Starting phenix.real_space_refine on Thu Apr 11 06:16:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oph_17053/04_2024/8oph_17053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oph_17053/04_2024/8oph_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oph_17053/04_2024/8oph_17053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oph_17053/04_2024/8oph_17053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oph_17053/04_2024/8oph_17053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oph_17053/04_2024/8oph_17053.pdb" } 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 Residue "Aa GLU 168": "OE1" <-> "OE2" Residue "Aa GLU 204": "OE1" <-> "OE2" Residue "Ac GLU 168": "OE1" <-> "OE2" Residue "Ac GLU 204": "OE1" <-> "OE2" Residue "Ae GLU 168": "OE1" <-> "OE2" Residue "Ae GLU 204": "OE1" <-> "OE2" Residue "Ag GLU 168": "OE1" <-> "OE2" Residue "Ag GLU 204": "OE1" <-> "OE2" Residue "Ai GLU 168": "OE1" <-> "OE2" Residue "Ai GLU 204": "OE1" <-> "OE2" Residue "Ak GLU 168": "OE1" <-> "OE2" Residue "Ak GLU 204": "OE1" <-> "OE2" Residue "Am GLU 168": "OE1" <-> "OE2" Residue "Am GLU 204": "OE1" <-> "OE2" Residue "Ao GLU 168": "OE1" <-> "OE2" Residue "Ao GLU 204": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 11.67, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 8.05 Conformation dependent library (CDL) restraints added in 3.7 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: 2.03 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: 5.92 Time building geometry restraints manager: 8.83 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: 99.12 - 106.10: 724 106.10 - 113.07: 11617 113.07 - 120.05: 7958 120.05 - 127.02: 9667 127.02 - 134.00: 290 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 2.440 nonbonded pdb=" OH TYRAi 203 " pdb=" OG1 THRAi 209 " model vdw 2.222 2.440 nonbonded pdb=" OH TYRAe 203 " pdb=" OG1 THRAe 209 " model vdw 2.222 2.440 nonbonded pdb=" OH TYRAm 203 " pdb=" OG1 THRAm 209 " model vdw 2.222 2.440 nonbonded pdb=" OH TYRAo 203 " pdb=" OG1 THRAo 209 " model vdw 2.222 2.440 ... (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 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: 3.700 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: 10.070 Check model and map are aligned: 0.300 Set scattering table: 0.220 Process input model: 56.060 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.730 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 14 poor density : 426 time to evaluate : 2.287 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: 1.4850 time to fit residues: 710.4016 Evaluate side-chains 424 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 421 time to evaluate : 2.378 ------------------------------------------------------------------------------- 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: 0.9980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22320 Z= 0.353 Angle : 0.640 7.279 30256 Z= 0.330 Chirality : 0.045 0.141 3248 Planarity : 0.006 0.057 3952 Dihedral : 4.670 26.564 3011 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.91 % Allowed : 19.56 % Favored : 76.53 % 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: -1.15 (0.16), residues: 2672 helix: -0.18 (0.14), residues: 1392 sheet: 0.27 (0.36), residues: 160 loop : -1.60 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAj 132 HIS 0.004 0.001 HISAa 217 PHE 0.025 0.004 PHEAd 202 TYR 0.020 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 623 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 531 time to evaluate : 2.314 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6456 (mmm) cc_final: 0.6123 (mmm) REVERT: Aa 72 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6750 (tm-30) REVERT: Aa 73 TYR cc_start: 0.8139 (t80) cc_final: 0.7855 (t80) REVERT: Ac 56 MET cc_start: 0.6393 (mmm) cc_final: 0.6161 (mmm) REVERT: Ac 220 MET cc_start: 0.6478 (mtm) cc_final: 0.6153 (mtm) REVERT: Ad 116 MET cc_start: 0.8019 (ttp) cc_final: 0.7594 (ttm) REVERT: Ad 122 ASN cc_start: 0.8489 (m-40) cc_final: 0.8224 (m-40) REVERT: Ad 160 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8211 (mmm) REVERT: Ad 188 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8005 (mtt90) REVERT: Ad 191 ARG cc_start: 0.6865 (mtt90) cc_final: 0.6504 (mtt90) REVERT: Ad 197 ARG cc_start: 0.8620 (ptm160) cc_final: 0.8415 (ptm160) REVERT: Ad 206 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8174 (p) REVERT: Ad 208 ARG cc_start: 0.7155 (mtm-85) cc_final: 0.6946 (mtm-85) REVERT: Ad 214 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7722 (mtm-85) REVERT: Ae 56 MET cc_start: 0.6240 (mmm) cc_final: 0.6021 (mmm) REVERT: Ag 122 ASN cc_start: 0.8422 (m-40) cc_final: 0.8193 (m110) REVERT: Ag 141 VAL cc_start: 0.8604 (t) cc_final: 0.8383 (p) REVERT: Ag 220 MET cc_start: 0.6341 (mtm) cc_final: 0.5973 (mtm) REVERT: Ah 116 MET cc_start: 0.7980 (ttp) cc_final: 0.7640 (ttm) REVERT: Ah 181 MET cc_start: 0.8070 (tpp) cc_final: 0.7851 (tpt) REVERT: Ah 188 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8061 (mtt90) REVERT: Ah 206 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8292 (p) REVERT: Ah 208 ARG cc_start: 0.7093 (mtm-85) cc_final: 0.6888 (mtm-85) REVERT: