Starting phenix.real_space_refine on Fri Jan 24 12:19:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oph_17053/01_2025/8oph_17053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oph_17053/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oph_17053/01_2025/8oph_17053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oph_17053/01_2025/8oph_17053.map" model { file = "/net/cci-nas-00/data/ceres_data/8oph_17053/01_2025/8oph_17053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oph_17053/01_2025/8oph_17053.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 12.24, per 1000 atoms: 0.56 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: 4.65 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.92 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: 6.18 Time building geometry restraints manager: 5.50 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: 0.03 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: 2.620 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: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 43.490 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.210 ------------------------------------------------------------------------------- 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= 0.270 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRPAh 118 HIS 0.003 0.001 HISAh 217 PHE 0.012 0.002 PHEAl 200 TYR 0.031 0.002 TYRAl 184 ARG 0.004 0.001 ARGAc 214 *********************** 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 : 2.276 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: 1.5511 time to fit residues: 742.0000 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 : 2.461 ------------------------------------------------------------------------------- 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 216 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.148071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134239 restraints weight = 28871.734| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.10 r_work: 0.3587 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22320 Z= 0.321 Angle : 0.638 8.728 30256 Z= 0.329 Chirality : 0.044 0.133 3248 Planarity : 0.006 0.057 3952 Dihedral : 4.602 25.575 3011 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.57 % Allowed : 18.45 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 2672 helix: -0.11 (0.14), residues: 1392 sheet: 0.29 (0.35), residues: 160 loop : -1.63 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAj 132 HIS 0.003 0.001 HISAp 217 PHE 0.023 0.003 PHEAd 202 TYR 0.019 0.002 TYRAc 143 ARG 0.008 0.001 ARGAn 188 *********************** 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 591 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 507 time to evaluate : 1.870 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6838 (mmm) cc_final: 0.6483 (mmm) REVERT: Aa 71 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7860 (mm) REVERT: Aa 72 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6986 (tm-30) REVERT: Ac 56 MET cc_start: 0.6754 (mmm) cc_final: 0.6482 (mmm) REVERT: Ac 220 MET cc_start: 0.6585 (mtm) cc_final: 0.6051 (mtm) REVERT: Ad 116 MET cc_start: 0.8009 (ttp) cc_final: 0.7599 (ttm) REVERT: Ad 122 ASN cc_start: 0.8513 (m-40) cc_final: 0.8238 (m-40) REVERT: Ad 183 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7551 (mtp85) REVERT: Ad 188 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.7993 (mtt90) REVERT: Ad 191 ARG cc_start: 0.7529 (mtt90) cc_final: 0.7165 (mtt90) REVERT: Ad 206 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8265 (p) REVERT: Ad 208 ARG cc_start: 0.7409 (mtm-85) cc_final: 0.7188 (mtm-85) REVERT: Ad 214 ARG cc_start: 0.8171 (mtm180) cc_final: 0.7898 (mtm-85) REVERT: Ae 56 MET cc_start: 0.6718 (mmm) cc_final: 0.6462 (mmm) REVERT: Ag 56 MET cc_start: 0.6788 (mmm) cc_final: 0.6391 (mmm) REVERT: Ag 220 MET cc_start: 0.6490 (mtm) cc_final: 0.6150 (mtm) REVERT: Ah 116 MET cc_start: 0.7939 (ttp) cc_final: 0.7637 (ttp) REVERT: Ah 122 ASN cc_start: 0.8538 (m-40) cc_final: 0.8273 (m-40) REVERT: Ah 188 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.8023 (mtt90) REVERT: Ah 206 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8410 (p) REVERT: Ah 208 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7249 (mtm-85) REVERT: Ah 214 ARG cc_start: 0.7966 (mtm180) cc_final: 0.7685 (mtm-85) REVERT: Ai 56 MET cc_start: 0.6766 (mmm) cc_final: 0.6489 (mmm) REVERT: Ai 72 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6844 (tm-30) REVERT: Ak 143 TYR cc_start: 0.8649 (m-80) cc_final: 0.8411 (m-80) REVERT: Ak 214 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8243 (mtm-85) REVERT: Ak 220 MET cc_start: 0.6844 (mtm) cc_final: 0.6484 (mtm) REVERT: Al 56 MET cc_start: 0.7188 (mpp) cc_final: 0.6802 (mpp) REVERT: Al 116 MET cc_start: 0.8086 (ttp) cc_final: 0.7692 (ttm) REVERT: Al 122 ASN cc_start: 0.8473 (m-40) cc_final: 0.8262 (m-40) REVERT: Al 188 ARG cc_start: 0.8565 (mtt90) cc_final: 0.8206 (mtt90) REVERT: Al 206 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8420 (p) REVERT: Am 56 MET cc_start: 0.6787 (mmm) cc_final: 0.6483 (mmm) REVERT: Am 72 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6939 (tm-30) REVERT: Am 95 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7070 (mt-10) REVERT: Ao 72 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6823 (tm-30) REVERT: Ao 139 GLU cc_start: 0.6733 (mp0) cc_final: 0.6504 (mp0) REVERT: Ao 172 GLU cc_start: 0.7699 (tp30) cc_final: 0.7457 (mm-30) REVERT: Ao 220 MET cc_start: 0.7123 (mtm) cc_final: 0.6586 (mtm) REVERT: Ap 116 MET cc_start: 0.8093 (ttp) cc_final: 0.7885 (ttm) REVERT: Ap 188 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7929 (mtt90) REVERT: Ap 206 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8265 (p) REVERT: Ap 208 ARG cc_start: 0.7461 (mtm-85) cc_final: 0.7197 (mtm-85) REVERT: Ap 214 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7839 (mtm-85) outliers start: 84 outliers final: 25 residues processed: 532 average time/residue: 1.6200 time to fit residues: 958.7409 Evaluate side-chains 526 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 496 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU 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 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 78 ILE 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 206 THR Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 133 VAL 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 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 6 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 230 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 239 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 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 77 GLN Aa 122 ASN Ac 77 GLN Af 158 GLN Ag 77 GLN Ak 77 GLN Am 77 GLN An 122 ASN Ao 77 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134857 restraints weight = 28500.635| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.09 r_work: 0.3593 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2268 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= 0.226 Angle : 0.572 9.168 30256 Z= 0.290 Chirality : 0.041 0.130 3248 Planarity : 0.006 0.053 3952 Dihedral : 4.417 25.961 3009 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.87 % Allowed : 20.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2672 helix: 0.49 (0.15), residues: 1296 sheet: 0.48 (0.33), residues: 160 loop : -1.17 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAj 132 HIS 0.002 0.001 HISAb 69 PHE 0.019 0.003 PHEAh 202 TYR 0.018 0.001 TYRAa 198 ARG 0.007 0.000 ARGAf 188 *********************** 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 546 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 502 time to evaluate : 2.383 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6825 (mmm) cc_final: 0.6517 (mmm) REVERT: Aa 72 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6928 (tm-30) REVERT: Aa 155 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8317 (p) REVERT: Ac 56 MET cc_start: 0.6689 (mmm) cc_final: 0.6469 (mmm) REVERT: Ac 220 MET cc_start: 0.6634 (mtm) cc_final: 0.6162 (mtm) REVERT: Ad 116 MET cc_start: 0.8025 (ttp) cc_final: 0.7589 (ttm) REVERT: Ad 183 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7490 (mtp85) REVERT: Ad 188 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8018 (mtt90) REVERT: Ad 191 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7172 (mtt90) REVERT: Ad 206 THR cc_start: 0.8623 (p) cc_final: 0.8268 (p) REVERT: Ad 208 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7297 (mtm-85) REVERT: Ad 214 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7777 (mtm-85) REVERT: Ae 72 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6744 (tm-30) REVERT: Ah 116 MET cc_start: 0.7885 (ttp) cc_final: 0.7558 (ttp) REVERT: Ah 188 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8045 (mtt90) REVERT: Ah 191 ARG cc_start: 0.7605 (mtt90) cc_final: 0.7278 (mtt90) REVERT: Ah 197 ARG cc_start: 0.8588 (ptm160) cc_final: 0.8340 (ptm-80) REVERT: Ah 206 THR cc_start: 0.8709 (p) cc_final: 0.8409 (p) REVERT: Ah 214 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7696 (mtm-85) REVERT: Ai 56 MET cc_start: 0.6844 (mmm) cc_final: 0.6610 (mmm) REVERT: Aj 112 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8061 (mtm) REVERT: Aj 206 THR cc_start: 0.8690 (p) cc_final: 0.8436 (p) REVERT: Ak 56 MET cc_start: 0.6850 (mpp) cc_final: 0.6503 (mpp) REVERT: Ak 108 MET cc_start: 0.8047 (tpt) cc_final: 0.7796 (tpt) REVERT: Ak 134 MET cc_start: 0.7813 (ttt) cc_final: 0.7594 (ttt) REVERT: Ak 220 MET cc_start: 0.6883 (mtm) cc_final: 0.6413 (mtm) REVERT: Al 56 MET cc_start: 0.7104 (mpp) cc_final: 0.6764 (mpp) REVERT: Al 116 MET cc_start: 0.7860 (ttp) cc_final: 0.7527 (ttm) REVERT: Al 188 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8228 (mtt90) REVERT: Al 206 THR cc_start: 0.8642 (p) cc_final: 0.8312 (p) REVERT: Am 56 MET cc_start: 0.6785 (mmm) cc_final: 0.6487 (mmm) REVERT: Am 72 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6883 (tm-30) REVERT: Ao 72 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6840 (tm-30) REVERT: Ao 116 MET cc_start: 0.7358 (ttp) cc_final: 0.6842 (ttp) REVERT: Ao 139 GLU cc_start: 0.6770 (mp0) cc_final: 0.6532 (mp0) REVERT: Ao 220 MET cc_start: 0.7082 (mtm) cc_final: 0.6712 (mtm) REVERT: Ap 116 MET cc_start: 0.8056 (ttp) cc_final: 0.7849 (ttm) REVERT: Ap 206 THR cc_start: 0.8630 (p) cc_final: 0.8279 (p) REVERT: Ap 208 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.7206 (mtm-85) REVERT: Ap 214 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7690 (mtm-85) outliers start: 44 outliers final: 23 residues processed: 514 average