) cc_final: 0.7734 (m-30) REVERT: F 125 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: G 108 ASP cc_start: 0.7977 (m-30) cc_final: 0.7756 (m-30) REVERT: G 125 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7901 (mt0) outliers start: 16 outliers final: 9 residues processed: 67 average time/residue: 0.2135 time to fit residues: 20.5367 Evaluate side-chains 65 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 132 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.086599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.069158 restraints weight = 34488.174| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 2.00 r_work: 0.2468 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2349 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8952 Z= 0.223 Angle : 0.528 4.179 12212 Z= 0.268 Chirality : 0.045 0.133 1360 Planarity : 0.004 0.047 1528 Dihedral : 11.380 70.597 1480 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.07 % Allowed : 20.09 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.14 (0.26), residues: 1112 helix: 0.48 (0.26), residues: 456 sheet: -1.85 (0.41), residues: 156 loop : -1.52 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 243 TYR 0.007 0.001 TYR A 134 PHE 0.013 0.001 PHE F 208 TRP 0.008 0.001 TRP B 123 HIS 0.004 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 8952) covalent geometry : angle 0.52832 (12212) hydrogen bonds : bond 0.04139 ( 314) hydrogen bonds : angle 3.69759 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ASP cc_start: 0.8006 (m-30) cc_final: 0.7686 (m-30) REVERT: F 108 ASP cc_start: 0.8034 (m-30) cc_final: 0.7718 (m-30) REVERT: G 125 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7891 (mt0) outliers start: 19 outliers final: 13 residues processed: 69 average time/residue: 0.2208 time to fit residues: 21.5340 Evaluate side-chains 68 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 132 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.087994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.070497 restraints weight = 34323.209| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 2.00 r_work: 0.2491 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2369 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8952 Z= 0.159 Angle : 0.489 4.076 12212 Z= 0.247 Chirality : 0.043 0.127 1360 Planarity : 0.004 0.048 1528 Dihedral : 11.116 71.107 1480 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.97 % Allowed : 20.20 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.02 (0.26), residues: 1112 helix: 0.61 (0.26), residues: 456 sheet: -1.86 (0.41), residues: 156 loop : -1.46 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 243 TYR 0.008 0.001 TYR A 149 PHE 0.011 0.001 PHE G 208 TRP 0.006 0.001 TRP B 123 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8952) covalent geometry : angle 0.48909 (12212) hydrogen bonds : bond 0.03630 ( 314) hydrogen bonds : angle 3.60778 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: B 108 ASP cc_start: 0.8022 (m-30) cc_final: 0.7708 (m-30) REVERT: B 125 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: F 108 ASP cc_start: 0.8017 (m-30) cc_final: 0.7705 (m-30) REVERT: F 125 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: G 125 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7870 (mt0) outliers start: 18 outliers final: 12 residues processed: 67 average time/residue: 0.2150 time to fit residues: 20.8101 Evaluate side-chains 69 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.088310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.070828 restraints weight = 34064.054| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 2.01 r_work: 0.2498 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8952 Z= 0.151 Angle : 0.486 4.043 12212 Z= 0.245 Chirality : 0.043 0.126 1360 Planarity : 0.004 0.047 1528 Dihedral : 10.912 73.192 1480 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.86 % Allowed : 20.31 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.95 (0.26), residues: 1112 helix: 0.71 (0.26), residues: 456 sheet: -1.78 (0.42), residues: 148 loop : -1.49 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG G 243 TYR 0.008 0.001 TYR A 149 PHE 0.011 0.001 PHE F 208 TRP 0.006 0.001 TRP B 123 HIS 0.004 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8952) covalent geometry : angle 0.48583 (12212) hydrogen bonds : bond 0.03547 ( 314) hydrogen bonds : angle 3.57602 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: B 108 ASP cc_start: 0.7981 (m-30) cc_final: 0.7660 (m-30) REVERT: B 125 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: F 108 ASP cc_start: 0.8015 (m-30) cc_final: 0.7696 (m-30) REVERT: F 125 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: G 108 ASP cc_start: 0.7949 (m-30) cc_final: 0.7594 (m-30) REVERT: G 125 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7891 (mt0) outliers start: 17 outliers final: 12 residues processed: 65 average time/residue: 0.2128 time to fit residues: 19.8360 Evaluate side-chains 68 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.086947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.069523 restraints weight = 33962.028| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 1.99 r_work: 0.2478 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2358 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8952 Z= 0.213 Angle : 0.523 4.183 12212 Z= 0.266 Chirality : 0.045 0.132 1360 Planarity : 0.004 0.048 1528 Dihedral : 11.323 72.936 1480 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.07 % Allowed : 20.20 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.12 (0.26), residues: 1112 helix: 0.56 (0.26), residues: 456 sheet: -1.88 (0.41), residues: 156 loop : -1.56 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 243 TYR 0.008 0.001 TYR A 134 PHE 0.013 0.001 PHE G 208 TRP 0.007 0.001 TRP G 64 HIS 0.004 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 8952) covalent geometry : angle 0.52318 (12212) hydrogen bonds : bond 0.04011 ( 314) hydrogen bonds : angle 3.67481 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ASP cc_start: 0.7994 (m-30) cc_final: 0.7660 (m-30) REVERT: F 125 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7777 (mt0) REVERT: G 125 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7864 (mt0) outliers start: 19 outliers final: 15 residues processed: 68 average time/residue: 0.2039 time to fit residues: 20.0048 Evaluate side-chains 71 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain G residue 125 GLN Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 171 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 103 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 63 optimal weight: 0.0270 chunk 49 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 184 GLN B 162 ASN B 179 ASN B 184 GLN F 179 ASN F 184 GLN G 179 ASN G 184 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.090534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.073113 restraints weight = 33692.038| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.00 r_work: 0.2541 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8952 Z= 0.092 Angle : 0.454 4.237 12212 Z= 0.227 Chirality : 0.042 0.131 1360 Planarity : 0.003 0.048 1528 Dihedral : 10.420 78.287 1480 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.20 % Allowed : 21.51 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.73 (0.26), residues: 1112 helix: 0.91 (0.26), residues: 456 sheet: -1.57 (0.47), residues: 124 loop : -1.45 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 243 TYR 0.009 0.001 TYR B 149 PHE 0.009 0.001 PHE G 208 TRP 0.006 0.001 TRP B 123 HIS 0.004 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8952) covalent geometry : angle 0.45416 (12212) hydrogen bonds : bond 0.02945 ( 314) hydrogen bonds : angle 3.46322 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.21 seconds wall clock time: 64 minutes 18.39 seconds (3858.39 seconds total)