Starting phenix.real_space_refine (version: dev) on Wed Feb 22 17:11:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2023/6tmj_10523.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2023/6tmj_10523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2023/6tmj_10523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2023/6tmj_10523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2023/6tmj_10523.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2023/6tmj_10523.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "K ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g2 PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g2 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g2 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g2 PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d2 GLU 98": "OE1" <-> "OE2" Residue "d2 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d2 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d2 PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d2 ASP 120": "OD1" <-> "OD2" Residue "e2 GLU 26": "OE1" <-> "OE2" Residue "e2 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e2 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H2 PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I2 GLU 136": "OE1" <-> "OE2" Residue "I2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J2 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J2 PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K2 GLU 136": "OE1" <-> "OE2" Residue "K2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M2 PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N2 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N2 PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O2 PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O2 PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P2 PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q2 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q2 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L2 TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18084 Number of models: 1 Model: "" Number of chains: 15 Chain: "Q" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 190 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Chain: "K" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1159 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "g2" Number of atoms: 3233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3233 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain: "d2" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2145 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "e2" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1077 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "H2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "I2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "J2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "K2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "M2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "N2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "O2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "P2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "Q2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "L2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Time building chain proxies: 8.86, per 1000 atoms: 0.49 Number of scatterers: 18084 At special positions: 0 Unit cell: (93.79, 84.66, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 1641 8.00 N 1428 7.00 C 5771 6.00 H 9178 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 16.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 3 sheets defined 77.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'Q' and resid 9 through 14 removed outlier: 3.663A pdb=" N GLU Q 14 " --> pdb=" O SER Q 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 185 Proline residue: K 167 - end of helix removed outlier: 3.760A pdb=" N ALA K 170 " --> pdb=" O ARG K 166 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE K 174 " --> pdb=" O ALA K 170 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY K 175 " --> pdb=" O PHE K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 218 Processing helix chain 'g2' and resid 68 through 80 Processing helix chain 'g2' and resid 81 through 93 removed outlier: 3.814A pdb=" N ALAg2 85 " --> pdb=" O GLYg2 81 " (cutoff:3.500A) Proline residue: g2 87 - end of helix Processing helix chain 'g2' and