time/residue: 1.7282 time to fit residues: 982.4508 Evaluate side-chains 519 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 492 time to evaluate : 2.534 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain Ac residue 107 GLU 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 Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL 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 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 204 GLU 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 173 MET Chi-restraints excluded: chain Ao residue 99 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 211 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 225 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 232 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 122 ASN Ac 77 GLN Ag 77 GLN Ah 122 ASN Aj 158 GLN Ak 77 GLN Am 77 GLN ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN Ao 77 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.136252 restraints weight = 28454.895| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.14 r_work: 0.3613 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22320 Z= 0.198 Angle : 0.559 8.962 30256 Z= 0.279 Chirality : 0.041 0.126 3248 Planarity : 0.005 0.046 3952 Dihedral : 4.358 24.473 3009 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.04 % Allowed : 21.64 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2672 helix: 1.11 (0.16), residues: 1200 sheet: 0.65 (0.34), residues: 160 loop : -0.61 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAj 132 HIS 0.002 0.001 HISAf 69 PHE 0.016 0.003 PHEAh 202 TYR 0.020 0.001 TYRAo 143 ARG 0.009 0.000 ARGAf 188 *********************** 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 547 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 499 time to evaluate : 2.527 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6826 (mmm) cc_final: 0.6498 (mmm) REVERT: Aa 72 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6865 (tm-30) REVERT: Aa 155 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8306 (p) REVERT: Aa 173 MET cc_start: 0.8827 (tmt) cc_final: 0.8618 (ttp) REVERT: Ac 56 MET cc_start: 0.6731 (mmm) cc_final: 0.6468 (mmm) REVERT: Ac 220 MET cc_start: 0.6712 (mtm) cc_final: 0.6312 (mtm) REVERT: Ad 56 MET cc_start: 0.6925 (mmm) cc_final: 0.6538 (mpp) REVERT: Ad 116 MET cc_start: 0.7919 (ttp) cc_final: 0.7502 (ttm) REVERT: Ad 183 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7431 (mtp85) REVERT: Ad 188 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8143 (mtt90) REVERT: Ad 191 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7169 (mtt90) REVERT: Ad 206 THR cc_start: 0.8635 (p) cc_final: 0.8306 (p) REVERT: Ad 208 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.7260 (mtm-85) REVERT: Ad 214 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7798 (mtm-85) REVERT: Ae 72 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6773 (tm-30) REVERT: Ag 220 MET cc_start: 0.6522 (mtm) cc_final: 0.6054 (mtm) REVERT: Ah 112 MET cc_start: 0.8138 (mtp) cc_final: 0.7924 (mtt) REVERT: Ah 188 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8096 (mtt90) REVERT: Ah 206 THR cc_start: 0.8694 (p) cc_final: 0.8437 (p) REVERT: Ai 56 MET cc_start: 0.6785 (mmm) cc_final: 0.6541 (mmm) REVERT: Ai 72 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6806 (tm-30) REVERT: Aj 112 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8153 (mtt) REVERT: Aj 206 THR cc_start: 0.8654 (p) cc_final: 0.8414 (p) REVERT: Ak 56 MET cc_start: 0.6851 (mpp) cc_final: 0.6457 (mpp) REVERT: Ak 108 MET cc_start: 0.8054 (tpt) cc_final: 0.7833 (tpt) REVERT: Al 56 MET cc_start: 0.7050 (mpp) cc_final: 0.6718 (mpp) REVERT: Al 116 MET cc_start: 0.7834 (ttp) cc_final: 0.7502 (ttm) REVERT: Al 206 THR cc_start: 0.8643 (p) cc_final: 0.8346 (p) REVERT: Am 56 MET cc_start: 0.6776 (mmm) cc_final: 0.6468 (mmm) REVERT: Am 72 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6926 (tm-30) REVERT: Am 188 ARG cc_start: 0.8395 (mmt90) cc_final: 0.7418 (mmt90) REVERT: Am 220 MET cc_start: 0.6886 (mtm) cc_final: 0.6246 (mtt) REVERT: Ao 54 MET cc_start: 0.6986 (ptt) cc_final: 0.6765 (ppp) REVERT: Ao 72 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6861 (tm-30) REVERT: Ao 139 GLU cc_start: 0.6801 (mp0) cc_final: 0.6518 (mp0) REVERT: Ao 220 MET cc_start: 0.7155 (mtm) cc_final: 0.6819 (mtm) REVERT: Ap 160 MET cc_start: 0.8285 (tpt) cc_final: 0.8072 (mmm) REVERT: Ap 206 THR cc_start: 0.8600 (p) cc_final: 0.8243 (p) REVERT: Ap 208 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.7182 (mtm-85) outliers start: 48 outliers final: 31 residues processed: 512 average time/residue: 1.6853 time to fit residues: 956.9462 Evaluate side-chains 532 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 497 time to evaluate : 2.480 ------------------------------------------------------------------------------- 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 188 ARG 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 141 VAL Chi-restraints excluded: chain Ag residue 204 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 Ah residue 211 VAL 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 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 173 MET Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 133 VAL 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 73 