Starting phenix.real_space_refine on Sun Aug 24 18:00:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oph_17053/08_2025/8oph_17053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oph_17053/08_2025/8oph_17053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oph_17053/08_2025/8oph_17053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oph_17053/08_2025/8oph_17053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oph_17053/08_2025/8oph_17053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oph_17053/08_2025/8oph_17053.map" } resolution = 2.93 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 13776 2.51 5 N 3760 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21824 Number of models: 1 Model: "" Number of chains: 16 Chain: "Aa" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ab" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ac" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ad" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ae" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Af" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ag" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ah" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ai" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Aj" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ak" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Al" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Am" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "An" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ao" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Chain: "Ap" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1364 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 158} Time building chain proxies: 5.36, per 1000 atoms: 0.25 Number of scatterers: 21824 At special positions: 0 Unit cell: (135.85, 135.85, 93.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 4096 8.00 N 3760 7.00 C 13776 6.00 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: 1.84 Conformation dependent library (CDL) restraints added in 891.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 54.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'Aa' and resid 68 through 72 Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 123 removed outlier: 3.894A pdb=" N GLYAa 114 " --> pdb=" O THRAa 110 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 151 removed outlier: 3.556A pdb=" N ASNAa 151 " --> pdb=" O PROAa 147 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 175 removed outlier: 3.656A pdb=" N GLUAa 168 " --> pdb=" O SERAa 164 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALAAa 169 " --> pdb=" O ASPAa 165 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 182 through 187 Processing helix chain 'Aa' and resid 195 through 199 Processing helix chain 'Aa' and resid 210 through 222 Processing helix chain 'Ab' and resid 68 through 73 Processing helix chain 'Ab' and resid 86 through 102 Processing helix chain 'Ab' and resid 107 through 123 removed outlier: 3.704A pdb=" N GLYAb 114 " --> pdb=" O THRAb 110 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 150 Processing helix chain 'Ab' and resid 155 through 161 Processing helix chain 'Ab' and resid 163 through 175 removed outlier: 3.666A pdb=" N ALAAb 169 " --> pdb=" O ASPAb 165 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 182 through 187 Processing helix chain 'Ab' and resid 192 through 199 removed outlier: 3.999A pdb=" N ARGAb 197 " --> pdb=" O SERAb 194 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 210 through 222 Processing helix chain 'Ac' and resid 68 through 72 Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 123 removed outlier: 3.893A pdb=" N GLYAc 114 " --> pdb=" O THRAc 110 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 151 removed outlier: 3.556A pdb=" N ASNAc 151 " --> pdb=" O PROAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 175 removed outlier: 3.656A pdb=" N GLUAc 168 " --> pdb=" O SERAc 164 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALAAc 169 " --> pdb=" O ASPAc 165 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 182 through 187 Processing helix chain 'Ac' and resid 195 through 199 Processing helix chain 'Ac' and resid 210 through 222 Processing helix chain 'Ad' and resid 68 through 73 Processing helix chain 'Ad' and resid 86 through 102 Processing helix chain 'Ad' and resid 107 through 123 removed outlier: 3.704A pdb=" N GLYAd 114 " --> pdb=" O THRAd 110 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 150 Processing helix chain 'Ad' and resid 155 through 161 Processing helix chain 'Ad' and resid 163 through 175 removed outlier: 3.667A pdb=" N ALAAd 169 " --> pdb=" O ASPAd 165 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 182 through 187 Processing helix chain 'Ad' and resid 192 through 199 removed outlier: 3.998A pdb=" N ARGAd 197 " --> pdb=" O SERAd 194 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 210 through 222 Processing helix chain 'Ae' and resid 68 through 72 Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 123 removed outlier: 3.894A pdb=" N GLYAe 114 " --> pdb=" O THRAe 110 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 removed outlier: 3.556A pdb=" N ASNAe 151 " --> pdb=" O PROAe 147 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 175 removed outlier: 3.655A pdb=" N GLUAe 168 " --> pdb=" O SERAe 164 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALAAe 169 " --> pdb=" O ASPAe 165 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 182 through 187 Processing helix chain 'Ae' and resid 195 through 199 Processing helix chain 'Ae' and resid 210 through 222 Processing helix chain 'Af' and resid 68 through 73 Processing helix chain 'Af' and resid 86 through 102 Processing helix chain 'Af' and resid 107 through 123 removed outlier: 3.704A pdb=" N GLYAf 114 " --> pdb=" O THRAf 110 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 150 Processing helix chain 'Af' and resid 155 through 161 Processing helix chain 'Af' and resid 163 through 175 removed outlier: 3.666A pdb=" N ALAAf 169 " --> pdb=" O ASPAf 165 " (cutoff:3.500A) Processing helix chain 'Af' and resid 182 through 187 Processing helix chain 'Af' and resid 192 through 199 removed outlier: 3.999A pdb=" N ARGAf 197 " --> pdb=" O SERAf 194 " (cutoff:3.500A) Processing helix chain 'Af' and resid 210 through 222 Processing helix chain 'Ag' and resid 68 through 72 Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 123 removed outlier: 3.894A pdb=" N GLYAg 114 " --> pdb=" O THRAg 110 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 removed outlier: 3.556A pdb=" N ASNAg 151 " --> pdb=" O PROAg 147 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 175 removed outlier: 3.656A pdb=" N GLUAg 168 " --> pdb=" O SERAg 164 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALAAg 169 " --> pdb=" O ASPAg 165 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 182 through 187 Processing helix chain 'Ag' and resid 195 through 199 Processing helix chain 'Ag' and resid 210 through 222 Processing helix chain 'Ah' and resid 68 through 73 Processing helix chain 'Ah' and resid 86 through 102 Processing helix chain 'Ah' and resid 107 through 123 removed outlier: 3.704A pdb=" N GLYAh 114 " --> pdb=" O THRAh 110 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 150 Processing helix chain 'Ah' and resid 155 through 161 Processing helix chain 'Ah' and resid 163 through 175 removed outlier: 3.668A pdb=" N ALAAh 169 " --> pdb=" O ASPAh 165 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 182 through 187 Processing helix chain 'Ah' and resid 192 through 199 removed outlier: 3.998A pdb=" N ARGAh 197 " --> pdb=" O SERAh 194 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 210 through 222 Processing helix chain 'Ai' and resid 68 through 72 Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 123 removed outlier: 3.894A pdb=" N GLYAi 114 " --> pdb=" O THRAi 110 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 151 removed outlier: 3.556A pdb=" N ASNAi 151 " --> pdb=" O PROAi 147 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 175 removed outlier: 3.655A pdb=" N GLUAi 168 " --> pdb=" O SERAi 164 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALAAi 169 " --> pdb=" O ASPAi 165 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 182 through 187 Processing helix chain 'Ai' and resid 195 through 199 Processing helix chain 'Ai' and resid 210 through 222 Processing helix chain 'Aj' and resid 68 through 73 Processing