resid 119 through 138 removed outlier: 3.547A pdb=" N METg2 137 " --> pdb=" O LYSg2 133 " (cutoff:3.500A) Processing helix chain 'g2' and resid 148 through 156 removed outlier: 3.958A pdb=" N ARGg2 152 " --> pdb=" O GLYg2 148 " (cutoff:3.500A) Processing helix chain 'g2' and resid 169 through 173 removed outlier: 3.551A pdb=" N ARGg2 172 " --> pdb=" O GLUg2 169 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHEg2 173 " --> pdb=" O VALg2 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'g2' and resid 169 through 173' Processing helix chain 'g2' and resid 177 through 190 removed outlier: 3.952A pdb=" N ILEg2 183 " --> pdb=" O GLNg2 179 " (cutoff:3.500A) Processing helix chain 'g2' and resid 217 through 223 removed outlier: 3.815A pdb=" N GLNg2 223 " --> pdb=" O THRg2 219 " (cutoff:3.500A) Processing helix chain 'g2' and resid 237 through 270 removed outlier: 5.299A pdb=" N LYSg2 243 " --> pdb=" O THRg2 239 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASPg2 244 " --> pdb=" O ASPg2 240 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASPg2 247 " --> pdb=" O LYSg2 243 " (cutoff:3.500A) Processing helix chain 'd2' and resid 142 through 158 removed outlier: 4.148A pdb=" N GLYd2 158 " --> pdb=" O GLNd2 154 " (cutoff:3.500A) Processing helix chain 'd2' and resid 161 through 182 Processing helix chain 'e2' and resid 1 through 6 Processing helix chain 'e2' and resid 8 through 23 removed outlier: 3.645A pdb=" N TYRe2 12 " --> pdb=" O SERe2 8 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEUe2 19 " --> pdb=" O GLUe2 15 " (cutoff:3.500A) Processing helix chain 'e2' and resid 25 through 36 removed outlier: 4.446A pdb=" N GLNe2 31 " --> pdb=" O PROe2 27 " (cutoff:3.500A) Processing helix chain 'e2' and resid 58 through 65 removed outlier: 3.516A pdb=" N ALAe2 62 " --> pdb=" O ASPe2 58 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALAe2 65 " --> pdb=" O LYSe2 61 " (cutoff:3.500A) Processing helix chain 'H2' and resid 97 through 107 removed outlier: 3.767A pdb=" N LEUH2 101 " --> pdb=" O GLYH2 97 " (cutoff:3.500A) Processing helix chain 'H2' and resid 109 through 131 removed outlier: 3.885A pdb=" N VALH2 113 " --> pdb=" O SERH2 109 " (cutoff:3.500A) Processing helix chain 'H2' and resid 134 through 166 removed outlier: 4.369A pdb=" N THRH2 140 " --> pdb=" O GLUH2 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THRH2 142 " --> pdb=" O LEUH2 138 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHEH2 148 " --> pdb=" O ILEH2 144 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHEH2 151 " --> pdb=" O GLYH2 147 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SERH2 160 " --> pdb=" O CYSH2 156 " (cutoff:3.500A) Processing helix chain 'I2' and resid 97 through 108 removed outlier: 3.600A pdb=" N LEUI2 101 " --> pdb=" O GLYI2 97 " (cutoff:3.500A) Processing helix chain 'I2' and resid 109 through 131 removed outlier: 3.689A pdb=" N VALI2 113 " --> pdb=" O SERI2 109 " (cutoff:3.500A) Processing helix chain 'I2' and resid 134 through 166 removed outlier: 3.502A pdb=" N LEUI2 138 " --> pdb=" O ILEI2 134 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHEI2 151 " --> pdb=" O GLYI2 147 " (cutoff:3.500A) Processing helix chain 'J2' and resid 97 through 107 Processing helix chain 'J2' and resid 110 through 131 removed outlier: 3.563A pdb=" N ALAJ2 114 " --> pdb=" O VALJ2 110 " (cutoff:3.500A) Processing helix chain 'J2' and resid 132 through 134 No H-bonds generated for 'chain 'J2' and resid 132 through 134' Processing helix chain 'J2' and resid 135 through 165 removed outlier: 3.797A pdb=" N THRJ2 140 " --> pdb=" O GLUJ2 136 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYRJ2 141 " --> pdb=" O ASPJ2 137 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHEJ2 151 " --> pdb=" O GLYJ2 147 " (cutoff:3.500A) Processing helix chain 'K2' and resid 97 through 107 removed outlier: 3.913A pdb=" N LEUK2 101 " --> pdb=" O GLYK2 97 " (cutoff:3.500A) Processing helix chain 'K2' and resid 108 through 131 removed outlier: 4.397A pdb=" N GLYK2 112 " --> pdb=" O METK2 108 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASNK2 131 " --> pdb=" O GLYK2 127 " (cutoff:3.500A) Processing helix chain 'K2' and resid 134 through 166 removed outlier: 3.637A pdb=" N LEUK2 138 " --> pdb=" O ILEK2 134 " (cutoff:3.500A) Processing helix chain 'M2' and resid 97 through 107 removed outlier: 3.537A pdb=" N LEUM2 101 " --> pdb=" O GLYM2 97 " (cutoff:3.500A) Processing