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 90 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 122 ASN Ac 77 GLN Ae 122 ASN Af 122 ASN Ag 77 GLN ** Ag 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Ak 77 GLN ** Ak 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 77 GLN ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN Ao 77 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141319 restraints weight = 28380.179| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.08 r_work: 0.3617 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22320 Z= 0.217 Angle : 0.559 9.249 30256 Z= 0.279 Chirality : 0.041 0.123 3248 Planarity : 0.005 0.047 3952 Dihedral : 4.377 23.575 3009 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.04 % Allowed : 22.11 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2672 helix: 1.18 (0.16), residues: 1200 sheet: 0.83 (0.33), residues: 160 loop : -0.53 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAn 132 HIS 0.002 0.001 HISAj 69 PHE 0.017 0.003 PHEAh 202 TYR 0.023 0.001 TYRAo 143 ARG 0.010 0.000 ARGAf 188 *********************** 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 543 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 495 time to evaluate : 2.333 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6821 (mmm) cc_final: 0.6544 (mmm) REVERT: Aa 72 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6889 (tm-30) REVERT: Aa 112 MET cc_start: 0.7961 (mtm) cc_final: 0.7725 (mtm) REVERT: Aa 155 THR cc_start: 0.8566 (p) cc_final: 0.8339 (p) REVERT: Ac 56 MET cc_start: 0.6706 (mmm) cc_final: 0.6481 (mmm) REVERT: Ac 220 MET cc_start: 0.6715 (mtm) cc_final: 0.6253 (mtm) REVERT: Ad 191 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7131 (mtt90) REVERT: Ad 206 THR cc_start: 0.8604 (p) cc_final: 0.8297 (p) REVERT: Ag 220 MET cc_start: 0.6646 (mtm) cc_final: 0.6156 (mtm) REVERT: Ah 112 MET cc_start: 0.8106 (mtp) cc_final: 0.7902 (mtt) REVERT: Ah 188 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8042 (mtt90) REVERT: Ah 206 THR cc_start: 0.8689 (p) cc_final: 0.8456 (p) REVERT: Ai 56 MET cc_start: 0.6883 (mmm) cc_final: 0.6660 (mmm) REVERT: Ai 72 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6776 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7181 (mt-10) REVERT: Aj 112 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8189 (mtt) REVERT: Aj 206 THR cc_start: 0.8672 (p) cc_final: 0.8451 (p) REVERT: Ak 56 MET cc_start: 0.6907 (mpp) cc_final: 0.6683 (mpp) REVERT: Ak 220 MET cc_start: 0.6863 (mtm) cc_final: 0.6451 (mtm) REVERT: Al 56 MET cc_start: 0.7026 (mpp) cc_final: 0.6693 (mpp) REVERT: Al 116 MET cc_start: 0.7851 (ttp) cc_final: 0.7502 (ttm) REVERT: Al 160 MET cc_start: 0.8332 (tpt) cc_final: 0.8106 (mmm) REVERT: Al 206 THR cc_start: 0.8635 (p) cc_final: 0.8358 (p) REVERT: Am 56 MET cc_start: 0.6746 (mmm) cc_final: 0.6475 (mmm) REVERT: Am 72 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6832 (tm-30) REVERT: Am 121 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7135 (mt-10) REVERT: Ao 54 MET cc_start: 0.7088 (ptt) cc_final: 0.6832 (ppp) REVERT: Ao 116 MET cc_start: 0.7351 (ttp) cc_final: 0.6763 (ttp) REVERT: Ao 220 MET cc_start: 0.7211 (mtm) cc_final: 0.6724 (mtm) REVERT: Ap 206 THR cc_start: 0.8621 (p) cc_final: 0.8289 (p) outliers start: 48 outliers final: 34 residues processed: 509 average time/residue: 1.7074 time to fit residues: 967.4766 Evaluate side-chains 522 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 486 time to evaluate : 2.383 ------------------------------------------------------------------------------- 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 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 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 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 141 VAL Chi-restraints excluded: chain Ag residue 204 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 Ah residue 211 VAL 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 54 MET Chi-restraints excluded: chain Ak residue 107 GLU 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 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 99 LEU 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 190 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 234 optimal weight: 0.5980 chunk 87 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 243 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** Ad 69 HIS ** 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 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 Ao 77 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141417 restraints weight = 28328.056| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.09 r_work: 0.3615 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2779 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= 0.205 Angle : 0.567 11.476 30256 Z= 0.280 Chirality : 0.041 0.128 3248 Planarity : 0.005 0.050 3952 Dihedral : 4.341 16.580 3008 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.13 % Allowed : 22.70 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.17), residues: 2672 helix: 1.26 (0.16), residues: 1200 sheet: 0.99 (0.33), residues: 160 loop : -0.49 (0.19), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAn 132 HIS 0.002 0.001 HISAb 217 PHE 0.016 0.003 PHEAh 202 TYR 0.022 0.001 TYRAo 143 ARG 0.010 0.000 ARGAn 