Ah 214 ARG cc_start: 0.7839 (mtm180) cc_final: 0.7589 (mtm-85) REVERT: Ai 56 MET cc_start: 0.6349 (mmm) cc_final: 0.6094 (mmm) REVERT: Ai 72 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6630 (tm-30) REVERT: Ak 214 ARG cc_start: 0.8612 (mtm-85) cc_final: 0.8265 (mtm-85) REVERT: Ak 220 MET cc_start: 0.6691 (mtm) cc_final: 0.6297 (mtm) REVERT: Al 56 MET cc_start: 0.7240 (mpp) cc_final: 0.6886 (mpp) REVERT: Al 116 MET cc_start: 0.8166 (ttp) cc_final: 0.7741 (ttm) REVERT: Al 122 ASN cc_start: 0.8432 (m-40) cc_final: 0.8196 (m-40) REVERT: Al 188 ARG cc_start: 0.8541 (mtt90) cc_final: 0.8336 (mtt90) REVERT: Al 206 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8224 (p) REVERT: Al 208 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.6818 (mtm-85) REVERT: Al 214 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7624 (mtm-85) REVERT: Am 56 MET cc_start: 0.6389 (mmm) cc_final: 0.6089 (mmm) REVERT: Am 72 GLU cc_start: 0.7010 (tm-30) cc_final: 0.6790 (tm-30) REVERT: Am 95 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6516 (mt-10) REVERT: Am 141 VAL cc_start: 0.8597 (t) cc_final: 0.8394 (p) REVERT: An 160 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8119 (mmm) REVERT: Ao 72 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6664 (tm-30) REVERT: Ao 139 GLU cc_start: 0.6452 (mp0) cc_final: 0.6218 (mp0) REVERT: Ao 220 MET cc_start: 0.7042 (mtm) cc_final: 0.6551 (mtm) REVERT: Ap 54 MET cc_start: 0.5667 (ptt) cc_final: 0.5451 (ptt) REVERT: Ap 122 ASN cc_start: 0.8447 (m-40) cc_final: 0.8189 (m-40) REVERT: Ap 188 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7899 (mtt90) REVERT: Ap 197 ARG cc_start: 0.8714 (ptm160) cc_final: 0.8474 (ptm160) REVERT: Ap 206 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8189 (p) REVERT: Ap 208 ARG cc_start: 0.7120 (mtm-85) cc_final: 0.6882 (mtm-85) REVERT: Ap 214 ARG cc_start: 0.7818 (mtm180) cc_final: 0.7528 (mtm-85) outliers start: 92 outliers final: 30 residues processed: 556 average time/residue: 1.6382 time to fit residues: 1011.6727 Evaluate side-chains 561 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 525 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 129 ASN 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 129 ASN Chi-restraints excluded: chain Ad residue 160 MET Chi-restraints excluded: chain Ad residue 206 THR Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 204 GLU Chi-restraints excluded: chain Af residue 206 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 204 GLU Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 206 THR Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 204 GLU 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 129 ASN Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 204 GLU Chi-restraints excluded: chain An residue 160 MET Chi-restraints excluded: chain An residue 206 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 chunk 232 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 207 optimal weight: 0.3980 chunk 230 optimal weight: 0.6980 chunk 79 optimal weight: 0.0370 chunk 186 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN Ab 122 ASN Ac 77 GLN Ac 122 ASN Af 122 ASN Af 158 GLN Ag 77 GLN Ah 122 ASN Aj 122 ASN Ak 77 GLN Am 77 GLN An 122 ASN Ao 77 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22320 Z= 0.169 Angle : 0.538 7.578 30256 Z= 0.273 Chirality : 0.040 0.127 3248 Planarity : 0.005 0.051 3952 Dihedral : 4.304 26.160 3009 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.62 % Allowed : 22.07 % 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: -0.73 (0.16), residues: 2672 helix: 0.24 (0.14), residues: 1392 sheet: 0.32 (0.34), residues: 160 loop : -1.49 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAj 132 HIS 0.002 0.001 HISAd 217 PHE 0.014 0.002 PHEAd 202 TYR 0.022 0.001 TYRAi 180 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 550 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 512 time to evaluate : 2.433 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6448 (mmm) cc_final: 0.6141 (mmm) REVERT: Ac 56 MET cc_start: 0.6361 (mmm) cc_final: 0.6152 (mmm) REVERT: Ac 220 MET cc_start: 0.6465 (mtm) cc_final: 0.6150 (mtm) REVERT: Ad 116 MET cc_start: 0.8029 (ttp) cc_final: 0.7574 (ttm) REVERT: Ad 160 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8244 (mmm) REVERT: Ad 188 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8138 (mtt90) REVERT: Ad 191 ARG cc_start: 0.6833 (mtt90) cc_final: 0.6457 (mtt90) REVERT: Ad 197 ARG cc_start: 0.8599 (ptm160) cc_final: 0.8386 (ptm160) REVERT: Ad 206 THR cc_start: 0.8449 (p) cc_final: 0.8050 (p) REVERT: Ad 208 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6896 (mtm-85) REVERT: Ae 72 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6458 (tm-30) REVERT: Ag 56 MET cc_start: 0.6196 (mpp) cc_final: 0.5924 (mpp) REVERT: Ag 77 GLN cc_start: 0.8511 (tt0) cc_final: 0.8297 (tt0) REVERT: Ag 122 ASN cc_start: 0.8377 (m-40) cc_final: 0.8163 (m110) REVERT: Ag 134 MET cc_start: 0.7556 (ttt) cc_final: 0.7331 (ttt) REVERT: Ag 220 MET cc_start: 0.6401 (mtm) cc_final: 0.6030 (mtm) REVERT: Ah 181 MET cc_start: 0.8016 (tpp) cc_final: 0.7782 (tpt) REVERT: Ah 188 