helix chain 'M2' and resid 108 through 131 removed outlier: 4.497A pdb=" N GLYM2 112 " --> pdb=" O METM2 108 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALAM2 129 " --> pdb=" O VALM2 125 " (cutoff:3.500A) Processing helix chain 'M2' and resid 136 through 166 Processing helix chain 'N2' and resid 97 through 107 Processing helix chain 'N2' and resid 109 through 131 Processing helix chain 'N2' and resid 135 through 165 Processing helix chain 'O2' and resid 97 through 106 removed outlier: 4.162A pdb=" N LEUO2 101 " --> pdb=" O GLYO2 97 " (cutoff:3.500A) Processing helix chain 'O2' and resid 109 through 130 Processing helix chain 'O2' and resid 131 through 133 No H-bonds generated for 'chain 'O2' and resid 131 through 133' Processing helix chain 'O2' and resid 134 through 165 removed outlier: 3.691A pdb=" N THRO2 140 " --> pdb=" O GLUO2 136 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHEO2 148 " --> pdb=" O ILEO2 144 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHEO2 151 " --> pdb=" O GLYO2 147 " (cutoff:3.500A) Processing helix chain 'P2' and resid 98 through 107 Processing helix chain 'P2' and resid 108 through 131 removed outlier: 3.671A pdb=" N GLNP2 115 " --> pdb=" O GLYP2 111 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLYP2 116 " --> pdb=" O GLYP2 112 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SERP2 119 " --> pdb=" O GLNP2 115 " (cutoff:3.500A) Processing helix chain 'P2' and resid 138 through 165 Processing helix chain 'Q2' and resid 97 through 108 removed outlier: 4.020A pdb=" N ALAQ2 104 " --> pdb=" O SERQ2 100 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 109 through 129 removed outlier: 3.690A pdb=" N VALQ2 113 " --> pdb=" O SERQ2 109 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLNQ2 115 " --> pdb=" O GLYQ2 111 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLYQ2 116 " --> pdb=" O GLYQ2 112 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 130 through 133 removed outlier: 6.389A pdb=" N SERQ2 133 " --> pdb=" O ARGQ2 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q2' and resid 130 through 133' Processing helix chain 'Q2' and resid 134 through 166 removed outlier: 3.551A pdb=" N THRQ2 140 " --> pdb=" O GLUQ2 136 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHEQ2 151 " --> pdb=" O GLYQ2 147 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SERQ2 160 " --> pdb=" O CYSQ2 156 " (cutoff:3.500A) Processing helix chain 'L2' and resid 97 through 107 Processing helix chain 'L2' and resid 108 through 110 No H-bonds generated for 'chain 'L2' and resid 108 through 110' Processing helix chain 'L2' and resid 112 through 131 Processing helix chain 'L2' and resid 134 through 165 removed outlier: 3.510A pdb=" N PHEL2 148 " --> pdb=" O ILEL2 144 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILEL2 155 " --> pdb=" O PHEL2 151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'g2' and resid 207 through 215 removed outlier: 6.863A pdb=" N ALAg2 207 " --> pdb=" O LYSg2 203 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYSg2 203 " --> pdb=" O ALAg2 207 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VALg2 215 " --> pdb=" O LEUg2 195 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEUg2 195 " --> pdb=" O VALg2 215 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASNg2 200 " --> pdb=" O LEUg2 110 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VALg2 107 " --> pdb=" O TYRg2 145 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VALg2 147 " --> pdb=" O VALg2 107 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALAg2 109 " --> pdb=" O VALg2 147 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VALg2 144 " --> pdb=" O LYSg2 164 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILEg2 166 " --> pdb=" O VALg2 144 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLYg2 146 " --> pdb=" O ILEg2 166 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THRg2 168 " --> pdb=" O GLYg2 146 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THRe2 52 " --> pdb=" O VALe2 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'g2' and resid 233 through 234 removed outlier: 5.826A pdb=" N GLUg2 233 " --> pdb=" O VALd2 84 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ARGd2 86 " --> pdb=" O GLUg2 233 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLYd2 111 " --> pdb=" O LEUd2 87 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEUd2 46 " --> pdb=" O ALAd2 127 