188 *********************** 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 537 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 487 time to evaluate : 2.260 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6816 (mmm) cc_final: 0.6525 (mmm) REVERT: Aa 72 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6843 (tm-30) REVERT: Aa 112 MET cc_start: 0.8021 (mtm) cc_final: 0.7768 (mtm) REVERT: Aa 155 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8336 (p) REVERT: Ac 56 MET cc_start: 0.6673 (mmm) cc_final: 0.6462 (mmm) REVERT: Ac 220 MET cc_start: 0.6750 (mtm) cc_final: 0.6374 (mtm) REVERT: Ad 191 ARG cc_start: 0.7535 (mtt90) cc_final: 0.7215 (mtt90) REVERT: Ad 206 THR cc_start: 0.8613 (p) cc_final: 0.8289 (p) REVERT: Ae 56 MET cc_start: 0.6546 (mmm) cc_final: 0.6344 (mmm) REVERT: Ah 112 MET cc_start: 0.8081 (mtp) cc_final: 0.7878 (mtt) REVERT: Ah 188 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8013 (mtt90) REVERT: Ah 206 THR cc_start: 0.8684 (p) cc_final: 0.8434 (p) REVERT: Ai 72 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6790 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7140 (mt-10) REVERT: Aj 112 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8155 (mtt) REVERT: Aj 206 THR cc_start: 0.8674 (p) cc_final: 0.8458 (p) REVERT: Ak 77 GLN cc_start: 0.8752 (tt0) cc_final: 0.8524 (tt0) REVERT: Ak 108 MET cc_start: 0.8039 (tpt) cc_final: 0.7806 (tpt) REVERT: Ak 220 MET cc_start: 0.6902 (mtm) cc_final: 0.6473 (mtm) REVERT: Al 56 MET cc_start: 0.7055 (mpp) cc_final: 0.6728 (mpp) REVERT: Al 116 MET cc_start: 0.7844 (ttp) cc_final: 0.7498 (ttm) REVERT: Al 206 THR cc_start: 0.8619 (p) cc_final: 0.8339 (p) REVERT: Am 56 MET cc_start: 0.6770 (mmm) cc_final: 0.6504 (mmm) REVERT: Am 121 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7160 (mt-10) REVERT: Am 188 ARG cc_start: 0.8373 (mmt90) cc_final: 0.7429 (mmt90) REVERT: Ao 54 MET cc_start: 0.7028 (ptt) cc_final: 0.6700 (ppp) REVERT: Ao 220 MET cc_start: 0.7245 (mtm) cc_final: 0.6767 (mtm) REVERT: Ap 188 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8104 (mtt90) REVERT: Ap 206 THR cc_start: 0.8480 (p) cc_final: 0.8143 (p) outliers start: 50 outliers final: 33 residues processed: 504 average time/residue: 1.6972 time to fit residues: 950.8320 Evaluate side-chains 515 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 479 time to evaluate : 2.340 ------------------------------------------------------------------------------- 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 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 141 VAL Chi-restraints excluded: chain Ag residue 204 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 Ah residue 211 VAL 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 54 MET Chi-restraints excluded: chain Ak residue 107 GLU 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 Ao residue 99 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 163 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 188 optimal weight: 0.0070 chunk 50 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN ** Ae 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Ag 77 GLN Ag 122 ASN ** 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136455 restraints weight = 28693.181| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.14 r_work: 0.3607 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2891 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= 0.207 Angle : 0.574 10.852 30256 Z= 0.282 Chirality : 0.041 0.121 3248 Planarity : 0.005 0.049 3952 Dihedral : 4.340 16.981 3008 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.04 % Allowed : 23.09 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2672 helix: 1.29 (0.16), residues: 1200 sheet: 1.17 (0.34), residues: 160 loop : -0.44 (0.19), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAn 132 HIS 0.002 0.001 HISAp 69 PHE 0.016 0.003 PHEAb 202 TYR 0.024 0.001 TYRAo 143 ARG 0.009 0.000 ARGAf 188 *********************** 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 531 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 483 time to evaluate : 2.796 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6835 (mmm) cc_final: 0.6544 (mmm) REVERT: Aa 112 MET cc_start: 0.7960 (mtm) cc_final: 0.7694 (mtm) REVERT: Aa 155 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8301 (p) REVERT: Aa 212 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6424 (ptm-80) REVERT: Ab 56 MET cc_start: 0.7174 (mmt) cc_final: 0.6847 (mmt) REVERT: Ab 108 MET cc_start: 0.7566 (tpp) cc_final: 0.7363 (tpp) REVERT: Ac 56 MET cc_start: 0.6713 (mmm) cc_final: 0.6457 (mmm) REVERT: Ac 220 MET cc_start: 0.6720 (mtm) cc_final: 0.6265 (mtm) REVERT: Ad 132 TRP cc_start: 0.8513 (p-90) cc_final: 0.8137 (p-90) REVERT: Ad 191 ARG cc_start: 0.7551 (mtt90) cc_final: 0.7214 (mtt90) REVERT: Ad 206 THR cc_start: 0.8593 (p) cc_final: 0.8280 (p) REVERT: Ah 112 MET cc_start: 0.8055 (mtp) cc_final: 0.7835 (mtt) REVERT: Ah 188 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8109 (mtt90) REVERT: Ah 206 THR cc_start: 0.8670 (p) cc_final: 0.8419 (p) REVERT: Ai 72 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6747 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7128 (mt-10) REVERT: Aj 112 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8066 (mtt) REVERT: Aj 158 GLN cc_start: 0.8640 (mt0) cc_final: 