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8065 (mtt90) REVERT: Ah 191 ARG cc_start: 0.6844 (mtt90) cc_final: 0.6609 (mtt90) REVERT: Ah 206 THR cc_start: 0.8637 (p) cc_final: 0.8308 (p) REVERT: Aj 206 THR cc_start: 0.8588 (p) cc_final: 0.8349 (p) REVERT: Ak 56 MET cc_start: 0.6580 (mpp) cc_final: 0.6210 (mpp) REVERT: Ak 108 MET cc_start: 0.7974 (tpt) cc_final: 0.7729 (tpt) REVERT: Ak 134 MET cc_start: 0.7540 (ttt) cc_final: 0.7280 (ttt) REVERT: Ak 135 MET cc_start: 0.8250 (mmm) cc_final: 0.8004 (mmt) REVERT: Ak 220 MET cc_start: 0.6733 (mtm) cc_final: 0.6416 (mtm) REVERT: Al 56 MET cc_start: 0.7104 (mpp) cc_final: 0.6740 (mpp) REVERT: Al 116 MET cc_start: 0.7955 (ttp) cc_final: 0.7625 (ttm) REVERT: Al 206 THR cc_start: 0.8560 (p) cc_final: 0.8157 (p) REVERT: Am 56 MET cc_start: 0.6331 (mmm) cc_final: 0.6005 (mmm) REVERT: Am 134 MET cc_start: 0.7553 (ttt) cc_final: 0.7281 (ttt) REVERT: Ao 72 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6569 (tm-30) REVERT: Ao 220 MET cc_start: 0.6966 (mtm) cc_final: 0.6629 (mtm) REVERT: Ap 84 ARG cc_start: 0.8490 (ptm160) cc_final: 0.8245 (ptp-170) REVERT: Ap 116 MET cc_start: 0.8082 (ttp) cc_final: 0.7881 (ttm) REVERT: Ap 197 ARG cc_start: 0.8680 (ptm160) cc_final: 0.8415 (ptm160) REVERT: Ap 206 THR cc_start: 0.8503 (p) cc_final: 0.8173 (p) outliers start: 38 outliers final: 16 residues processed: 521 average time/residue: 1.7361 time to fit residues: 1000.7338 Evaluate side-chains 524 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 505 time to evaluate : 2.473 ------------------------------------------------------------------------------- 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 160 MET Chi-restraints excluded: chain Ad residue 188 ARG Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 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 Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 204 GLU Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 173 MET Chi-restraints excluded: chain Ao residue 107 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 120 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 111 optimal weight: 0.0060 chunk 156 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 221 optimal weight: 0.0670 chunk 66 optimal weight: 0.8980 overall best weight: 0.2934 ------------------------------------------------------------------------------- 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 ** Ac 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Aj 122 ASN Aj 158 GLN Ak 77 GLN Am 77 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN Ao 77 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22320 Z= 0.152 Angle : 0.534 10.113 30256 Z= 0.265 Chirality : 0.039 0.142 3248 Planarity : 0.005 0.044 3952 Dihedral : 4.194 23.396 3009 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.49 % Allowed : 24.11 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.17), residues: 2672 helix: 1.26 (0.16), residues: 1200 sheet: 0.37 (0.34), residues: 160 loop : -0.57 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAj 132 HIS 0.002 0.001 HISAd 69 PHE 0.012 0.002 PHEAd 202 TYR 0.022 0.001 TYRAa 198 ARG 0.009 0.000 ARGAj 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 557 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 522 time to evaluate : 2.442 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6332 (mmm) cc_final: 0.6008 (mmm) REVERT: Aa 155 THR cc_start: 0.8611 (p) cc_final: 0.8382 (p) REVERT: Ac 56 MET cc_start: 0.6352 (mmm) cc_final: 0.6141 (mmm) REVERT: Ac 220 MET cc_start: 0.6519 (mtm) cc_final: 0.6140 (mtm) REVERT: Ad 116 MET cc_start: 0.8033 (ttp) cc_final: 0.7570 (ttm) REVERT: Ad 160 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8220 (mmm) REVERT: Ad 188 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8146 (mtt90) REVERT: Ad 191 ARG cc_start: 0.6744 (mtt90) cc_final: 0.6365 (mtt90) REVERT: Ad 197 ARG cc_start: 0.8599 (ptm160) cc_final: 0.8303 (ptm160) REVERT: Ad 206 THR cc_start: 0.8453 (p) cc_final: 0.8080 (p) REVERT: Ae 56 MET cc_start: 0.6418 (mmm) cc_final: 0.5898 (mmm) REVERT: Ag 56 MET cc_start: 0.6189 (mpp) cc_final: 0.5594 (mpp) REVERT: Ag 122 ASN cc_start: 0.8383 (m-40) cc_final: 0.8144 (m-40) REVERT: Ag 134 MET cc_start: 0.7548 (ttt) cc_final: 0.7347 (ttt) REVERT: Ag 220 MET cc_start: 0.6436 (mtm) cc_final: 0.6132 (mtm) REVERT: Ah 112 MET cc_start: 0.8131 (mtp) cc_final: 0.7900 (mtt) REVERT: Ah 181 MET cc_start: 0.8033 (tpp) cc_final: 0.7821 (tpt) REVERT: Ah 188 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8060 (mtt90) REVERT: Ah 206 THR cc_start: 0.8660 (p) cc_final: 0.8357 (p) REVERT: Aj 206 THR cc_start: 0.8546 (p) cc_final: 0.8314 (p) REVERT: Ak 108 MET cc_start: 0.7950 (tpt) cc_final: 0.7693 (tpt) REVERT: Ak 135 MET cc_start: 0.8208 (mmm) cc_final: 0.8002 (mmt) REVERT: Al 56 MET cc_start: 0.7001 (mpp) cc_final: 0.6603 (mpp) REVERT: Al 116 MET cc_start: 0.7951 (ttp) cc_final: 0.7627 (ttm) REVERT: Al 206 THR cc_start: 0.8577 (p) cc_final: 0.8219 (p) REVERT: Am 56 MET cc_start: 0.6332 (mmm) cc_final: 0.6006 (mmm) REVERT: Ao 220 MET cc_start: 0.7062 (mtm) cc_final: 0.6577 (mtm) REVERT: Ap 84 ARG cc_start: 0.8453 (ptm160) cc_final: 0.8186 (ptp-170) REVERT: Ap 197 