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VALd2 129 " --> pdb=" O LEUd2 46 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THRd2 48 " --> pdb=" O VALd2 129 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLYd2 131 " --> pdb=" O THRd2 48 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SERd2 50 " --> pdb=" O GLYd2 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'g2' and resid 233 through 234 removed outlier: 5.826A pdb=" N GLUg2 233 " --> pdb=" O VALd2 84 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ARGd2 86 " --> pdb=" O GLUg2 233 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLYd2 111 " --> pdb=" O LEUd2 87 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEUd2 46 " --> pdb=" O ALAd2 127 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VALd2 129 " --> pdb=" O LEUd2 46 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THRd2 48 " --> pdb=" O VALd2 129 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLYd2 131 " --> pdb=" O THRd2 48 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SERd2 50 " --> pdb=" O GLYd2 131 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLUd2 91 " --> pdb=" O PROd2 68 " (cutoff:3.500A) 734 hydrogen bonds defined for protein. 2169 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.94 Time building geometry restraints manager: 16.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9160 1.03 - 1.22: 19 1.22 - 1.42: 3656 1.42 - 1.61: 5270 1.61 - 1.81: 114 Bond restraints: 18219 Sorted by residual: bond pdb=" CB VALd2 113 " pdb=" CG1 VALd2 113 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.31e+00 bond pdb=" CB VALI2 125 " pdb=" CG2 VALI2 125 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.06e+00 bond pdb=" CG1 ILEI2 134 " pdb=" CD1 ILEI2 134 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.06e+00 bond pdb=" CG LEUL2 120 " pdb=" CD1 LEUL2 120 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.49e+00 bond pdb=" CG LEUI2 120 " pdb=" CD2 LEUI2 120 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 ... (remaining 18214 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.42: 135 105.42 - 112.59: 21640 112.59 - 119.76: 4507 119.76 - 126.93: 6638 126.93 - 134.09: 40 Bond angle restraints: 32960 Sorted by residual: angle pdb=" N LYSP2 135 " pdb=" CA LYSP2 135 " pdb=" C LYSP2 135 " ideal model delta sigma weight residual 112.04 108.43 3.61 1.44e+00 4.82e-01 6.30e+00 angle pdb=" C ILEI2 134 " pdb=" N LYSI2 135 " pdb=" CA LYSI2 135 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.91e+00 angle pdb=" C METP2 108 " pdb=" N SERP2 109 " pdb=" CA SERP2 109 " ideal model delta sigma weight residual 120.38 123.51 -3.13 1.46e+00 4.69e-01 4.61e+00 angle pdb=" C ILEg2 198 " pdb=" N TYRg2 199 " pdb=" CA TYRg2 199 " ideal model delta sigma weight residual 122.09 118.14 3.95 1.86e+00 2.89e-01 4.52e+00 angle pdb=" N LEUg2 245 " pdb=" CA LEUg2 245 " pdb=" C LEUg2 245 " ideal model delta sigma weight residual 112.23 109.60 2.63 1.26e+00 6.30e-01 4.36e+00 ... (remaining 32955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 6547 17.26 - 34.53: 582 34.53 - 51.79: 73 51.79 - 69.06: 7 69.06 - 86.32: 10 Dihedral angle restraints: 7219 sinusoidal: 3273 harmonic: 3946 Sorted by residual: dihedral pdb=" CA GLUg2 235 " pdb=" C GLUg2 235 " pdb=" N PROg2 236 " pdb=" CA PROg2 236 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ALAP2 114 " pdb=" C ALAP2 114 " pdb=" N GLNP2 115 " pdb=" CA GLNP2 115 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLNe2 47 " pdb=" C GLNe2 47 " pdb=" N GLYe2 48 " pdb=" CA GLYe2 48 " ideal model delta harmonic sigma weight residual 180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 7216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 833 0.030 - 0.060: 393 0.060 - 0.091: 174 0.091 - 0.121: 77 0.121 - 0.151: 9 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CG LEUd2 87 " pdb=" CB LEUd2 87 " pdb=" CD1 LEUd2 87 " pdb=" CD2 LEUd2 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CB VAL K 173 " pdb=" CA VAL K 173 " pdb=" CG1 VAL K 173 " pdb=" CG2 VAL K 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA PHEI2 121 " pdb=" N PHEI2 121 " pdb=" C PHEI2 121 " pdb=" CB PHEI2 121 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 1483 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHEO2 148 " -0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C PHEO2 148 " 0.076 2.00e-02 2.50e+03 pdb=" O PHEO2 148 " -0.028 2.00e-02 2.50e+03 pdb=" N LEUO2 