0.8439 (mt0) REVERT: Aj 206 THR cc_start: 0.8654 (p) cc_final: 0.8434 (p) REVERT: Ak 77 GLN cc_start: 0.8757 (tt0) cc_final: 0.8470 (tt0) REVERT: Al 56 MET cc_start: 0.7043 (mpp) cc_final: 0.6683 (mpp) REVERT: Al 116 MET cc_start: 0.7820 (ttp) cc_final: 0.7483 (ttm) REVERT: Al 206 THR cc_start: 0.8600 (p) cc_final: 0.8321 (p) REVERT: Am 56 MET cc_start: 0.6801 (mmm) cc_final: 0.6529 (mmm) REVERT: Am 72 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6853 (tm-30) REVERT: Am 121 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7220 (mt-10) REVERT: Am 188 ARG cc_start: 0.8410 (mmt90) cc_final: 0.7389 (mmt90) REVERT: Ao 54 MET cc_start: 0.6997 (ptt) cc_final: 0.6690 (ppp) REVERT: Ao 220 MET cc_start: 0.7141 (mtm) cc_final: 0.6880 (mtm) REVERT: Ap 188 ARG cc_start: 0.8412 (mtt90) cc_final: 0.8064 (mtt90) outliers start: 48 outliers final: 28 residues processed: 500 average time/residue: 1.7424 time to fit residues: 964.7575 Evaluate side-chains 512 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 480 time to evaluate : 2.374 ------------------------------------------------------------------------------- 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 Aa residue 212 ARG 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 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 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 141 VAL 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 Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 112 MET 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 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 134 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 93 optimal weight: 0.0970 chunk 137 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 145 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 247 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN ** Ae 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Ag 77 GLN 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 Ao 77 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137170 restraints weight = 28651.751| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.14 r_work: 0.3623 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22320 Z= 0.181 Angle : 0.578 12.602 30256 Z= 0.279 Chirality : 0.040 0.120 3248 Planarity : 0.005 0.048 3952 Dihedral : 4.281 18.718 3008 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.79 % Allowed : 24.02 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2672 helix: 1.41 (0.16), residues: 1200 sheet: 0.58 (0.32), residues: 192 loop : -0.42 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAf 132 HIS 0.002 0.001 HISAp 69 PHE 0.014 0.002 PHEAf 202 TYR 0.021 0.001 TYRAe 198 ARG 0.009 0.000 ARGAb 188 *********************** 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 510 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 468 time to evaluate : 3.032 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6875 (mmm) cc_final: 0.6573 (mmm) REVERT: Aa 72 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6808 (tm-30) REVERT: Aa 95 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7099 (mt-10) REVERT: Aa 112 MET cc_start: 0.7950 (mtm) cc_final: 0.7677 (mtm) REVERT: Aa 155 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8318 (p) REVERT: Ab 56 MET cc_start: 0.7162 (mmt) cc_final: 0.6873 (mmt) REVERT: Ac 56 MET cc_start: 0.6728 (mmm) cc_final: 0.6479 (mmm) REVERT: Ad 132 TRP cc_start: 0.8487 (p-90) cc_final: 0.8109 (p-90) REVERT: Ad 191 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7219 (mtt90) REVERT: Ad 206 THR cc_start: 0.8510 (p) cc_final: 0.8222 (p) REVERT: Af 65 LEU cc_start: 0.8181 (mp) cc_final: 0.7903 (mt) REVERT: Af 188 ARG cc_start: 0.8401 (mtt90) cc_final: 0.8147 (mtt-85) REVERT: Af 206 THR cc_start: 0.8647 (p) cc_final: 0.8407 (p) REVERT: Ah 112 MET cc_start: 0.8013 (mtp) cc_final: 0.7806 (mtt) REVERT: Ah 188 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8124 (mtt90) REVERT: Ah 206 THR cc_start: 0.8654 (p) cc_final: 0.8390 (p) REVERT: Ai 72 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6643 (tm-30) REVERT: Ai 121 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7171 (mt-10) REVERT: Aj 108 MET cc_start: 0.7386 (tpp) cc_final: 0.7114 (tpp) REVERT: Aj 112 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8118 (mtt) REVERT: Aj 206 THR cc_start: 0.8605 (p) cc_final: 0.8400 (p) REVERT: Ak 77 GLN cc_start: 0.8759 (tt0) cc_final: 0.8463 (tt0) REVERT: Ak 108 MET cc_start: 0.7984 (tpt) cc_final: 0.7755 (tpt) REVERT: Al 56 MET cc_start: 0.7034 (mpp) cc_final: 0.6675 (mpp) REVERT: Al 116 MET cc_start: 0.7807 (ttp) cc_final: 0.7486 (ttm) REVERT: Al 206 THR cc_start: 0.8571 (p) cc_final: 0.8283 (p) REVERT: Am 56 MET cc_start: 0.6779 (mmm) cc_final: 0.6488 (mmm) REVERT: Am 72 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6752 (tm-30) REVERT: Am 121 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7219 (mt-10) REVERT: Am 188 ARG cc_start: 0.8371 (mmt90) cc_final: 0.7322 (mmt90) REVERT: An 188 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8112 (mtt-85) REVERT: Ao 54 MET cc_start: 0.6954 (ptt) cc_final: 0.6672 (ppp) REVERT: Ao 151 ASN cc_start: 0.7581 (m-40) cc_final: 0.7315 (m-40) REVERT: Ao 220 MET cc_start: 0.7206 (mtm) cc_final: 0.6953 (mtt) REVERT: Ap 84 ARG cc_start: 0.8485 (ptp-170) cc_final: 0.8177 (ptp-170) REVERT: Ap 188 ARG cc_start: 