ARG cc_start: 0.8685 (ptm160) cc_final: 0.8418 (ptm160) REVERT: Ap 206 THR cc_start: 0.8472 (p) cc_final: 0.8121 (p) outliers start: 35 outliers final: 20 residues processed: 531 average time/residue: 1.6848 time to fit residues: 992.3371 Evaluate side-chains 537 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 514 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 160 MET Chi-restraints excluded: chain Ad residue 188 ARG Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 107 GLU 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 206 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 184 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 222 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** Ac 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 122 ASN Af 122 ASN Ag 77 GLN Ai 122 ASN Aj 122 ASN Aj 158 GLN Ak 77 GLN ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN Ao 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2607 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= 0.215 Angle : 0.559 10.170 30256 Z= 0.278 Chirality : 0.041 0.122 3248 Planarity : 0.005 0.046 3952 Dihedral : 4.288 16.386 3008 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.34 % Allowed : 23.98 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.16), residues: 2672 helix: 0.51 (0.15), residues: 1392 sheet: 0.53 (0.32), residues: 160 loop : -1.09 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAm 132 HIS 0.002 0.001 HISAj 217 PHE 0.018 0.003 PHEAd 202 TYR 0.021 0.001 TYRAa 198 ARG 0.010 0.000 ARGAn 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 581 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 526 time to evaluate : 2.369 Fit side-chains REVERT: Aa 56 MET cc_start: 0.6444 (mmm) cc_final: 0.6163 (mmm) REVERT: Aa 155 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8378 (p) REVERT: Ac 220 MET cc_start: 0.6525 (mtm) cc_final: 0.6160 (mtm) REVERT: Ad 56 MET cc_start: 0.6877 (mmm) cc_final: 0.6502 (mpp) REVERT: Ad 116 MET cc_start: 0.8056 (ttp) cc_final: 0.7575 (ttm) REVERT: Ad 160 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8248 (mmm) REVERT: Ad 191 ARG cc_start: 0.6831 (mtt90) cc_final: 0.6461 (mtt90) REVERT: Ad 197 ARG cc_start: 0.8619 (ptm160) cc_final: 0.8333 (ptm160) REVERT: Ad 206 THR cc_start: 0.8486 (p) cc_final: 0.8125 (p) REVERT: Ae 56 MET cc_start: 0.6441 (mmm) cc_final: 0.6205 (mmm) REVERT: Af 206 THR cc_start: 0.8585 (p) cc_final: 0.8337 (p) REVERT: Ag 122 ASN cc_start: 0.8309 (m-40) cc_final: 0.8074 (m110) REVERT: Ag 220 MET cc_start: 0.6450 (mtm) cc_final: 0.6103 (mtm) REVERT: Ah 112 MET cc_start: 0.8111 (mtp) cc_final: 0.7877 (mtt) REVERT: Ah 181 MET cc_start: 0.8020 (tpp) cc_final: 0.7795 (tpt) REVERT: Ah 188 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7992 (mtt90) REVERT: Ah 206 THR cc_start: 0.8656 (p) cc_final: 0.8361 (p) REVERT: Ai 56 MET cc_start: 0.6487 (mmm) cc_final: 0.6280 (mmm) REVERT: Aj 158 GLN cc_start: 0.8570 (mt0) cc_final: 0.8336 (mt0) REVERT: Aj 206 THR cc_start: 0.8583 (p) cc_final: 0.8335 (p) REVERT: Ak 56 MET cc_start: 0.6537 (mpp) cc_final: 0.6321 (mpp) REVERT: Ak 220 MET cc_start: 0.6693 (mtm) cc_final: 0.6409 (mtm) REVERT: Al 56 MET cc_start: 0.7001 (mpp) cc_final: 0.6614 (mpp) REVERT: Al 116 MET cc_start: 0.7957 (ttp) cc_final: 0.7604 (ttm) REVERT: Al 206 THR cc_start: 0.8578 (p) cc_final: 0.8254 (p) REVERT: Am 56 MET cc_start: 0.6331 (mmm) cc_final: 0.5896 (mmm) REVERT: Ao 220 MET cc_start: 0.7084 (mtm) cc_final: 0.6605 (mtm) REVERT: Ap 84 ARG cc_start: 0.8525 (ptm160) cc_final: 0.8320 (ptp-170) REVERT: Ap 188 ARG cc_start: 0.8475 (mtt90) cc_final: 0.8154 (mtt90) REVERT: Ap 197 ARG cc_start: 0.8724 (ptm160) cc_final: 0.8478 (ptm160) REVERT: Ap 206 THR cc_start: 0.8482 (p) cc_final: 0.8148 (p) outliers start: 55 outliers final: 31 residues processed: 543 average time/residue: 1.6256 time to fit residues: 982.3206 Evaluate side-chains 556 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 522 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 129 ASN 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 129 ASN Chi-restraints excluded: chain Ac residue 204 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 160 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ah residue 211 VAL Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 204 GLU Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Al residue 211 VAL Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 129 ASN Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 54 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 247 optimal weight: 0.0470 chunk 205 optimal weight: 0.0070 chunk 114 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 130 optimal weight: 0.1980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN ** Aa 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN ** Ac 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Ag 77 GLN ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22320 Z= 0.153 Angle : 0.539 11.117 30256 Z= 0.266 Chirality : 0.039 0.144 3248 Planarity : 0.005 0.047 3952 Dihedral : 4.158 17.072 3008 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.70 % Allowed : 24.87 % Favored : 73.43 % 