149 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYI2 118 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLYI2 118 " -0.067 2.00e-02 2.50e+03 pdb=" O GLYI2 118 " 0.025 2.00e-02 2.50e+03 pdb=" N SERI2 119 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYN2 118 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.46e+01 pdb=" C GLYN2 118 " 0.066 2.00e-02 2.50e+03 pdb=" O GLYN2 118 " -0.025 2.00e-02 2.50e+03 pdb=" N SERN2 119 " -0.022 2.00e-02 2.50e+03 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 796 2.17 - 2.78: 36999 2.78 - 3.39: 50843 3.39 - 3.99: 64269 3.99 - 4.60: 104944 Nonbonded interactions: 257851 Sorted by model distance: nonbonded pdb=" OG SERM2 100 " pdb=" HG SERL2 102 " model vdw 1.564 1.850 nonbonded pdb=" HG SERN2 109 " pdb=" O LEUO2 107 " model vdw 1.569 1.850 nonbonded pdb=" OE2 GLUg2 233 " pdb=" HG SERd2 81 " model vdw 1.572 1.850 nonbonded pdb=" O VALK2 157 " pdb=" HG SERK2 160 " model vdw 1.575 1.850 nonbonded pdb="HH21 ARG K 166 " pdb=" OE2 GLUP2 150 " model vdw 1.584 1.850 ... (remaining 257846 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 'H2' selection = chain 'I2' selection = chain 'J2' selection = chain 'K2' selection = chain 'L2' selection = chain 'M2' selection = chain 'N2' selection = chain 'O2' selection = chain 'P2' selection = chain 'Q2' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 5771 2.51 5 N 1428 2.21 5 O 1641 1.98 5 H 9178 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 12.400 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: 0.280 Extract box with map and model: 38.410 Check model and map are aligned: 0.280 Process input model: 60.690 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 9041 Z= 0.468 Angle : 0.616 5.989 12223 Z= 0.346 Chirality : 0.044 0.151 1486 Planarity : 0.007 0.044 1518 Dihedral : 13.813 86.321 3163 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.51 (0.20), residues: 1174 helix: -2.43 (0.15), residues: 867 sheet: -3.57 (0.40), residues: 97 loop : -3.92 (0.30), residues: 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.4707 time to fit residues: 77.2821 Evaluate side-chains 96 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g2 179 GLN e2 57 ASN ** H2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9041 Z= 0.214 Angle : 0.532 5.230 12223 Z= 0.294 Chirality : 0.037 0.145 1486 Planarity : 0.004 0.036 1518 Dihedral : 4.371 22.806 1264 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.24), residues: 1174 helix: -0.28 (0.17), residues: 903 sheet: -2.85 (0.45), residues: 93 loop : -2.56 (0.41), residues: 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 109 average time/residue: 0.4941 time to fit residues: 74.5851 Evaluate side-chains 103 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2082 time to fit residues: 2.9117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g2 261 ASN e2 36 ASN ** H2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9041 Z= 0.259 Angle : 0.536 5.165 12223 Z= 0.295 Chirality : 0.038 0.147 1486 Planarity : 0.003 0.033 1518 Dihedral : 4.304 22.259 1264 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1174 helix: 0.96 (0.18), residues: 897 sheet: -2.36 (0.48), residues: 94 loop : -1.83 (0.47), residues: 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 132 average time/residue: 0.5463 time to fit residues: 99.2284 Evaluate side-chains 116 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2347 time to fit residues: 4.4310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H2 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9041 Z= 0.259 Angle : 0.538 5.029 12223 Z= 0.294 Chirality : 0.038 0.157 1486 Planarity : 0.003 0.035 1518 Dihedral : 4.294 22.000 1264 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.26), residues: 1174 helix: 1.30 (0.18), residues: 902 sheet: -2.30 (0.49), residues: 92 loop : -1.31 (0.48), residues: 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 132 average time/residue: 0.4986 time to fit residues: 91.4807 Evaluate side-chains 121 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2103 time to fit residues: 2.1322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.0070 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H2 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9041 Z= 0.192 Angle : 0.493 4.964 12223 Z= 0.266 Chirality : 0.036 0.151 1486 Planarity : 0.003 0.031 1518 Dihedral : 4.128 22.706 1264 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.26), residues: 