0.8393 (mtt90) cc_final: 0.7953 (mtt90) outliers start: 42 outliers final: 27 residues processed: 486 average time/residue: 1.8995 time to fit residues: 1020.1395 Evaluate side-chains 496 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 466 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 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 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 141 VAL 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 212 ARG 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 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 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 236 optimal weight: 0.1980 chunk 76 optimal weight: 0.4980 chunk 135 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 210 optimal weight: 0.0570 chunk 194 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 77 GLN ** 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 = 0.3919 r_free = 0.3919 target = 0.152209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137879 restraints weight = 28730.340| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.17 r_work: 0.3642 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3075 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= 0.157 Angle : 0.567 12.338 30256 Z= 0.274 Chirality : 0.040 0.120 3248 Planarity : 0.005 0.047 3952 Dihedral : 4.234 20.949 3008 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.45 % Allowed : 24.40 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2672 helix: 1.04 (0.15), residues: 1296 sheet: 0.62 (0.33), residues: 192 loop : -0.78 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAa 132 HIS 0.002 0.001 HISAp 69 PHE 0.014 0.002 PHEAl 200 TYR 0.020 0.001 TYRAa 198 ARG 0.009 0.000 ARGAe 208 *********************** 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 496 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 462 time to evaluate : 2.398 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6580 (mmm) cc_final: 0.6286 (mmm) REVERT: Aa 95 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6796 (mt-10) REVERT: Aa 112 MET cc_start: 0.7703 (mtm) cc_final: 0.7430 (mtm) REVERT: Aa 155 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8271 (p) REVERT: Ab 56 MET cc_start: 0.6902 (mmt) cc_final: 0.6691 (mmt) REVERT: Ac 56 MET cc_start: 0.6484 (mmm) cc_final: 0.6279 (mmm) REVERT: Ad 132 TRP cc_start: 0.8333 (p-90) cc_final: 0.7873 (p-90) REVERT: Ad 134 MET cc_start: 0.7527 (ttt) cc_final: 0.7300 (ttp) REVERT: Ad 191 ARG cc_start: 0.7251 (mtt90) cc_final: 0.6905 (mtt90) REVERT: Ad 206 THR cc_start: 0.8376 (p) cc_final: 0.8052 (p) REVERT: Af 65 LEU cc_start: 0.8017 (mp) cc_final: 0.7802 (mt) REVERT: Af 188 ARG cc_start: 0.8326 (mtt90) cc_final: 0.8083 (mtt-85) REVERT: Af 206 THR cc_start: 0.8612 (p) cc_final: 0.8388 (p) REVERT: Ah 135 MET cc_start: 0.8312 (mmm) cc_final: 0.8066 (mmt) REVERT: Ah 188 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7931 (mtt90) REVERT: Ah 206 THR cc_start: 0.8566 (p) cc_final: 0.8271 (p) REVERT: Ai 56 MET cc_start: 0.6548 (mmm) cc_final: 0.6139 (mmm) REVERT: Ai 188 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7020 (mmt90) REVERT: Ai 220 MET cc_start: 0.6549 (mtp) cc_final: 0.6081 (mpp) REVERT: Aj 112 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8000 (mtt) REVERT: Ak 77 GLN cc_start: 0.8646 (tt0) cc_final: 0.8358 (tt0) REVERT: Ak 108 MET cc_start: 0.7783 (tpt) cc_final: 0.7556 (tpt) REVERT: Al 56 MET cc_start: 0.6897 (mpp) cc_final: 0.6500 (mpp) REVERT: Al 116 MET cc_start: 0.7646 (ttp) cc_final: 0.7353 (ttm) REVERT: Al 206 THR cc_start: 0.8507 (p) cc_final: 0.8183 (p) REVERT: Am 56 MET cc_start: 0.6475 (mmm) cc_final: 0.6091 (mmm) REVERT: An 188 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.8096 (mtt-85) REVERT: An 217 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6902 (m-70) REVERT: Ao 151 ASN cc_start: 0.7424 (m-40) cc_final: 0.7177 (m-40) REVERT: Ao 220 MET cc_start: 0.7239 (mtm) cc_final: 0.7022 (mtt) REVERT: Ap 56 MET cc_start: 0.6833 (mmt) cc_final: 0.6330 (mmt) REVERT: Ap 84 ARG cc_start: 0.8370 (ptp-170) cc_final: 0.8038 (ptp-170) REVERT: Ap 158 GLN cc_start: 0.8497 (mt0) cc_final: 0.8293 (mt0) outliers start: 34 outliers final: 20 residues processed: 477 average time/residue: 1.7866 time to fit residues: 941.1429 Evaluate side-chains 484 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 460 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 107 GLU 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 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 141 VAL Chi-restraints excluded: chain Ah residue 166 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 Ai residue 212 ARG Chi-restraints excluded: chain Aj residue 112 MET Chi-restraints excluded: chain Ak residue 107 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 An residue 217 HIS Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 10 optimal weight: 0.0000 chunk 44 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 201 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 0.0370 chunk 14 optimal weight: 0.5980 chunk 223 optimal weight: 0.3980 overall best weight: 0.3262 ------------------------------------------------------------------------------- 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 Ag 77 GLN Ag 122 ASN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Ak 