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: 0.44 (0.17), residues: 2672 helix: 1.06 (0.15), residues: 1296 sheet: 0.77 (0.33), residues: 160 loop : -0.56 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAj 132 HIS 0.002 0.001 HISAb 217 PHE 0.012 0.002 PHEAp 200 TYR 0.020 0.001 TYRAi 180 ARG 0.008 0.000 ARGAb 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 559 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 519 time to evaluate : 2.585 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6382 (mmm) cc_final: 0.6068 (mmm) REVERT: Aa 155 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8372 (p) REVERT: Ac 220 MET cc_start: 0.6587 (mtm) cc_final: 0.6240 (mtm) REVERT: Ad 56 MET cc_start: 0.6810 (mmm) cc_final: 0.6439 (mpp) REVERT: Ad 141 VAL cc_start: 0.8439 (t) cc_final: 0.8197 (p) REVERT: Ad 160 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8233 (mmm) REVERT: Ad 191 ARG cc_start: 0.6723 (mtt90) cc_final: 0.6357 (mtt90) REVERT: Ad 197 ARG cc_start: 0.8596 (ptm160) cc_final: 0.8367 (ptm160) REVERT: Ad 206 THR cc_start: 0.8399 (p) cc_final: 0.8064 (p) REVERT: Ag 122 ASN cc_start: 0.8287 (m-40) cc_final: 0.8048 (m-40) REVERT: Ah 56 MET cc_start: 0.7161 (mmt) cc_final: 0.6845 (mpp) REVERT: Ah 112 MET cc_start: 0.8047 (mtp) cc_final: 0.7826 (mtt) REVERT: Ah 181 MET cc_start: 0.7989 (tpp) cc_final: 0.7784 (tpt) REVERT: Ah 188 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7985 (mtt90) REVERT: Ah 206 THR cc_start: 0.8667 (p) cc_final: 0.8379 (p) REVERT: Ai 180 TYR cc_start: 0.8464 (t80) cc_final: 0.8216 (t80) REVERT: Aj 206 THR cc_start: 0.8529 (p) cc_final: 0.8313 (p) REVERT: Ak 220 MET cc_start: 0.6721 (mtm) cc_final: 0.6441 (mtm) REVERT: Al 56 MET cc_start: 0.6966 (mpp) cc_final: 0.6574 (mpp) REVERT: Al 116 MET cc_start: 0.7938 (ttp) cc_final: 0.7601 (ttm) REVERT: Al 160 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8127 (mmm) REVERT: Al 188 ARG cc_start: 0.8482 (mtt90) cc_final: 0.8261 (mtt90) REVERT: Al 206 THR cc_start: 0.8576 (p) cc_final: 0.7925 (p) REVERT: Al 208 ARG cc_start: 0.6991 (mtm-85) cc_final: 0.6501 (mtm-85) REVERT: Am 135 MET cc_start: 0.8330 (mmm) cc_final: 0.8104 (mmm) REVERT: Ao 220 MET cc_start: 0.6975 (mtm) cc_final: 0.6552 (mtm) REVERT: Ap 188 ARG cc_start: 0.8435 (mtt90) cc_final: 0.8099 (mtt90) REVERT: Ap 197 ARG cc_start: 0.8674 (ptm160) cc_final: 0.8442 (ptm160) outliers start: 40 outliers final: 25 residues processed: 539 average time/residue: 1.7199 time to fit residues: 1026.1772 Evaluate side-chains 540 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 511 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 129 ASN 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 Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 160 MET 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 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 107 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 212 ARG Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Al residue 160 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 54 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 140 optimal weight: 0.0370 chunk 208 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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** ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Af 158 GLN Ag 77 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22320 Z= 0.232 Angle : 0.604 12.232 30256 Z= 0.291 Chirality : 0.042 0.143 3248 Planarity : 0.005 0.049 3952 Dihedral : 4.335 16.903 3008 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.04 % Allowed : 24.83 % Favored : 73.13 % 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: 0.41 (0.17), residues: 2672 helix: 1.21 (0.16), residues: 1200 sheet: 0.85 (0.33), residues: 160 loop : -0.67 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAk 132 HIS 0.002 0.001 HISAb 217 PHE 0.018 0.003 PHEAl 202 TYR 0.022 0.001 TYRAk 198 ARG 0.011 0.000 ARGAb 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 542 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 494 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6523 (mmm) cc_final: 0.6195 (mmm) REVERT: Aa 155 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8387 (p) REVERT: Ac 54 MET cc_start: 0.6705 (ptp) cc_final: 0.6486 (ppp) REVERT: Ac 220 MET cc_start: 0.6604 (mtm) cc_final: 0.6234 (mtm) REVERT: Ad 56 MET cc_start: 0.6865 (mmm) cc_final: 0.6490 (mpp) REVERT: Ad 160 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8269 (mmm) REVERT: Ad 191 ARG cc_start: 0.6855 (mtt90) cc_final: 0.6508 (mtt90) REVERT: Ad 197 ARG cc_start: 0.8608 (ptm160) cc_final: 0.8403 (ptm160) REVERT: Ad 206 THR cc_start: 0.8461 (p) cc_final: 0.8136 (p) REVERT: Ae 212 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6912 (ptt90) REVERT: Ag 122 ASN cc_start: 0.8290 (m-40) cc_final: 0.8034 (m110) REVERT: Ag 220 MET cc_start: 0.6392 (mtm) cc_final: 0.6013 (mtm) REVERT: Ah 112 MET cc_start: 0.8082 (mtp) cc_final: 0.7864 (mtt) REVERT: Ah 181 MET cc_start: 0.8019 (tpp) cc_final: 0.7796 (tpt) REVERT: Ah 188 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8068 (mtt90) REVERT: Ah 206 THR cc_start: 0.8672 (p) cc_final: 0.8377 (p) REVERT: Aj 158 GLN cc_start: 