1174 helix: 1.67 (0.18), residues: 903 sheet: -2.02 (0.50), residues: 94 loop : -1.16 (0.48), residues: 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 130 average time/residue: 0.4813 time to fit residues: 86.4369 Evaluate side-chains 122 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2244 time to fit residues: 3.1977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 113 optimal weight: 1.1980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g2 135 ASN H2 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 9041 Z= 0.291 Angle : 0.541 5.132 12223 Z= 0.298 Chirality : 0.037 0.137 1486 Planarity : 0.003 0.033 1518 Dihedral : 4.216 22.783 1264 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.26), residues: 1174 helix: 1.63 (0.18), residues: 901 sheet: -2.11 (0.49), residues: 94 loop : -1.13 (0.48), residues: 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 131 average time/residue: 0.4998 time to fit residues: 91.0298 Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2500 time to fit residues: 2.6931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H2 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 9041 Z= 0.266 Angle : 0.528 4.962 12223 Z= 0.289 Chirality : 0.037 0.149 1486 Planarity : 0.003 0.034 1518 Dihedral : 4.215 23.116 1264 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.26), residues: 1174 helix: 1.70 (0.18), residues: 901 sheet: -2.01 (0.50), residues: 94 loop : -1.15 (0.47), residues: 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 133 average time/residue: 0.4668 time to fit residues: 88.7292 Evaluate side-chains 130 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2181 time to fit residues: 4.2854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H2 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 9041 Z= 0.262 Angle : 0.531 5.137 12223 Z= 0.291 Chirality : 0.037 0.142 1486 Planarity : 0.003 0.037 1518 Dihedral : 4.173 23.019 1264 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.26), residues: 1174 helix: 1.76 (0.18), residues: 902 sheet: -2.04 (0.50), residues: 94 loop : -1.19 (0.48), residues: 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 132 average time/residue: 0.4789 time to fit residues: 88.4589 Evaluate side-chains 121 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 2.039 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2144 time to fit residues: 2.6815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 108 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H2 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 9041 Z= 0.205 Angle : 0.500 4.789 12223 Z= 0.271 Chirality : 0.036 0.149 1486 Planarity : 0.003 0.036 1518 Dihedral : 4.073 23.163 1264 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.26), residues: 1174 helix: 1.90 (0.18), residues: 903 sheet: -2.06 (0.50), residues: 94 loop : -1.14 (0.47), residues: 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.5108 time to fit residues: 88.6024 Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H2 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 9041 Z= 0.258 Angle : 0.531 5.757 12223 Z= 0.290 Chirality : 0.037 0.151 1486 Planarity : 0.003 0.037 1518 Dihedral : 4.135 23.063 1264 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1174 helix: 1.85 (0.18), residues: 909 sheet: -2.14 (0.49), residues: 94 loop : -1.22 (0.48), residues: 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.5192 time to fit residues: 88.3826 Evaluate side-chains 122 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d2 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.154320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.136637 restraints weight = 28431.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141152 restraints weight = 13428.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143950 restraints weight = 7873.063| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 9041 Z= 0.208 Angle : 0.503 5.049 12223 Z= 0.271 Chirality : 0.036 0.142 1486 Planarity : 0.003 0.036 1518 Dihedral : 4.033 23.196 1264 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.26), residues: 1174 helix: 1.98 (0.18), residues: 910 sheet: -2.11 (0.49), residues: 94 loop : -1.22 (0.48), residues: 170 =============================================================================== Job complete usr+sys time: 4103.20 seconds wall clock time: 73 minutes 43.62 seconds (4423.62 seconds total)