helix chain 'Aj' and resid 86 through 102 Processing helix chain 'Aj' and resid 107 through 123 removed outlier: 3.704A pdb=" N GLYAj 114 " --> pdb=" O THRAj 110 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 145 through 150 Processing helix chain 'Aj' and resid 155 through 161 Processing helix chain 'Aj' and resid 163 through 175 removed outlier: 3.667A pdb=" N ALAAj 169 " --> pdb=" O ASPAj 165 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 182 through 187 Processing helix chain 'Aj' and resid 192 through 199 removed outlier: 3.999A pdb=" N ARGAj 197 " --> pdb=" O SERAj 194 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 210 through 222 Processing helix chain 'Ak' and resid 68 through 72 Processing helix chain 'Ak' and resid 86 through 102 Processing helix chain 'Ak' and resid 107 through 123 removed outlier: 3.893A pdb=" N GLYAk 114 " --> pdb=" O THRAk 110 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 151 removed outlier: 3.556A pdb=" N ASNAk 151 " --> pdb=" O PROAk 147 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 175 removed outlier: 3.656A pdb=" N GLUAk 168 " --> pdb=" O SERAk 164 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALAAk 169 " --> pdb=" O ASPAk 165 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 182 through 187 Processing helix chain 'Ak' and resid 195 through 199 Processing helix chain 'Ak' and resid 210 through 222 Processing helix chain 'Al' and resid 68 through 73 Processing helix chain 'Al' and resid 86 through 102 Processing helix chain 'Al' and resid 107 through 123 removed outlier: 3.704A pdb=" N GLYAl 114 " --> pdb=" O THRAl 110 " (cutoff:3.500A) Processing helix chain 'Al' and resid 145 through 150 Processing helix chain 'Al' and resid 155 through 161 Processing helix chain 'Al' and resid 163 through 175 removed outlier: 3.667A pdb=" N ALAAl 169 " --> pdb=" O ASPAl 165 " (cutoff:3.500A) Processing helix chain 'Al' and resid 182 through 187 Processing helix chain 'Al' and resid 192 through 199 removed outlier: 3.999A pdb=" N ARGAl 197 " --> pdb=" O SERAl 194 " (cutoff:3.500A) Processing helix chain 'Al' and resid 210 through 222 Processing helix chain 'Am' and resid 68 through 72 Processing helix chain 'Am' and resid 86 through 102 Processing helix chain 'Am' and resid 107 through 123 removed outlier: 3.894A pdb=" N GLYAm 114 " --> pdb=" O THRAm 110 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 151 removed outlier: 3.557A pdb=" N ASNAm 151 " --> pdb=" O PROAm 147 " (cutoff:3.500A) Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 175 removed outlier: 3.655A pdb=" N GLUAm 168 " --> pdb=" O SERAm 164 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALAAm 169 " --> pdb=" O ASPAm 165 " (cutoff:3.500A) Processing helix chain 'Am' and resid 182 through 187 Processing helix chain 'Am' and resid 195 through 199 Processing helix chain 'Am' and resid 210 through 222 Processing helix chain 'An' and resid 68 through 73 Processing helix chain 'An' and resid 86 through 102 Processing helix chain 'An' and resid 107 through 123 removed outlier: 3.704A pdb=" N GLYAn 114 " --> pdb=" O THRAn 110 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 150 Processing helix chain 'An' and resid 155 through 161 Processing helix chain 'An' and resid 163 through 175 removed outlier: 3.667A pdb=" N ALAAn 169 " --> pdb=" O ASPAn 165 " (cutoff:3.500A) Processing helix chain 'An' and resid 182 through 187 Processing helix chain 'An' and resid 192 through 199 removed outlier: 3.998A pdb=" N ARGAn 197 " --> pdb=" O SERAn 194 " (cutoff:3.500A) Processing helix chain 'An' and resid 210 through 222 Processing helix chain 'Ao' and resid 68 through 72 Processing helix chain 'Ao' and resid 86 through 102 Processing helix chain 'Ao' and resid 107 through 123 removed outlier: 3.894A pdb=" N GLYAo 114 " --> pdb=" O THRAo 110 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 151 removed outlier: 3.556A pdb=" N ASNAo 151 " --> pdb=" O PROAo 147 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 175 removed outlier: 3.656A pdb=" N GLUAo 168 " --> pdb=" O SERAo 164 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALAAo 169 " --> pdb=" O ASPAo 165 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 182 through 187 Processing helix chain 'Ao' and resid 195 through 199 Processing helix chain 'Ao' and resid 210 through 222 Processing helix chain 'Ap' and resid 68 through 73 Processing helix chain 'Ap' and resid 86 through 102 Processing helix chain 'Ap' and resid 107 through 123 removed outlier: 3.704A pdb=" N GLYAp 114 " --> pdb=" O THRAp 110 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 150 Processing helix chain 'Ap' and resid 155 through 161 Processing helix chain 'Ap' and resid 163 through 175 removed outlier: 3.666A pdb=" N ALAAp 169 " --> pdb=" O ASPAp 165 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 182 through 187 Processing helix chain 'Ap' and resid 192 through 199 removed outlier: 3.998A pdb=" N ARGAp 197 " --> pdb=" O SERAp 194 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 210 through 222 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 131 through 136 Processing sheet with id=AA2, first strand: chain 'Ab' and resid 131 through 136 Processing sheet with id=AA3, first strand: chain 'Ac' and resid 131 through 136 Processing sheet with id=AA4, first strand: chain 'Ad' and resid 131 through 136 Processing sheet with id=AA5, first strand: chain 'Ae' and resid 131 through 136 Processing sheet with id=AA6, first strand: chain 'Af' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'Ag' and resid 131 through 136 Processing sheet with id=AA8, first strand: chain 'Ah' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'Ai' and resid 131 through 136 Processing sheet with id=AB1, first strand: chain 'Aj' and resid 131 through 136 Processing sheet with id=AB2, first strand: chain 'Ak' and resid 131 through 136 Processing sheet with id=AB3, first strand: chain 'Al' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'Am' and resid 131 through 136 Processing sheet with id=AB5, first strand: chain 'An' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'Ao' and resid 131 through 136 Processing sheet with id=AB7, first strand: chain 'Ap' and resid 131 through 136 952 hydrogen bonds defined for protein. 2616 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: 3.44 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5706 1.33 - 1.45: 4050 1.45 - 1.57: 12196 1.57 - 1.69: 0 1.69 - 1.81: 368 Bond restraints: 22320 Sorted by residual: bond pdb=" CA GLUAo 150 " pdb=" C GLUAo 150 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.27e-02 6.20e+03 2.88e+01 bond pdb=" CA GLUAa 150 " pdb=" C GLUAa 150 " ideal model delta sigma weight residual 1.524 1.456 0.067 1.27e-02 6.20e+03 2.82e+01 bond pdb=" CA GLUAi 150 " pdb=" C GLUAi 150 " ideal model delta sigma weight residual 1.524 1.456 0.067 1.27e-02 6.20e+03 2.82e+01 bond pdb=" CA GLUAe 150 " pdb=" C GLUAe 150 " ideal model delta sigma weight residual 1.524 1.456 0.067 1.27e-02 6.20e+03 2.81e+01 bond pdb=" CA GLUAg 150 " pdb=" C GLUAg 150 " ideal model delta sigma weight residual 1.524 1.457 0.067 1.27e-02 6.20e+03 2.80e+01 ... (remaining 22315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 28853 1.33 - 2.67: 965 2.67 - 4.00: 302 4.00 - 5.33: 89 5.33 - 6.66: 47 Bond angle restraints: 30256 Sorted by residual: angle pdb=" C METAa 56 " pdb=" N PROAa 57 " pdb=" CA PROAa 57 " ideal model delta sigma weight residual 119.84 126.41 -6.57 1.25e+00 6.40e-01 2.76e+01 angle pdb=" C METAm 56 " pdb=" N PROAm 57 " pdb=" CA PROAm 57 " ideal model delta sigma weight residual 119.84 126.41 -6.57 1.25e+00 6.40e-01 2.76e+01 angle pdb=" C METAe 56 " pdb=" N PROAe 57 " pdb=" CA PROAe 57 " ideal model delta sigma weight residual 119.84 126.41 -6.57 1.25e+00 6.40e-01 2.76e+01 angle pdb=" C METAo 56 " pdb=" N PROAo 57 " pdb=" CA PROAo 57 " ideal model delta sigma weight residual 119.84 126.40 -6.56 1.25e+00 6.40e-01 2.76e+01 angle pdb=" C METAk 56 " pdb=" N PROAk 57 " pdb=" CA PROAk 57 " ideal model delta sigma weight residual 119.84 126.40 -6.56 1.25e+00 6.40e-01 2.75e+01 ... (remaining 30251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 11864 16.20 - 32.40: 1211 32.40 - 48.60: 421 48.60 - 64.80: 128 64.80 - 81.00: 24 Dihedral angle restraints: 13648 sinusoidal: 5664 harmonic: 7984 Sorted by residual: dihedral pdb=" N GLUAo 204 " pdb=" CA GLUAo 204 " pdb=" CB GLUAo 204 " pdb=" CG GLUAo 204 " ideal model delta sinusoidal sigma weight residual -60.00 -119.41 59.41 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLUAg 204 " pdb=" CA GLUAg 204 " pdb=" CB GLUAg 204 " pdb=" CG GLUAg 204 " ideal model delta sinusoidal sigma weight residual -60.00 -119.41 59.41 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLUAk 204 " pdb=" CA GLUAk 204 " pdb=" CB GLUAk 204 " pdb=" CG GLUAk 204 " ideal model delta sinusoidal sigma weight residual -60.00 -119.41 59.41 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 13645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1928 0.032 - 0.063: 932 0.063 - 0.095: 325 0.095 - 0.127: 48 0.127 - 0.158: 15 Chirality restraints: 3248 Sorted by residual: chirality pdb=" CA ARGAg 183 " pdb=" N ARGAg 183 " pdb=" C ARGAg 183 " pdb=" CB ARGAg 183 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ARGAe 183 " pdb=" N ARGAe 183 " pdb=" C ARGAe 183 " pdb=" CB ARGAe 183 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ARGAm 183 " pdb=" N ARGAm 183 " pdb=" C ARGAm 183 " pdb=" CB ARGAm 183 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 3245 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYSAp 146 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PROAp 147 " -0.084 5.00e-02 4.00e+02 pdb=" CA PROAp 147 " 0.025 5.00e-02 4.00e+02 pdb=" CD PROAp 147 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYSAj 146 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PROAj 147 " -0.084 5.00e-02 4.00e+02 pdb=" CA PROAj 147 " 0.024 5.00e-02 4.00e+02 pdb=" CD PROAj 147 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYSAf 146 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PROAf 147 " -0.084 5.00e-02 4.00e+02 pdb=" CA PROAf 147 " 0.024 5.00e-02 4.00e+02 pdb=" CD PROAf 147 " 0.027 5.00e-02 4.00e+02 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3453 2.76 - 3.29: 20622 3.29 - 3.83: 36581 3.83 - 4.36: 44172 4.36 - 4.90: 72545 Nonbonded interactions: 177373 Sorted by model distance: nonbonded pdb=" OH TYRAk 203 " pdb=" OG1 THRAk 209 " model vdw 2.221 3.040 nonbonded pdb=" OH TYRAi 203 " pdb=" OG1 THRAi 209 " model vdw 2.222 3.040 nonbonded pdb=" OH TYRAe 203 " pdb=" OG1 THRAe 209 " model vdw 2.222 3.040 nonbonded pdb=" OH TYRAm 203 " pdb=" OG1 THRAm 209 " model vdw 2.222 3.040 nonbonded pdb=" OH TYRAo 203 " pdb=" OG1 THRAo 209 " model vdw 2.222 3.040 ... (remaining 177368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' } 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: 2.940 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.860 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.004 0.068 22320 Z= 0.266 Angle : 0.673 6.663 30256 Z= 0.386 Chirality : 0.041 0.158 3248 Planarity : 0.005 0.049 3952 Dihedral : 15.928 81.002 8496 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.60 % Allowed : 24.45 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: -1.59 (0.16), residues: 2672 helix: -0.63 (0.14), residues: 1392 sheet: 0.28 (0.38), residues: 160 loop : -1.72 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGAc 214 TYR 0.031 0.002 TYRAl 184 PHE 0.012 0.002 PHEAl 200 TRP 0.008 0.001 TRPAh 118 HIS 0.003 0.001 HISAh 217 Details of bonding type rmsd covalent geometry : bond 0.00420 (22320) covalent geometry : angle 0.67300 (30256) hydrogen bonds : bond 0.29462 ( 952) hydrogen bonds : angle 7.61417 ( 2616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 426 time to evaluate : 0.832 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6076 (mmm) cc_final: 0.5768 (mmm) REVERT: Ac 56 MET cc_start: 0.6147 (mmm) cc_final: 0.5940 (mmm) REVERT: Ac 116 MET cc_start: 0.7216 (ttp) cc_final: 0.6791 (ttp) REVERT: Ac 141 VAL cc_start: 0.8454 (t) cc_final: 0.8147 (p) REVERT: Ac 155 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8476 (m) REVERT: Ad 111 VAL cc_start: 0.7211 (t) cc_final: 0.6999 (t) REVERT: Ad 116 MET cc_start: 0.7933 (ttp) cc_final: 0.7324 (ttp) REVERT: Ad 160 MET cc_start: 0.8421 (tpt) cc_final: 0.8134 (mmm) REVERT: Ad 188 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7748 (mtt90) REVERT: Ad 206 THR cc_start: 0.8420 (p) cc_final: 0.8203 (p) REVERT: Ae 56 MET cc_start: 0.5855 (mmm) cc_final: 0.5552 (mmm) REVERT: Ae 141 VAL cc_start: 0.8495 (t) cc_final: 0.8219 (p) REVERT: Ae 151 ASN cc_start: 0.7833 (m-40) cc_final: 0.7295 (m-40) REVERT: Af 108 MET cc_start: 0.7847 (tpp) cc_final: 0.7523 (tpp) REVERT: Af 139 GLU cc_start: 0.7265 (mp0) cc_final: 0.6606 (mp0) REVERT: Ag 56 MET cc_start: 0.6127 (mmm) cc_final: 0.5800 (mmm) REVERT: Ag 116 MET cc_start: 0.7185 (ttp) cc_final: 0.6912 (ttp) REVERT: Ag 141 VAL cc_start: 0.8540 (t) cc_final: 0.8216 (p) REVERT: Ag 220 MET cc_start: 0.6132 (mtm) cc_final: 0.5821 (mtm) REVERT: Ah 116 MET cc_start: 0.7989 (ttp) cc_final: 0.7574 (ttp) REVERT: Ah 160 MET cc_start: 0.8342 (tpt) cc_final: 0.8058 (mmm) REVERT: Ah 181 MET cc_start: 0.8104 (tpp) cc_final: 0.7883 (tpt) REVERT: Ah 188 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7760 (mtt90) REVERT: Ah 206 THR cc_start: 0.8558 (p) cc_final: 0.8355 (p) REVERT: Ai 56 MET cc_start: 0.6035 (mmm) cc_final: 0.5685 (mmm) REVERT: Aj 108 MET cc_start: 0.7854 (tpp) cc_final: 0.7530 (tpp) REVERT: Aj 112 MET cc_start: 0.8570 (mtp) cc_final: 0.8250 (mtt) REVERT: Aj 206 THR cc_start: 0.8498 (p) cc_final: 0.8248 (p) REVERT: Ak 56 MET cc_start: 0.6180 (mmm) cc_final: 0.5758 (mmm) REVERT: Ak 116 MET cc_start: 0.7529 (ttp) cc_final: 0.7056 (ttp) REVERT: Ak 220 MET cc_start: 0.6494 (mtm) cc_final: 0.6204 (mtm) REVERT: Al 108 MET cc_start: 0.7980 (tpp) cc_final: 0.7626 (tpp) REVERT: Al 116 MET cc_start: 0.8048 (ttp) cc_final: 0.7754 (ttm) REVERT: Al 143 TYR cc_start: 0.8398 (m-80) cc_final: 0.7953 (m-80) REVERT: Al 206 THR cc_start: 0.8501 (p) cc_final: 0.8282 (p) REVERT: Am 56 MET cc_start: 0.6056 (mmm) cc_final: 0.5754 (mmm) REVERT: Am 141 VAL cc_start: 0.8531 (t) cc_final: 0.8236 (p) REVERT: An 108 MET cc_start: 0.7923 (tpp) cc_final: 0.7516 (tpp) REVERT: An 143 TYR cc_start: 0.8448 (m-80) cc_final: 0.7918 (m-80) REVERT: Ao 56 MET cc_start: 0.6126 (mmm) cc_final: 0.5750 (mmm) REVERT: Ao 116 MET cc_start: 0.7411 (ttp) cc_final: 0.6782 (ttp) REVERT: Ao 139 GLU cc_start: 0.6676 (mp0) cc_final: 0.6341 (mp0) REVERT: Ao 141 VAL cc_start: 0.8566 (t) cc_final: 0.8290 (p) REVERT: Ap 84 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8190 (ptp-170) REVERT: Ap 112 MET cc_start: 0.8414 (mtp) cc_final: 0.8179 (mtt) REVERT: Ap 116 MET cc_start: 0.8029 (ttp) cc_final: 0.7725 (ttm) REVERT: Ap 188 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7718 (mtt90) REVERT: Ap 206 THR cc_start: 0.8447 (p) cc_final: 0.8209 (p) outliers start: 14 outliers final: 2 residues processed: 426 average time/residue: 0.7370 time to fit residues: 352.4699 Evaluate side-chains 424 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 421 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ae residue 155 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 0.0270 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN Ac 77 GLN Ag 77 GLN Ak 77 GLN Am 77 GLN Ao 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.148791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134917 restraints weight = 28890.894| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.13 r_work: 0.3594 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22320 Z= 0.192 Angle : 0.624 8.779 30256 Z= 0.320 Chirality : 0.043 0.125 3248 Planarity : 0.006 0.055 3952 Dihedral : 4.530 24.869 3011 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.49 % Allowed : 18.11 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: -1.08 (0.16), residues: 2672 helix: -0.08 (0.14), residues: 1392 sheet: 0.24 (0.36), residues: 160 loop : -1.64 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAn 188 TYR 0.018 0.002 TYRAc 143 PHE 0.022 0.003 PHEAd 202 TRP 0.013 0.002 TRPAj 132 HIS 0.003 0.001 HISAp 217 Details of bonding type rmsd covalent geometry : bond 0.00448 (22320) covalent geometry : angle 0.62401 (30256) hydrogen bonds : bond 0.04384 ( 952) hydrogen bonds : angle 5.10620 ( 2616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 498 time to evaluate : 0.827 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6864 (mmm) cc_final: 0.6513 (mmm) REVERT: Aa 72 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6970 (tm-30) REVERT: Aa 134 MET cc_start: 0.7809 (ttt) cc_final: 0.7518 (ttt) REVERT: Ac 56 MET cc_start: 0.6795 (mmm) cc_final: 0.6497 (mmm) REVERT: Ac 220 MET cc_start: 0.6562 (mtm) cc_final: 0.6072 (mtm) REVERT: Ad 116 MET cc_start: 0.8015 (ttp) cc_final: 0.7594 (ttm) REVERT: Ad 122 ASN cc_start: 0.8501 (m-40) cc_final: 