0.8573 (mt0) cc_final: 0.8338 (mt0) REVERT: Aj 206 THR cc_start: 0.8579 (p) cc_final: 0.8336 (p) REVERT: Ak 220 MET cc_start: 0.6648 (mtm) cc_final: 0.6346 (mtm) REVERT: Al 56 MET cc_start: 0.7014 (mpp) cc_final: 0.6601 (mpp) REVERT: Al 116 MET cc_start: 0.7953 (ttp) cc_final: 0.7594 (ttm) REVERT: Al 206 THR cc_start: 0.8577 (p) cc_final: 0.7929 (p) REVERT: Al 208 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.6550 (mtm-85) REVERT: Am 56 MET cc_start: 0.6765 (mmm) cc_final: 0.6330 (mpp) REVERT: An 133 VAL cc_start: 0.8816 (m) cc_final: 0.8534 (p) REVERT: Ao 220 MET cc_start: 0.6997 (mtm) cc_final: 0.6642 (mtm) REVERT: Ap 197 ARG cc_start: 0.8707 (ptm160) cc_final: 0.8488 (ptm160) outliers start: 48 outliers final: 30 residues processed: 517 average time/residue: 1.7293 time to fit residues: 989.0460 Evaluate side-chains 526 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 492 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 206 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ac residue 204 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 160 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 212 ARG Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 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 Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 212 ARG Chi-restraints excluded: chain Ai residue 220 MET Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 212 ARG 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 152 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 147 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 0.0470 chunk 168 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 193 optimal weight: 0.3980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 122 ASN ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 122 ASN Ac 77 GLN ** Ac 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Ag 77 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Ak 77 GLN ** Am 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2919 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= 0.184 Angle : 0.579 11.693 30256 Z= 0.280 Chirality : 0.040 0.129 3248 Planarity : 0.005 0.048 3952 Dihedral : 4.267 18.653 3008 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.96 % Allowed : 25.04 % 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: 0.52 (0.17), residues: 2672 helix: 1.30 (0.16), residues: 1200 sheet: 1.03 (0.33), residues: 160 loop : -0.62 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAa 132 HIS 0.002 0.001 HISAb 217 PHE 0.014 0.002 PHEAl 202 TYR 0.022 0.001 TYRAe 198 ARG 0.008 0.000 ARGAf 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 540 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 494 time to evaluate : 2.330 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6552 (mmm) cc_final: 0.6206 (mmm) REVERT: Aa 155 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8399 (p) REVERT: Ab 84 ARG cc_start: 0.8656 (ptp-170) cc_final: 0.8399 (ptp-170) REVERT: Ac 220 MET cc_start: 0.6602 (mtm) cc_final: 0.6228 (mtm) REVERT: Ad 56 MET cc_start: 0.6819 (mmm) cc_final: 0.6474 (mpp) REVERT: Ad 160 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8264 (mmm) REVERT: Ad 191 ARG cc_start: 0.6845 (mtt90) cc_final: 0.6501 (mtt90) REVERT: Ad 197 ARG cc_start: 0.8593 (ptm160) cc_final: 0.8388 (ptm160) REVERT: Ad 206 THR cc_start: 0.8403 (p) cc_final: 0.8076 (p) REVERT: Ae 56 MET cc_start: 0.6236 (mmm) cc_final: 0.6010 (mmm) REVERT: Ae 212 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6874 (ptt90) REVERT: Af 206 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8329 (p) REVERT: Ag 54 MET cc_start: 0.5785 (pp-130) cc_final: 0.5395 (pp-130) REVERT: Ag 122 ASN cc_start: 0.8259 (m-40) cc_final: 0.8022 (m-40) REVERT: Ag 220 MET cc_start: 0.6422 (mtm) cc_final: 0.6046 (mtm) REVERT: Ah 112 MET cc_start: 0.8036 (mtp) cc_final: 0.7826 (mtt) REVERT: Ah 188 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8056 (mtt90) REVERT: Ah 206 THR cc_start: 0.8663 (p) cc_final: 0.8364 (p) REVERT: Ai 135 MET cc_start: 0.8370 (mmm) cc_final: 0.8165 (mpt) REVERT: Aj 158 GLN cc_start: 0.8569 (mt0) cc_final: 0.8340 (mt0) REVERT: Aj 206 THR cc_start: 0.8553 (p) cc_final: 0.8325 (p) REVERT: Ak 220 MET cc_start: 0.6651 (mtm) cc_final: 0.6327 (mtm) REVERT: Al 56 MET cc_start: 0.7003 (mpp) cc_final: 0.6589 (mpp) REVERT: Al 116 MET cc_start: 0.7912 (ttp) cc_final: 0.7585 (ttm) REVERT: Al 160 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8131 (mmm) REVERT: Al 206 THR cc_start: 0.8571 (p) cc_final: 0.7920 (p) REVERT: Al 208 ARG cc_start: 0.7016 (mtm-85) cc_final: 0.6516 (mtm-85) REVERT: Am 56 MET cc_start: 0.6764 (mmm) cc_final: 0.6357 (mpp) REVERT: An 133 VAL cc_start: 0.8776 (m) cc_final: 0.8497 (p) REVERT: Ao 116 MET cc_start: 0.7507 (ttp) cc_final: 0.6938 (ttp) REVERT: Ao 220 MET cc_start: 0.6969 (mtm) cc_final: 0.6603 (mtm) REVERT: Ap 160 MET cc_start: 0.8403 (tpt) cc_final: 0.8125 (mmm) REVERT: Ap 188 ARG cc_start: 0.8445 (mtt90) cc_final: 0.8135 (mtt90) REVERT: Ap 197 ARG cc_start: 0.8669 (ptm160) cc_final: 0.8434 (ptm160) outliers start: 46 outliers final: 30 residues processed: 516 average time/residue: 1.7149 time to fit residues: 