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 Ao 77 GLN Ap 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.152244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138355 restraints weight = 28749.761| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.07 r_work: 0.3655 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22320 Z= 0.168 Angle : 0.589 12.593 30256 Z= 0.283 Chirality : 0.040 0.143 3248 Planarity : 0.005 0.045 3952 Dihedral : 4.260 21.743 3008 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.45 % Allowed : 24.96 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2672 helix: 1.03 (0.15), residues: 1296 sheet: 0.57 (0.33), residues: 192 loop : -0.76 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAa 132 HIS 0.002 0.001 HISAp 69 PHE 0.014 0.002 PHEAl 200 TYR 0.020 0.001 TYRAo 143 ARG 0.008 0.000 ARGAe 208 ********************** 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 509 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 475 time to evaluate : 2.382 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6786 (mmm) cc_final: 0.6464 (mmm) REVERT: Aa 155 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8342 (p) REVERT: Aa 212 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.7039 (ptt-90) REVERT: Ab 56 MET cc_start: 0.7052 (mmt) cc_final: 0.6850 (mmt) REVERT: Ac 56 MET cc_start: 0.6739 (mmm) cc_final: 0.6503 (mmm) REVERT: Ac 122 ASN cc_start: 0.8339 (m-40) cc_final: 0.8123 (m-40) REVERT: Ad 132 TRP cc_start: 0.8441 (p-90) cc_final: 0.8045 (p-90) REVERT: Ad 134 MET cc_start: 0.7959 (ttt) cc_final: 0.7754 (ttp) REVERT: Ad 191 ARG cc_start: 0.7481 (mtt90) cc_final: 0.7162 (mtt90) REVERT: Ad 206 THR cc_start: 0.8396 (p) cc_final: 0.8102 (p) REVERT: Af 65 LEU cc_start: 0.8165 (mp) cc_final: 0.7877 (mt) REVERT: Af 206 THR cc_start: 0.8648 (p) cc_final: 0.8438 (p) REVERT: Ah 135 MET cc_start: 0.8323 (mmm) cc_final: 0.8075 (mmt) REVERT: Ah 188 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8102 (mtt90) REVERT: Ah 206 THR cc_start: 0.8602 (p) cc_final: 0.8327 (p) REVERT: Ai 56 MET cc_start: 0.6761 (mmm) cc_final: 0.6447 (mmm) REVERT: Ai 188 ARG cc_start: 0.8171 (mmt90) cc_final: 0.7724 (mmt90) REVERT: Aj 112 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8093 (mtt) REVERT: Ak 108 MET cc_start: 0.7962 (tpt) cc_final: 0.7753 (tpt) REVERT: Ak 121 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6927 (mt-10) REVERT: Ak 139 GLU cc_start: 0.7107 (mp0) cc_final: 0.6652 (mp0) REVERT: Al 116 MET cc_start: 0.7810 (ttp) cc_final: 0.7510 (ttm) REVERT: Al 132 TRP cc_start: 0.8352 (p-90) cc_final: 0.8073 (p-90) REVERT: Al 206 THR cc_start: 0.8547 (p) cc_final: 0.7943 (p) REVERT: Al 208 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.6987 (mtm-85) REVERT: Am 56 MET cc_start: 0.6779 (mmm) cc_final: 0.6366 (mpp) REVERT: Am 77 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7957 (tp-100) REVERT: Am 188 ARG cc_start: 0.8323 (mmt90) cc_final: 0.7330 (mmt90) REVERT: Ao 151 ASN cc_start: 0.7520 (m-40) cc_final: 0.7265 (m-40) REVERT: Ap 56 MET cc_start: 0.6972 (mmt) cc_final: 0.6497 (mmt) REVERT: Ap 73 TYR cc_start: 0.7570 (t80) cc_final: 0.7349 (t80) REVERT: Ap 84 ARG cc_start: 0.8403 (ptp-170) cc_final: 0.8091 (ptp-170) REVERT: Ap 191 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7273 (mmt180) outliers start: 34 outliers final: 24 residues processed: 491 average time/residue: 1.7903 time to fit residues: 969.1192 Evaluate side-chains 499 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 471 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 212 ARG 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 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 141 VAL Chi-restraints excluded: chain Ah residue 166 VAL 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 212 ARG 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 Al residue 176 LYS 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 133 VAL Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ap residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 85 optimal weight: 0.2980 chunk 140 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 239 optimal weight: 0.0670 chunk 64 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 254 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Af 158 GLN Ag 77 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Aj 158 GLN Ak 77 GLN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN ** 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 Ap 77 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136997 restraints weight = 28930.228| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.18 r_work: 0.3639 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22320 Z= 0.179 Angle : 0.590 12.473 30256 Z= 0.285 Chirality : 0.040 0.144 3248 Planarity : 0.005 0.046 3952 Dihedral : 4.304 21.652 3008 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.53 % Allowed : 25.47 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2672 helix: 1.04 (0.15), residues: 1296 sheet: 0.61 (0.33), residues: 192 loop : -0.74 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAj 132 HIS 0.002 0.001 HISAp 69 PHE 0.015 0.002 PHEAl 200 TYR 0.026 0.001 TYRAa 198 ARG 0.009 0.000 ARGAe 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16653.45 seconds wall clock time: 296 minutes 38.77 seconds (17798.77 seconds total)