0.8221 (m-40) REVERT: Ad 183 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7551 (mtp85) REVERT: Ad 188 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.8133 (mtt90) REVERT: Ad 191 ARG cc_start: 0.7503 (mtt90) cc_final: 0.7139 (mtt90) REVERT: Ad 206 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8278 (p) REVERT: Ad 208 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.7175 (mtm-85) REVERT: Ad 214 ARG cc_start: 0.8150 (mtm180) cc_final: 0.7888 (mtm-85) REVERT: Ae 56 MET cc_start: 0.6725 (mmm) cc_final: 0.6457 (mmm) REVERT: Ag 220 MET cc_start: 0.6473 (mtm) cc_final: 0.6112 (mtm) REVERT: Ah 116 MET cc_start: 0.7944 (ttp) cc_final: 0.7645 (ttp) REVERT: Ah 122 ASN cc_start: 0.8468 (m-40) cc_final: 0.8194 (m-40) REVERT: Ah 188 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.8017 (mtt90) REVERT: Ah 206 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8501 (p) REVERT: Ai 56 MET cc_start: 0.6754 (mmm) cc_final: 0.6468 (mmm) REVERT: Ai 72 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6831 (tm-30) REVERT: Ai 141 VAL cc_start: 0.8690 (t) cc_final: 0.8480 (p) REVERT: Ak 56 MET cc_start: 0.6860 (mmm) cc_final: 0.6572 (mpp) REVERT: Ak 143 TYR cc_start: 0.8631 (m-80) cc_final: 0.8394 (m-80) REVERT: Ak 220 MET cc_start: 0.6866 (mtm) cc_final: 0.6491 (mtm) REVERT: Al 56 MET cc_start: 0.7161 (mpp) cc_final: 0.6765 (mpp) REVERT: Al 116 MET cc_start: 0.8108 (ttp) cc_final: 0.7717 (ttm) REVERT: Al 122 ASN cc_start: 0.8444 (m-40) cc_final: 0.8229 (m-40) REVERT: Al 188 ARG cc_start: 0.8537 (mtt90) cc_final: 0.8215 (mtt90) REVERT: Al 206 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8421 (p) REVERT: Am 56 MET cc_start: 0.6790 (mmm) cc_final: 0.6469 (mmm) REVERT: Am 72 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6956 (tm-30) REVERT: Am 95 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7076 (mt-10) REVERT: An 160 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8105 (mmm) REVERT: Ao 56 MET cc_start: 0.6731 (mmm) cc_final: 0.6464 (mmm) REVERT: Ao 72 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6838 (tm-30) REVERT: Ao 101 TYR cc_start: 0.8342 (m-10) cc_final: 0.8112 (m-10) REVERT: Ao 116 MET cc_start: 0.7378 (ttp) cc_final: 0.6803 (ttp) REVERT: Ao 220 MET cc_start: 0.7131 (mtm) cc_final: 0.6571 (mtm) REVERT: Ap 188 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7880 (mtt90) REVERT: Ap 206 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8261 (p) REVERT: Ap 208 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7204 (mtm-85) REVERT: Ap 214 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7827 (mtm-85) outliers start: 82 outliers final: 25 residues processed: 520 average time/residue: 0.7260 time to fit residues: 421.3188 Evaluate side-chains 519 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 489 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 206 THR Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Af residue 206 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 204 GLU Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 206 THR Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 173 MET Chi-restraints excluded: chain Aj residue 206 THR Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 204 GLU Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Al residue 206 THR Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 160 MET Chi-restraints excluded: chain An residue 173 MET Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 134 MET Chi-restraints excluded: chain Ap residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 5 optimal weight: 0.0170 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 30 optimal weight: 0.0010 chunk 127 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 144 optimal weight: 0.3980 chunk 232 optimal weight: 0.0050 chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN Aa 122 ASN Ab 122 ASN Ac 77 GLN Af 158 GLN Ag 77 GLN Aj 122 ASN Ak 77 GLN Am 77 GLN An 122 ASN Ao 77 GLN Ao 129 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138217 restraints weight = 28884.331| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.19 r_work: 0.3649 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22320 Z= 0.098 Angle : 0.525 7.467 30256 Z= 0.267 Chirality : 0.039 0.122 3248 Planarity : 0.005 0.046 3952 Dihedral : 4.194 22.111 3009 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.49 % Allowed : 20.62 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 0.35 (0.17), residues: 2672 helix: 1.15 (0.16), residues: 1200 sheet: 0.24 (0.34), residues: 160 loop : -0.59 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAn 188 TYR 0.019 0.001 TYRAa 198 PHE 0.013 0.002 PHEAp 200 TRP 0.012 0.001 TRPAf 132 HIS 0.002 0.001 HISAf 69 Details of bonding type rmsd covalent geometry : bond 0.00229 (22320) covalent geometry : angle 0.52495 (30256) hydrogen bonds : bond 0.03242 ( 952) hydrogen bonds : angle 4.50088 ( 2616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 506 time to evaluate : 0.619 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6472 (mmm) cc_final: 0.6128 (mmm) REVERT: Aa 155 THR cc_start: 0.8461 (p) cc_final: 0.8226 (p) REVERT: Ac 56 MET cc_start: 0.6480 (mmm) cc_final: 0.6277 (mmm) REVERT: Ac 220 MET cc_start: 0.6686 (mtm) cc_final: 0.6290 (mtm) REVERT: Ad 116 MET cc_start: 0.7905 (ttp) cc_final: 0.7470 (ttm) REVERT: Ad 188 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7834 (mtt90) REVERT: Ad 191 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6861 (mtt90) REVERT: Ad 206 THR cc_start: 0.8428 (p) cc_final: 0.8094 (p) REVERT: Ad 214 ARG cc_start: 0.8074 (mtm180) cc_final: 0.7770 (mtm-85) REVERT: Af 116 MET cc_start: 0.7980 (ttp) cc_final: 0.7698 (ttp) REVERT: Ag 56 MET cc_start: 0.6241 (mpp) cc_final: 0.5842 (mpp) REVERT: Ag 73 TYR cc_start: 0.7665 (t80) cc_final: 0.7463 (t80) REVERT: Ah 56 MET cc_start: 0.6991 (mmt) cc_final: 0.6745 (mpp) REVERT: Ah 84 ARG cc_start: 0.8288 (ptm160) cc_final: 0.8074 (ptp-170) REVERT: Ah 112 MET cc_start: 0.8034 (mtp) cc_final: 0.7811 (mtm) REVERT: Ah 122 ASN cc_start: 0.8347 (m-40) cc_final: 0.8047 (m-40) REVERT: Ah 188 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7960 (mtt90) REVERT: Ah 197 ARG cc_start: 0.8448 (ptm160) cc_final: 0.8144 (ptm-80) REVERT: Ah 206 THR cc_start: 0.8653 (p) cc_final: 0.8340 (p) REVERT: Ah 214 ARG cc_start: 0.7855 (mtm180) cc_final: 0.7575 (mtm-85) REVERT: Ai 56 MET cc_start: 0.6510 (mmm) cc_final: 0.6304 (mmm) REVERT: Ai 101 TYR cc_start: 0.7975 (m-10) cc_final: 0.7644 (m-80) REVERT: Aj 112 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.8005 (mtm) REVERT: Aj 206 THR cc_start: 0.8521 (p) cc_final: 0.8294 (p) REVERT: Ak 56 MET cc_start: 0.6467 (mmm) cc_final: 0.6237 (mmm) REVERT: Ak 108 MET cc_start: 0.7844 (tpt) cc_final: 0.7639 (tpt) REVERT: Ak 134 MET cc_start: 0.7475 (ttt) cc_final: 0.7233 (ttt) REVERT: Ak 135 MET cc_start: 0.8300 (mmm) cc_final: 0.8080 (mmt) REVERT: Ak 143 TYR cc_start: 0.8410 (m-80) cc_final: 0.8057 (m-80) REVERT: Al 56 MET cc_start: 0.6873 (mpp) cc_final: 0.6577 (mpp) REVERT: Al 116 MET cc_start: 0.7707 (ttp) cc_final: 0.7411 (ttm) REVERT: Al 188 ARG cc_start: 0.8404 (mtt90) cc_final: 0.8096 (mtt90) REVERT: Al 206 THR cc_start: 0.8543 (p) cc_final: 0.8315 (p) REVERT: Am 56 MET cc_start: 0.6372 (mmm) cc_final: 0.6070 (mmm) REVERT: Am 73 TYR cc_start: 0.7856 (t80) cc_final: 0.7538 (t80) REVERT: Ao 116 MET cc_start: 0.7216 (ttp) cc_final: 0.6632 (ttp) REVERT: Ao 141 VAL cc_start: 0.8525 (m) cc_final: 0.8315 (p) REVERT: Ao 220 MET cc_start: 0.7157 (mtm) cc_final: 0.6812 (mtm) REVERT: Ap 84 ARG cc_start: 0.8269 (ptm160) cc_final: 0.7932 (ptp-170) REVERT: Ap 116 MET cc_start: 0.7865 (ttp) cc_final: 0.7644 (ttm) REVERT: Ap 135 MET cc_start: 0.8297 (mmm) cc_final: 0.8079 (mmt) REVERT: Ap 188 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7878 (mtt90) REVERT: Ap 206 THR cc_start: 0.8422 (p) cc_final: 0.8072 (p) REVERT: Ap 214 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7580 (mtm-85) outliers start: 35 outliers final: 17 residues processed: 514 average time/residue: 0.8239 time to fit residues: 469.6803 Evaluate side-chains 516 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 495 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 173 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ad residue 188 ARG Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 112 MET Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 204 GLU Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 188 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 