977.8543 Evaluate side-chains 529 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 493 time to evaluate : 2.538 ------------------------------------------------------------------------------- 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 129 ASN 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 129 ASN Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 160 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 212 ARG Chi-restraints excluded: chain Af residue 206 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 166 VAL Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 212 ARG Chi-restraints excluded: chain Ai residue 220 MET Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 134 MET Chi-restraints excluded: chain Al residue 160 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 An residue 116 MET Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 212 ARG Chi-restraints excluded: chain Ap residue 134 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.8980 chunk 236 optimal weight: 0.0870 chunk 215 optimal weight: 0.3980 chunk 229 optimal weight: 0.0970 chunk 138 optimal weight: 0.0050 chunk 100 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 122 ASN ** Aa 151 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** ** Ae 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Af 158 GLN Ag 77 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 77 GLN ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Ak 77 GLN Al 77 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 122 ASN Ao 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22320 Z= 0.156 Angle : 0.574 12.404 30256 Z= 0.276 Chirality : 0.039 0.119 3248 Planarity : 0.005 0.048 3952 Dihedral : 4.196 19.036 3008 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.87 % Allowed : 25.13 % 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: 0.13 (0.17), residues: 2672 helix: 1.01 (0.15), residues: 1296 sheet: 0.50 (0.32), residues: 192 loop : -1.00 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAf 132 HIS 0.002 0.001 HISAl 217 PHE 0.013 0.002 PHEAd 200 TYR 0.019 0.001 TYRAe 198 ARG 0.008 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 538 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 494 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6553 (mmm) cc_final: 0.6104 (mpp) REVERT: Aa 155 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8405 (p) REVERT: Ab 84 ARG cc_start: 0.8590 (ptp-170) cc_final: 0.8315 (ptp-170) REVERT: Ac 220 MET cc_start: 0.6633 (mtm) cc_final: 0.6269 (mtm) REVERT: Ad 56 MET cc_start: 0.6780 (mmm) cc_final: 0.6434 (mpp) REVERT: Ad 132 TRP cc_start: 0.8536 (p-90) cc_final: 0.8131 (p-90) REVERT: Ad 160 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8248 (mmm) REVERT: Ad 181 MET cc_start: 0.7974 (tpp) cc_final: 0.7686 (tpp) REVERT: Ad 191 ARG cc_start: 0.6828 (mtt90) cc_final: 0.6463 (mtt90) REVERT: Ad 206 THR cc_start: 0.8348 (p) cc_final: 0.7992 (p) REVERT: Ae 56 MET cc_start: 0.6226 (mmm) cc_final: 0.6001 (mmm) REVERT: Af 188 ARG cc_start: 0.8409 (mtt90) cc_final: 0.8121 (mtt-85) REVERT: Ag 122 ASN cc_start: 0.8268 (m-40) cc_final: 0.8016 (m-40) REVERT: Ag 220 MET cc_start: 0.6428 (mtm) cc_final: 0.6044 (mtm) REVERT: Ah 56 MET cc_start: 0.7001 (mmt) cc_final: 0.6684 (mpp) REVERT: Ah 188 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8025 (mtt90) REVERT: Ah 206 THR cc_start: 0.8531 (p) cc_final: 0.8239 (p) REVERT: Ai 56 MET cc_start: 0.6344 (mmm) cc_final: 0.6050 (mmm) REVERT: Aj 158 GLN cc_start: 0.8568 (mt0) cc_final: 0.8348 (mt0) REVERT: Aj 206 THR cc_start: 0.8493 (p) cc_final: 0.8290 (p) REVERT: Ak 220 MET cc_start: 0.6752 (mtm) cc_final: 0.6404 (mtm) REVERT: Al 56 MET cc_start: 0.6979 (mpp) cc_final: 0.6574 (mpp) REVERT: Al 160 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8115 (mmm) REVERT: Al 181 MET cc_start: 0.7771 (tpp) cc_final: 0.7439 (tpt) REVERT: Al 206 THR cc_start: 0.8534 (p) cc_final: 0.7871 (p) REVERT: Al 208 ARG cc_start: 0.6994 (mtm-85) cc_final: 0.6508 (mtm-85) REVERT: Am 56 MET cc_start: 0.6735 (mmm) cc_final: 0.6327 (mpp) REVERT: An 108 MET cc_start: 0.7306 (tpp) cc_final: 0.7095 (tpp) REVERT: Ap 188 ARG cc_start: 0.8422 (mtt90) cc_final: 0.8110 (mtt90) REVERT: Ap 197 ARG cc_start: 0.8653 (ptm160) cc_final: 0.8421 (ptm160) outliers start: 44 outliers final: 28 residues processed: 516 average time/residue: 1.7877 time to fit residues: 1022.5432 Evaluate side-chains 525 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 493 time to evaluate : 2.449 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain Ab residue 206 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 160 MET 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 Af residue 206 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 166 VAL Chi-restraints excluded: chain Ah residue 188 ARG Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 212 ARG Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 160 MET Chi-restraints excluded: chain Al residue 211 VAL Chi-restraints excluded: chain Am residue 54 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 204 GLU Chi-restraints excluded: chain Ao residue 212 ARG Chi-restraints excluded: chain Ap