181 optimal weight: 0.7980 chunk 222 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 240 optimal weight: 0.0870 chunk 145 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN ** Aa 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN Af 122 ASN Ag 77 GLN Aj 122 ASN Ak 77 GLN Am 77 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN Ao 77 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.153859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139596 restraints weight = 28545.441| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.19 r_work: 0.3595 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22320 Z= 0.147 Angle : 0.575 10.416 30256 Z= 0.285 Chirality : 0.041 0.139 3248 Planarity : 0.005 0.044 3952 Dihedral : 4.326 16.422 3008 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.87 % Allowed : 22.45 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 0.42 (0.17), residues: 2672 helix: 1.43 (0.16), residues: 1104 sheet: 0.53 (0.33), residues: 160 loop : -0.68 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAj 188 TYR 0.023 0.001 TYRAi 198 PHE 0.019 0.003 PHEAd 202 TRP 0.012 0.001 TRPAm 132 HIS 0.002 0.001 HISAj 69 Details of bonding type rmsd covalent geometry : bond 0.00349 (22320) covalent geometry : angle 0.57475 (30256) hydrogen bonds : bond 0.03554 ( 952) hydrogen bonds : angle 4.47803 ( 2616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 527 time to evaluate : 0.883 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6525 (mmm) cc_final: 0.6226 (mmm) REVERT: Aa 155 THR cc_start: 0.8474 (p) cc_final: 0.8226 (p) REVERT: Ac 56 MET cc_start: 0.6479 (mmm) cc_final: 0.6278 (mmm) REVERT: Ac 220 MET cc_start: 0.6738 (mtm) cc_final: 0.6408 (mtm) REVERT: Ad 116 MET cc_start: 0.7911 (ttp) cc_final: 0.7470 (ttm) REVERT: Ad 188 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8011 (mtt90) REVERT: Ad 191 ARG cc_start: 0.7233 (mtt90) cc_final: 0.6882 (mtt90) REVERT: Ad 206 THR cc_start: 0.8561 (p) cc_final: 0.8274 (p) REVERT: Ad 214 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7719 (mtm-85) REVERT: Ae 56 MET cc_start: 0.6313 (mmm) cc_final: 0.5955 (mmm) REVERT: Af 206 THR cc_start: 0.8587 (p) cc_final: 0.8345 (p) REVERT: Ag 220 MET cc_start: 0.6585 (mtm) cc_final: 0.6133 (mtm) REVERT: Ah 188 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8028 (mtt90) REVERT: Ah 206 THR cc_start: 0.8634 (p) cc_final: 0.8366 (p) REVERT: Aj 112 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7831 (mtm) REVERT: Aj 206 THR cc_start: 0.8641 (p) cc_final: 0.8395 (p) REVERT: Ak 108 MET cc_start: 0.7923 (tpt) cc_final: 0.7721 (tpt) REVERT: Ak 135 MET cc_start: 0.8262 (mmm) cc_final: 0.8049 (mmt) REVERT: Ak 220 MET cc_start: 0.6813 (mtm) cc_final: 0.6411 (mtm) REVERT: Al 56 MET cc_start: 0.6900 (mpp) cc_final: 0.6525 (mpp) REVERT: Al 108 MET cc_start: 0.7134 (tpp) cc_final: 0.6884 (tpp) REVERT: Al 116 MET cc_start: 0.7733 (ttp) cc_final: 0.7372 (ttm) REVERT: Al 160 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: Al 188 ARG cc_start: 0.8487 (mtt90) cc_final: 0.8209 (mtt90) REVERT: Al 206 THR cc_start: 0.8558 (p) cc_final: 0.8225 (p) REVERT: Al 214 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7751 (mtm-85) REVERT: Am 56 MET cc_start: 0.6422 (mmm) cc_final: 0.6133 (mmm) REVERT: An 108 MET cc_start: 0.7183 (tpp) cc_final: 0.6898 (tpp) REVERT: Ao 72 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6796 (tm-30) REVERT: Ao 220 MET cc_start: 0.7194 (mtm) cc_final: 0.6861 (mtm) REVERT: Ap 84 ARG cc_start: 0.8396 (ptm160) cc_final: 0.8170 (ptp-170) REVERT: Ap 135 MET cc_start: 0.8305 (mmm) cc_final: 0.8097 (mmt) REVERT: Ap 160 MET cc_start: 0.8218 (tpt) cc_final: 0.8001 (mmm) REVERT: Ap 206 THR cc_start: 0.8467 (p) cc_final: 0.8128 (p) REVERT: Ap 214 ARG cc_start: 0.7956 (mtm180) cc_final: 0.7605 (mtm-85) outliers start: 44 outliers final: 28 residues processed: 537 average time/residue: 0.7808 time to fit residues: 465.1428 Evaluate side-chains 548 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 516 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 204 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 188 ARG Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Aj residue 112 MET Chi-restraints excluded: chain Ak residue 173 MET Chi-restraints excluded: chain Ak residue 204 GLU Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Al residue 160 MET Chi-restraints excluded: chain Al residue 211 VAL Chi-restraints excluded: chain Am residue 54 MET Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 134 MET Chi-restraints excluded: chain Ap residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 159 optimal weight: 0.0870 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 193 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN ** Aa 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN ** Ac 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 122 ASN Af 122 ASN Ag 77 GLN ** Ag 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Aj 158 GLN Ak 77 GLN ** Ak 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN Ao 77 GLN ** Ao 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 129 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.149794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135592 restraints weight = 28527.941| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.11 r_work: 0.3581 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22320 Z= 0.180 Angle : 0.600 10.826 30256 Z= 0.297 Chirality : 0.043 0.149 3248 Planarity : 0.006 0.045 3952 Dihedral : 4.463 17.321 3008 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.30 % Allowed : 22.45 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: -0.04 (0.16), residues: 2672 helix: 0.73 (0.15), residues: 1328 sheet: 0.63 (0.33), residues: 160 loop : -0.96 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGAj 188 TYR 0.025 0.002 TYRAa 198 PHE 0.021 0.003 PHEAl 202 TRP 0.011 0.002 TRPAj 132 HIS 0.002 0.001 HISAf 217 Details of bonding type rmsd covalent geometry : bond 0.00426 (22320) covalent geometry : angle 0.60025 (30256) hydrogen bonds : bond 0.03714 ( 952) hydrogen bonds : angle 4.51951 ( 2616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 508 time to evaluate : 0.852 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6840 (mmm) cc_final: 0.6554 (mmm) REVERT: Aa 72 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6846 (tm-30) REVERT: Aa 155 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8342 (p) REVERT: Ab 84 ARG cc_start: 0.8575 (ptp-170) cc_final: 0.8318 (ptp-170) REVERT: Ac 56 MET cc_start: 0.6741 (mmm) cc_final: 0.6523 (mmm) REVERT: Ac 122 ASN cc_start: 0.8412 (m110) cc_final: 0.8073 (m-40) REVERT: Ac 220 MET cc_start: 0.6737 (mtm) cc_final: 0.6245 (mtm) REVERT: Ad 56 MET cc_start: 0.6932 (mmm) cc_final: 0.6550 (mpp) REVERT: Ad 116 MET cc_start: 0.8034 (ttp) cc_final: 0.7578 (ttm) REVERT: Ad 191 ARG cc_start: 0.7625 (mtt90) cc_final: 0.7275 (mtt90) REVERT: Ad 206 THR cc_start: 0.8601 (p) cc_final: 0.8327 (p) REVERT: Ag 220 MET cc_start: 0.6559 (mtm) cc_final: 0.5997 (mtm) REVERT: Ah 135 MET cc_start: 0.8439 (mmm) cc_final: 0.8200 (mmt) REVERT: Ah 188 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8034 (mtt90) REVERT: Ah 206 THR cc_start: 0.8702 (p) cc_final: 0.8443 (p) REVERT: Ai 72 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6732 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7186 (mt-10) REVERT: Aj 112 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8173 (mtt) REVERT: Aj 206 THR cc_start: 0.8690 (p) cc_final: 0.8424 (p) REVERT: Ak 108 MET cc_start: 0.8050 (tpt) cc_final: 0.7836 (tpt) REVERT: Ak 122 ASN cc_start: 0.8387 (m110) cc_final: 0.8066 (m-40) REVERT: Ak 220 MET cc_start: 0.6850 (mtm) cc_final: 0.6359 (mtm) REVERT: Al 56 MET cc_start: 0.7088 (mpp) cc_final: 0.6747 (mpp) REVERT: Al 116 MET cc_start: 0.8042 (ttp) cc_final: 0.7640 (ttm) REVERT: Al 206 THR cc_start: 0.8627 (p) cc_final: 0.8338 (p) REVERT: Am 56 MET cc_start: 0.6887 (mmm) cc_final: 0.6627 (mmm) REVERT: Am 135 MET cc_start: 0.8416 (mmm) cc_final: 0.8213 (mmm) REVERT: An 108 MET cc_start: 0.7456 (tpp) cc_final: 0.7145 (tpp) REVERT: An 190 LEU cc_start: 0.8270 (tp) cc_final: 0.8066 (tp) REVERT: Ao 101 TYR cc_start: 0.8378 (m-10) cc_final: 0.8115 (m-10) REVERT: Ao 220 MET cc_start: 0.7203 (mtm) cc_final: 0.6877 (mtt) REVERT: Ap 160 MET cc_start: 0.8387 (tpt) cc_final: 0.8177 (mmm) REVERT: Ap 206 THR cc_start: 0.8574 (p) cc_final: 0.8251 (p) outliers start: 54 outliers final: 34 residues processed: 523 average time/residue: 0.7673 time to fit residues: 446.1153 Evaluate side-chains 537 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 500 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 204 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 120 ILE Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 204 GLU Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Aj residue 112 MET Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 173 MET Chi-restraints excluded: chain Ak residue 204 GLU Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Al residue 211 VAL Chi-restraints excluded: chain Am residue 54 MET Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 134 MET Chi-restraints excluded: chain Ap residue 211 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 151 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 187 optimal weight: 0.0970 chunk 107 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN ** Aa 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN ** Ac 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Af 158 GLN Ag 77 GLN ** Ag 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Aj 158 GLN Ak 77 GLN ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN An 158 GLN Ao 77 GLN ** Ao 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.149695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135226 restraints weight = 28475.665| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.13 r_work: 0.3602 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22320 Z= 0.164 Angle : 0.592 12.680 30256 Z= 0.292 Chirality : 0.042 0.127 3248 Planarity : 0.006 0.046 3952 Dihedral : 4.460 17.706 3008 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.17 % Allowed : 22.62 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 0.45 (0.17), residues: 2672 helix: 1.40 (0.16), residues: 1104 sheet: 0.80 (0.34), residues: 160 loop : -0.65 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAj 188 TYR 0.022 0.001 TYRAc 198 PHE 0.019 0.003 PHEAh 202 TRP 0.012 0.002 TRPAn 132 HIS 0.002 0.001 HISAb 217 Details of bonding type rmsd covalent geometry : bond 0.00391 (22320) covalent geometry : angle 0.59176 (30256) hydrogen bonds : bond 0.03517 ( 952) hydrogen bonds : angle 4.48676 ( 2616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 504 time to evaluate : 0.867 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6846 (mmm) cc_final: 0.6550 (mmm) REVERT: Aa 72 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6912 (tm-30) REVERT: Aa 155 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8298 (p) REVERT: Ab 84 ARG cc_start: 0.8579 (ptp-170) cc_final: 0.8289 (ptp-170) REVERT: Ac 56 MET cc_start: 0.6789 (mmm) cc_final: 0.6536 (mmm) REVERT: Ac 122 ASN cc_start: 0.8429 (m110) cc_final: 0.8162 (m-40) REVERT: Ad 56 MET cc_start: 0.6911 (mmm) cc_final: 0.6539 (mpp) REVERT: Ad 116 MET cc_start: 0.7924 (ttp) cc_final: 0.7508 (ttm) REVERT: Ad 188 ARG cc_start: 0.8420 (mtt90) cc_final: 0.8220 (mtt90) REVERT: Ad 191 ARG cc_start: 0.7567 (mtt90) cc_final: 0.7243 (mtt90) REVERT: Ad 206 THR cc_start: 0.8612 (p) cc_final: 0.8318 (p) REVERT: Ae 56 MET cc_start: 0.6647 (mmm) cc_final: 0.6440 (mmm) REVERT: Ae 173 MET cc_start: 0.8714 (tmt) cc_final: 0.8511 (ttp) REVERT: Ah 135 MET cc_start: 0.8474 (mmm) cc_final: 0.8239 (mmt) REVERT: Ah 188 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7975 (mtt90) REVERT: Ah 206 THR cc_start: 0.8696 (p) cc_final: 0.8438 (p) REVERT: Ai 72 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6802 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7122 (mt-10) REVERT: Aj 112 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8160 (mtt) REVERT: Aj 158 GLN cc_start: 0.8654 (mt0) cc_final: 0.8428 (mt0) REVERT: Aj 206 THR cc_start: 0.8667 (p) cc_final: 0.8422 (p) REVERT: Ak 77 GLN cc_start: 0.8754 (tt0) cc_final: 0.8501 (tt0) REVERT: Ak 108 MET cc_start: 0.8031 (tpt) cc_final: 0.7814 (tpt) REVERT: Ak 122 ASN cc_start: 0.8364 (m110) cc_final: 0.8049 (m-40) REVERT: Ak 220 MET cc_start: 0.6841 (mtm) cc_final: 0.6417 (mtm) REVERT: Al 56 MET cc_start: 0.7047 (mpp) cc_final: 0.6783 (mpp) REVERT: Al 116 MET cc_start: 0.7794 (ttp) cc_final: 0.7457 (ttm) REVERT: Al 206 THR cc_start: 0.8623 (p) cc_final: 0.8345 (p) REVERT: Am 56 MET cc_start: 0.6820 (mmm) cc_final: 0.6547 (mmm) REVERT: Am 188 ARG cc_start: 0.8406 (mmt90) cc_final: 0.7393 (mmt90) REVERT: An 108 MET cc_start: 0.7464 (tpp) cc_final: 0.7174 (tpp) REVERT: An 112 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8106 (mtm) REVERT: Ao 116 MET cc_start: 0.7246 (ttp) cc_final: 0.6727 (ttp) REVERT: Ao 220 MET cc_start: 0.7225 (mtm) cc_final: 0.6877 (mtm) REVERT: Ap 160 MET cc_start: 0.8312 (tpt) cc_final: 0.8106 (mmm) REVERT: Ap 206 THR cc_start: 0.8642 (p) cc_final: 0.8333 (p) outliers start: 51 outliers final: 35 residues processed: 519 average time/residue: 0.7780 time to fit residues: 448.1949 Evaluate side-chains 540 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 501 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 173 MET Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 204 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 120 ILE Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 204 GLU Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 204 GLU Chi-restraints excluded: chain Aj residue 112 MET Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 173 MET Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Al residue 211 VAL Chi-restraints excluded: chain Am residue 54 MET Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain An residue 112 MET Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 134 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 88 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 156 optimal weight: 0.0070 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN ** Aa 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN ** Ac 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Ag 77 GLN Ag 122 ASN ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 77 GLN ** Ao 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.141764 restraints weight = 28347.492| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.07 r_work: 0.3599 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22320 Z= 0.141 Angle : 0.590 12.931 30256 Z= 0.287 Chirality : 0.041 0.121 3248 Planarity : 0.006 0.048 3952 Dihedral : 4.423 17.275 3008 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.21 % Allowed : 23.43 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 0.59 (0.17), residues: 2672 helix: 1.51 (0.16), residues: 1104 sheet: 1.00 (0.33), residues: 160 loop : -0.59 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGAj 188 TYR 0.021 0.001 TYRAc 198 PHE 0.017 0.003 PHEAj 202 TRP 0.014 0.001 TRPAn 132 HIS 0.002 0.001 HISAb 217 Details of bonding type rmsd covalent geometry : bond 0.00339 (22320) covalent geometry : angle 0.59005 (30256) hydrogen bonds : bond 0.03280 ( 952) hydrogen bonds : angle 4.41996 ( 2616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 502 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6825 (mmm) cc_final: 0.6549 (mmm) REVERT: Aa 112 MET cc_start: 0.7945 (mtm) cc_final: 0.7704 (mtm) REVERT: Aa 155 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8325 (p) REVERT: Ab 84 ARG cc_start: 0.8594 (ptp-170) cc_final: 0.8300 (ptp-170) REVERT: Ac 56 MET cc_start: 0.6758 (mmm) cc_final: 0.6528 (mmm) REVERT: Ac 122 ASN cc_start: 0.8399 (m110) cc_final: 0.8145 (m-40) REVERT: Ac 220 MET cc_start: 0.6647 (mtm) cc_final: 0.6441 (mtt) REVERT: Ad 56 MET cc_start: 0.6877 (mmm) cc_final: 0.6561 (mpp) REVERT: Ad 116 MET cc_start: 0.7894 (ttp) cc_final: 0.7474 (ttm) REVERT: Ad 188 ARG cc_start: 0.8449 (mtt90) cc_final: 0.8232 (mtt90) REVERT: Ad 191 ARG cc_start: 0.7536 (mtt90) cc_final: 0.7219 (mtt90) REVERT: Ad 206 THR cc_start: 0.8591 (p) cc_final: 0.8278 (p) REVERT: Ad 214 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7341 (mtm-85) REVERT: Ag 220 MET cc_start: 0.6468 (mtm) cc_final: 0.6225 (mtt) REVERT: Ah 188 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8035 (mtt90) REVERT: Ah 206 THR cc_start: 0.8691 (p) cc_final: 0.8436 (p) REVERT: Ai 72 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6753 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7098 (mt-10) REVERT: Aj 112 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8106 (mtt) REVERT: Aj 206 THR cc_start: 0.8662 (p) cc_final: 0.8419 (p) REVERT: Ak 77 GLN cc_start: 0.8776 (tt0) cc_final: 0.8479 (tt0) REVERT: Ak 108 MET cc_start: 0.8041 (tpt) cc_final: 0.7802 (tpt) REVERT: Ak 122 ASN cc_start: 0.8307 (m110) cc_final: 0.8075 (m-40) REVERT: Ak 220 MET cc_start: 0.6848 (mtm) cc_final: 0.6384 (mtm) REVERT: Al 56 MET cc_start: 0.7037 (mpp) cc_final: 0.6675 (mpp) REVERT: Al 116 MET cc_start: 0.7791 (ttp) cc_final: 0.7469 (ttm) REVERT: Al 206 THR cc_start: 0.8603 (p) cc_final: 0.8319 (p) REVERT: Am 56 MET cc_start: 0.6803 (mmm) cc_final: 0.6559 (mmm) REVERT: Am 150 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6608 (pt0) REVERT: Am 188 ARG cc_start: 0.8393 (mmt90) cc_final: 0.7453 (mmt90) REVERT: Am 190 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8087 (mp) REVERT: An 112 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8020 (mtm) REVERT: Ao 116 MET cc_start: 0.7256 (ttp) cc_final: 0.6785 (ttp) REVERT: Ao 220 MET cc_start: 0.7157 (mtm) cc_final: 0.6874 (mtm) REVERT: Ap 188 ARG cc_start: 0.8428 (mtt90) cc_final: 0.8143 (mtt90) REVERT: Ap 206 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8280 (p) outliers start: 52 outliers final: 29 residues processed: 518 average time/residue: 0.8357 time to fit residues: 480.1601 Evaluate side-chains 532 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 496 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 204 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 120 ILE Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Aj residue 112 MET Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Am residue 54 MET Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 150 GLU Chi-restraints excluded: chain Am residue 190 LEU Chi-restraints excluded: chain An residue 112 MET Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 134 MET Chi-restraints excluded: chain Ap residue 206 THR Chi-restraints excluded: chain Ap residue 211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 248 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 176 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 chunk 226 optimal weight: 0.5980 chunk 92 optimal weight: 0.0040 chunk 169 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN ** Ac 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Af 158 GLN Ag 77 GLN Ag 122 ASN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Aj 158 GLN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN Ao 77 GLN Ao 122 ASN ** Ap 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.151224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136660 restraints weight = 28525.965| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.15 r_work: 0.3601 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22320 Z= 0.123 Angle : 0.584 12.311 30256 Z= 0.283 Chirality : 0.041 0.126 3248 Planarity : 0.005 0.049 3952 Dihedral : 4.370 18.268 3008 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.04 % Allowed : 23.68 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 0.71 (0.17), residues: 2672 helix: 1.60 (0.16), residues: 1104 sheet: 1.14 (0.34), residues: 160 loop : -0.52 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAj 188 TYR 0.021 0.001 TYRAo 143 PHE 0.015 0.002 PHEAf 202 TRP 0.013 0.001 TRPAf 132 HIS 0.002 0.001 HISAl 69 Details of bonding type rmsd covalent geometry : bond 0.00298 (22320) covalent geometry : angle 0.58418 (30256) hydrogen bonds : bond 0.03074 ( 952) hydrogen bonds : angle 4.36613 ( 2616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 478 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6558 (mmm) cc_final: 0.6289 (mmm) REVERT: Aa 72 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6641 (tm-30) REVERT: Aa 95 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6795 (mt-10) REVERT: Aa 112 MET cc_start: 0.7703 (mtm) cc_final: 0.7450 (mtm) REVERT: Aa 155 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8274 (p) REVERT: Aa 188 ARG cc_start: 0.8061 (mmt90) cc_final: 0.7328 (mmt90) REVERT: Ab 84 ARG cc_start: 0.8557 (ptp-170) cc_final: 0.8285 (ptp-170) REVERT: Ad 191 ARG cc_start: 0.7238 (mtt90) cc_final: 0.6923 (mtt90) REVERT: Ad 206 THR cc_start: 0.8564 (p) cc_final: 0.8261 (p) REVERT: Ad 214 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7279 (mtm-85) REVERT: Af 84 ARG cc_start: 0.8524 (ptp-170) cc_final: 0.8250 (ptp-170) REVERT: Af 206 THR cc_start: 0.8611 (p) cc_final: 0.8367 (p) REVERT: Ah 135 MET cc_start: 0.8382 (mmm) cc_final: 0.8137 (mmt) REVERT: Ah 188 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7983 (mtt90) REVERT: Ah 206 THR cc_start: 0.8623 (p) cc_final: 0.8357 (p) REVERT: Ai 72 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6593 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6869 (mt-10) REVERT: Aj 54 MET cc_start: 0.4972 (ptt) cc_final: 0.4668 (ptt) REVERT: Aj 112 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7993 (mtt) REVERT: Aj 206 THR cc_start: 0.8622 (p) cc_final: 0.8406 (p) REVERT: Ak 77 GLN cc_start: 0.8628 (tt0) cc_final: 0.8261 (tt0) REVERT: Al 56 MET cc_start: 0.6872 (mpp) cc_final: 0.6482 (mpp) REVERT: Al 116 MET cc_start: 0.7637 (ttp) cc_final: 0.7327 (ttm) REVERT: Al 206 THR cc_start: 0.8548 (p) cc_final: 0.8246 (p) REVERT: Am 56 MET cc_start: 0.6467 (mmm) cc_final: 0.6085 (mmm) REVERT: An 112 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7982 (mtm) REVERT: Ao 116 MET cc_start: 0.7090 (ttp) cc_final: 0.6587 (ttp) REVERT: Ao 220 MET cc_start: 0.7213 (mtm) cc_final: 0.6986 (mtt) REVERT: Ap 188 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7927 (mtt90) outliers start: 48 outliers final: 28 residues processed: 499 average time/residue: 0.7984 time to fit residues: 440.3109 Evaluate side-chains 504 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 472 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 204 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 120 ILE Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 212 ARG Chi-restraints excluded: chain Aj residue 112 MET Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 212 ARG Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain An residue 112 MET Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 134 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 93 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 248 optimal weight: 0.0570 chunk 255 optimal weight: 0.9980 chunk 153 optimal weight: 0.1980 chunk 170 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 122 ASN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 122 ASN Af 122 ASN Af 158 GLN Ag 77 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Aj 158 GLN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 77 GLN ** Ao 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136513 restraints weight = 28553.369| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.13 r_work: 0.3594 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 22320 Z= 0.147 Angle : 0.609 13.684 30256 Z= 0.293 Chirality : 0.042 0.136 3248 Planarity : 0.005 0.048 3952 Dihedral : 4.423 18.241 3008 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.66 % Allowed : 24.45 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 0.67 (0.17), residues: 2672 helix: 1.55 (0.16), residues: 1104 sheet: 1.17 (0.34), residues: 160 loop : -0.53 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAe 208 TYR 0.024 0.001 TYRAo 143 PHE 0.017 0.003 PHEAj 202 TRP 0.012 0.001 TRPAf 132 HIS 0.002 0.001 HISAb 217 Details of bonding type rmsd covalent geometry : bond 0.00352 (22320) covalent geometry : angle 0.60902 (30256) hydrogen bonds : bond 0.03298 ( 952) hydrogen bonds : angle 4.40692 ( 2616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 479 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6855 (mmm) cc_final: 0.6577 (mmm) REVERT: Aa 72 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6836 (tm-30) REVERT: Aa 112 MET cc_start: 0.8013 (mtm) cc_final: 0.7754 (mtm) REVERT: Aa 155 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8335 (p) REVERT: Aa 188 ARG cc_start: 0.8342 (mmt90) cc_final: 0.7595 (mmt90) REVERT: Ab 84 ARG cc_start: 0.8605 (ptp-170) cc_final: 0.8302 (ptp-170) REVERT: Ad 191 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7289 (mtt90) REVERT: Ad 206 THR cc_start: 0.8601 (p) cc_final: 0.8303 (p) REVERT: Ad 214 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7372 (mtm-85) REVERT: Af 65 LEU cc_start: 0.8122 (mt) cc_final: 0.7861 (mp) REVERT: Af 84 ARG cc_start: 0.8587 (ptp-170) cc_final: 0.8267 (ptp-170) REVERT: Af 206 THR cc_start: 0.8665 (p) cc_final: 0.8415 (p) REVERT: Ag 72 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6842 (tm-30) REVERT: Ah 112 MET cc_start: 0.8042 (mtm) cc_final: 