residue 79 ASP Chi-restraints excluded: chain Ap residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 255 optimal weight: 0.0170 chunk 234 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 124 optimal weight: 0.0370 chunk 161 optimal weight: 0.0770 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 122 ASN Aa 151 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 Ag 77 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 77 GLN ** Ai 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 122 ASN Ak 77 GLN Al 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 Ap 77 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22320 Z= 0.173 Angle : 0.595 12.842 30256 Z= 0.285 Chirality : 0.040 0.143 3248 Planarity : 0.005 0.048 3952 Dihedral : 4.246 20.644 3008 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.62 % Allowed : 25.85 % Favored : 72.53 % 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: 0.12 (0.17), residues: 2672 helix: 0.98 (0.15), residues: 1296 sheet: 0.52 (0.32), residues: 192 loop : -0.99 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAa 132 HIS 0.002 0.001 HISAp 69 PHE 0.013 0.002 PHEAd 200 TYR 0.022 0.001 TYRAp 180 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 547 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 509 time to evaluate : 2.287 Fit side-chains revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.6589 (mmm) cc_final: 0.6090 (mpp) REVERT: Aa 141 VAL cc_start: 0.8637 (m) cc_final: 0.8424 (p) REVERT: Aa 155 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8399 (p) REVERT: Ab 56 MET cc_start: 0.7265 (tpp) cc_final: 0.6913 (mpp) REVERT: Ab 84 ARG cc_start: 0.8581 (ptp-170) cc_final: 0.8316 (ptp-170) REVERT: Ab 188 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.8046 (mtt90) REVERT: Ac 220 MET cc_start: 0.6638 (mtm) cc_final: 0.6254 (mtm) REVERT: Ad 56 MET cc_start: 0.6783 (mmm) cc_final: 0.6453 (mpp) REVERT: Ad 132 TRP cc_start: 0.8548 (p-90) cc_final: 0.8165 (p-90) REVERT: Ad 160 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8265 (mmm) REVERT: Ad 191 ARG cc_start: 0.6717 (mtt90) cc_final: 0.6359 (mtt90) REVERT: Ag 122 ASN cc_start: 0.8264 (m-40) cc_final: 0.8018 (m-40) REVERT: Ag 220 MET cc_start: 0.6449 (mtm) cc_final: 0.5973 (mtm) REVERT: Ah 188 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7925 (mtt90) REVERT: Ah 206 THR cc_start: 0.8488 (p) cc_final: 0.8183 (p) REVERT: Ai 56 MET cc_start: 0.6367 (mmm) cc_final: 0.6139 (mmm) REVERT: Aj 158 GLN cc_start: 0.8576 (mt0) cc_final: 0.8351 (mt0) REVERT: Ak 220 MET cc_start: 0.6774 (mtm) cc_final: 0.6414 (mtm) REVERT: Al 56 MET cc_start: 0.6988 (mpp) cc_final: 0.6570 (mpp) REVERT: Al 160 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8128 (mmm) REVERT: Al 208 ARG cc_start: 0.6997 (mtm-85) cc_final: 0.6721 (mtm-85) REVERT: An 108 MET cc_start: 0.7337 (tpp) cc_final: 0.7131 (tpp) REVERT: Ao 220 MET cc_start: 0.6939 (mtt) cc_final: 0.6656 (mtt) REVERT: Ap 188 ARG cc_start: 0.8416 (mtt90) cc_final: 0.8109 (mtt90) REVERT: Ap 197 ARG cc_start: 0.8662 (ptm160) cc_final: 0.8432 (ptm160) outliers start: 38 outliers final: 27 residues processed: 526 average time/residue: 1.7240 time to fit residues: 1002.3179 Evaluate side-chains 536 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 505 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 71 LEU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 206 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 160 MET Chi-restraints excluded: chain Ad residue 211 VAL Chi-restraints excluded: chain Ae residue 129 ASN 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 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 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 212 ARG Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 160 MET 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 An residue 206 THR Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 204 GLU Chi-restraints excluded: chain Ap residue 134 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 178 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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** Ah 77 GLN Aj 122 ASN Ak 77 GLN Al 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 ** Ao 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 77 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.156906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142799 restraints weight = 28518.461| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.10 r_work: 0.3639 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22320 Z= 0.219 Angle : 0.628 14.531 30256 Z= 0.299 Chirality : 0.041 0.135 3248 Planarity : 0.005 0.048 3952 Dihedral : 4.371 21.343 3008 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.79 % Allowed : 25.94 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.17), residues: 2672 helix: 1.02 (0.15), residues: 1296 sheet: 0.41 (0.32), residues: 192 loop : -0.42 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAo 132 HIS 0.002 0.001 HISAe 217 PHE 0.017 0.002 PHEAd 202 TYR 0.028 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: 12374.10 seconds wall clock time: 220 minutes 15.78 seconds (13215.78 seconds total)