0.7827 (mtt) REVERT: Ah 116 MET cc_start: 0.7645 (ttm) cc_final: 0.7435 (ttp) REVERT: Ah 135 MET cc_start: 0.8468 (mmm) cc_final: 0.8208 (mmt) REVERT: Ah 188 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8047 (mtt90) REVERT: Ah 206 THR cc_start: 0.8687 (p) cc_final: 0.8419 (p) REVERT: Ai 72 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6692 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7104 (mt-10) REVERT: Ai 122 ASN cc_start: 0.8407 (m110) cc_final: 0.8167 (m-40) REVERT: Aj 112 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8074 (mtt) REVERT: Aj 206 THR cc_start: 0.8665 (p) cc_final: 0.8445 (p) REVERT: Ak 77 GLN cc_start: 0.8749 (tt0) cc_final: 0.8424 (tt0) REVERT: Ak 139 GLU cc_start: 0.7081 (mp0) cc_final: 0.6580 (mp0) REVERT: Al 56 MET cc_start: 0.7045 (mpp) cc_final: 0.6655 (mpp) REVERT: Al 116 MET cc_start: 0.7805 (ttp) cc_final: 0.7480 (ttm) REVERT: Al 206 THR cc_start: 0.8639 (p) cc_final: 0.8342 (p) REVERT: Am 56 MET cc_start: 0.6898 (mmm) cc_final: 0.6673 (mmm) REVERT: Am 188 ARG cc_start: 0.8394 (mmt90) cc_final: 0.7391 (mmt90) REVERT: An 112 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7955 (mtm) REVERT: An 133 VAL cc_start: 0.8862 (m) cc_final: 0.8593 (p) REVERT: An 188 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.8236 (mtt-85) REVERT: Ao 220 MET cc_start: 0.7204 (mtm) cc_final: 0.6953 (mtt) REVERT: Ap 188 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8011 (mtt90) REVERT: Ap 208 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.7150 (mtm-85) outliers start: 39 outliers final: 27 residues processed: 497 average time/residue: 0.7931 time to fit residues: 435.9049 Evaluate side-chains 508 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 477 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 204 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 120 ILE Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 212 ARG Chi-restraints excluded: chain Aj residue 112 MET Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 212 ARG Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Al residue 176 LYS Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain An residue 112 MET Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 218 optimal weight: 1.9990 chunk 246 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 220 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 122 ASN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 76 GLN Ab 122 ASN Ac 77 GLN ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Af 158 GLN Ag 77 GLN ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Aj 158 GLN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN Ao 77 GLN ** Ao 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136739 restraints weight = 28668.780| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.07 r_work: 0.3611 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22320 Z= 0.135 Angle : 0.614 13.698 30256 Z= 0.294 Chirality : 0.041 0.130 3248 Planarity : 0.005 0.047 3952 Dihedral : 4.424 20.609 3008 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.40 % Allowed : 24.87 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 0.72 (0.17), residues: 2672 helix: 1.59 (0.16), residues: 1104 sheet: 1.15 (0.34), residues: 160 loop : -0.50 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAe 208 TYR 0.026 0.001 TYRAa 198 PHE 0.015 0.002 PHEAh 202 TRP 0.013 0.001 TRPAf 132 HIS 0.002 0.001 HISAl 69 Details of bonding type rmsd covalent geometry : bond 0.00326 (22320) covalent geometry : angle 0.61381 (30256) hydrogen bonds : bond 0.03159 ( 952) hydrogen bonds : angle 4.38895 ( 2616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 474 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6863 (mmm) cc_final: 0.6581 (mmm) REVERT: Aa 112 MET cc_start: 0.7931 (mtm) cc_final: 0.7667 (mtm) REVERT: Aa 155 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8313 (p) REVERT: Aa 188 ARG cc_start: 0.8318 (mmt90) cc_final: 0.7570 (mmt90) REVERT: Ab 84 ARG cc_start: 0.8591 (ptp-170) cc_final: 0.8292 (ptp-170) REVERT: Ad 132 TRP cc_start: 0.8473 (p-90) cc_final: 0.8094 (p-90) REVERT: Ad 191 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7258 (mtt90) REVERT: Ad 206 THR cc_start: 0.8579 (p) cc_final: 0.8272 (p) REVERT: Ad 214 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7246 (mtm-85) REVERT: Af 65 LEU cc_start: 0.8135 (mt) cc_final: 0.7878 (mp) REVERT: Af 84 ARG cc_start: 0.8552 (ptp-170) cc_final: 0.8225 (ptp-170) REVERT: Af 206 THR cc_start: 0.8635 (p) cc_final: 0.8387 (p) REVERT: Ag 214 ARG cc_start: 0.8431 (mtm180) cc_final: 0.8207 (mtm-85) REVERT: Ah 56 MET cc_start: 0.7217 (mmt) cc_final: 0.6772 (mmt) REVERT: Ah 132 TRP cc_start: 0.8383 (p-90) cc_final: 0.8068 (p-90) REVERT: Ah 135 MET cc_start: 0.8443 (mmm) cc_final: 0.8201 (mmt) REVERT: Ah 188 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8042 (mtt90) REVERT: Ah 206 THR cc_start: 0.8672 (p) cc_final: 0.8397 (p) REVERT: Ai 72 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6620 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7108 (mt-10) REVERT: Ai 220 MET cc_start: 0.7014 (mtm) cc_final: 0.6743 (mtt) REVERT: Aj 112 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8052 (mtt) REVERT: Aj 188 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7760 (mtt90) REVERT: Aj 206 THR cc_start: 0.8665 (p) cc_final: 0.8452 (p) REVERT: Ak 77 GLN cc_start: 0.8765 (tt0) cc_final: 0.8526 (tt0) REVERT: Ak 139 GLU cc_start: 0.7008 (mp0) cc_final: 0.6506 (mp0) REVERT: Al 116 MET cc_start: 0.7818 (ttp) cc_final: 0.7501 (ttm) REVERT: Al 206 THR cc_start: 0.8622 (p) cc_final: 0.8310 (p) REVERT: Am 56 MET cc_start: 0.6833 (mmm) cc_final: 0.6622 (mmm) REVERT: Am 188 ARG cc_start: 0.8355 (mmt90) cc_final: 0.7362 (mmt90) REVERT: An 112 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8005 (mtm) REVERT: An 133 VAL cc_start: 0.8818 (m) cc_final: 0.8547 (p) REVERT: An 188 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.8188 (mtt-85) REVERT: An 217 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6948 (m-70) REVERT: Ao 220 MET cc_start: 0.7209 (mtm) cc_final: 0.6963 (mtt) REVERT: Ap 208 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.7130 (mtm-85) outliers start: 33 outliers final: 25 residues processed: 488 average time/residue: 0.7667 time to fit residues: 413.6219 Evaluate side-chains 499 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 469 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 204 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 120 ILE Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 166 VAL Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Aj residue 112 MET Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 173 MET Chi-restraints excluded: chain Ak residue 212 ARG Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain An residue 112 MET Chi-restraints excluded: chain An residue 217 HIS Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 107 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 174 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 255 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 122 ASN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN Ac 122 ASN ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Ag 77 GLN Ai 122 ASN Aj 122 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 77 GLN ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 77 GLN ** Ao 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135985 restraints weight = 28614.861| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.13 r_work: 0.3593 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22320 Z= 0.153 Angle : 0.630 13.395 30256 Z= 0.301 Chirality : 0.042 0.131 3248 Planarity : 0.005 0.047 3952 Dihedral : 4.488 21.394 3008 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.45 % Allowed : 25.04 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 aren not related in a simple way. whole: 0.66 (0.17), residues: 2672 helix: 1.53 (0.16), residues: 1104 sheet: 1.15 (0.35), residues: 160 loop : -0.52 (0.18), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAe 208 TYR 0.025 0.001 TYRAo 143 PHE 0.017 0.003 PHEAh 202 TRP 0.012 0.001 TRPAf 132 HIS 0.002 0.001 HISAl 69 Details of bonding type rmsd covalent geometry : bond 0.00369 (22320) covalent geometry : angle 0.62985 (30256) hydrogen bonds : bond 0.03335 ( 952) hydrogen bonds : angle 4.42473 ( 2616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8070.12 seconds wall clock time: 138 minutes 0.51 seconds (8280.51 seconds total)