Starting phenix.real_space_refine on Sat Feb 17 07:50:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2024/6tmj_10523.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2024/6tmj_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_2024/6tmj_10523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2024/6tmj_10523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2024/6tmj_10523.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tmj_10523/02_2024/6tmj_10523.pdb" } resolution = 3.5 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= 0.004 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.06, per 1000 atoms: 0.45 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: 14.11 Conformation dependent library (CDL) restraints added in 1.8 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: 1.36 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: 6.44 Time building geometry restraints manager: 14.52 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: 7617 17.26 - 34.53: 642 34.53 - 51.79: 187 51.79 - 69.06: 91 69.06 - 86.32: 10 Dihedral angle restraints: 8547 sinusoidal: 4601 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 8544 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 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: 10.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.290 Extract box with map and model: 35.370 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 56.640 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 % Allowed : 3.83 % Favored : 96.17 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPe2 2 HIS 0.004 0.002 HISe2 39 PHE 0.022 0.002 PHEg2 84 TYR 0.020 0.002 TYRg2 199 ARG 0.005 0.001 ARGN2 130 *********************** 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 : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d2 54 GLU cc_start: 0.7913 (tt0) cc_final: 0.7584 (pm20) REVERT: e2 45 TYR cc_start: 0.8825 (m-80) cc_final: 0.8600 (m-80) REVERT: J2 137 ASP cc_start: 0.7880 (t70) cc_final: 0.7417 (t0) REVERT: M2 165 TYR cc_start: 0.6908 (m-10) cc_final: 0.6322 (m-80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.4651 time to fit residues: 76.2057 Evaluate side-chains 96 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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: 0.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 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: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g2 179 GLN e2 36 ASN e2 57 ASN ** H2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9041 Z= 0.215 Angle : 0.536 5.101 12223 Z= 0.297 Chirality : 0.038 0.132 1486 Planarity : 0.004 0.039 1518 Dihedral : 4.391 22.473 1264 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.43 % Allowed : 9.78 % Favored : 89.80 % 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: -1.23 (0.24), residues: 1174 helix: -0.13 (0.17), residues: 903 sheet: -2.88 (0.45), residues: 96 loop : -2.41 (0.43), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPe2 2 HIS 0.003 0.001 HISd2 80 PHE 0.015 0.001 PHEI2 121 TYR 0.009 0.001 TYRg2 249 ARG 0.004 0.000 ARGN2 130 *********************** 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 113 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.5183 (tpp) cc_final: 0.4835 (tpp) REVERT: g2 260 ASP cc_start: 0.8140 (m-30) cc_final: 0.7839 (m-30) REVERT: d2 91 GLU cc_start: 0.7334 (pt0) cc_final: 0.7111 (pt0) REVERT: e2 53 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7193 (ptp90) REVERT: I2 146 MET cc_start: 0.7232 (mmm) cc_final: 0.6708 (tmm) REVERT: J2 137 ASP cc_start: 0.7872 (t70) cc_final: 0.7193 (t0) REVERT: M2 165 TYR cc_start: 0.7001 (m-10) cc_final: 0.6446 (m-80) REVERT: N2 108 MET cc_start: 0.7476 (mtm) cc_final: 0.7205 (mtm) REVERT: Q2 146 MET cc_start: 0.7620 (mmm) cc_final: 0.7164 (mmm) outliers start: 4 outliers final: 4 residues processed: 111 average time/residue: 0.4857 time to fit residues: 74.6385 Evaluate side-chains 106 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g2 residue 153 SER Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g2 261 ASN ** H2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9041 Z= 0.246 Angle : 0.523 5.007 12223 Z= 0.287 Chirality : 0.037 0.134 1486 Planarity : 0.004 0.037 1518 Dihedral : 4.283 22.317 1264 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.49 % Allowed : 9.78 % Favored : 88.74 % 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: 0.46 (0.26), residues: 1174 helix: 1.08 (0.18), residues: 897 sheet: -2.58 (0.48), residues: 92 loop : -1.62 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPg2 175 HIS 0.003 0.001 HISd2 80 PHE 0.014 0.001 PHEI2 121 TYR 0.008 0.001 TYRg2 249 ARG 0.004 0.000 ARGM2 130 *********************** 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 141 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.5743 (tpp) cc_final: 0.5453 (tpp) REVERT: g2 164 LYS cc_start: 0.8133 (tptt) cc_final: 0.7648 (tptt) REVERT: d2 141 ASP cc_start: 0.6822 (t0) cc_final: 0.6299 (t0) REVERT: d2 176 SER cc_start: 0.8319 (m) cc_final: 0.8071 (t) REVERT: I2 146 MET cc_start: 0.7468 (mmm) cc_final: 0.7233 (mmm) REVERT: J2 137 ASP cc_start: 0.7995 (t70) cc_final: 0.7274 (t0) REVERT: J2 146 MET cc_start: 0.8012 (mmp) cc_final: 0.7724 (mmp) REVERT: M2 165 TYR cc_start: 0.6921 (m-10) cc_final: 0.6518 (m-80) REVERT: N2 146 MET cc_start: 0.7206 (mmm) cc_final: 0.6857 (mmm) REVERT: L2 159 MET cc_start: 0.7135 (mmt) cc_final: 0.6832 (mmt) outliers start: 14 outliers final: 10 residues processed: 138 average time/residue: 0.5169 time to fit residues: 96.8602 Evaluate side-chains 127 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 153 SER Chi-restraints excluded: chain g2 residue 212 THR Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 109 SER Chi-restraints excluded: chain H2 residue 137 ASP Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7871 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9041 Z= 0.250 Angle : 0.525 5.147 12223 Z= 0.288 Chirality : 0.037 0.162 1486 Planarity : 0.003 0.038 1518 Dihedral : 4.229 21.932 1264 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.96 % Allowed : 12.86 % Favored : 86.18 % 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: 0.93 (0.26), residues: 1174 helix: 1.38 (0.18), residues: 896 sheet: -2.35 (0.49), residues: 92 loop : -1.31 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 PHE 0.014 0.001 PHEI2 121 TYR 0.007 0.001 TYRg2 249 ARG 0.003 0.000 ARGQ2 130 *********************** 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 134 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6155 (tpp) cc_final: 0.5756 (tpp) REVERT: g2 164 LYS cc_start: 0.8202 (tptt) cc_final: 0.7709 (tptt) REVERT: d2 139 MET cc_start: 0.6400 (mmt) cc_final: 0.6039 (mmt) REVERT: H2 146 MET cc_start: 0.8001 (mmm) cc_final: 0.7691 (mmm) REVERT: I2 146 MET cc_start: 0.7538 (mmm) cc_final: 0.6909 (tmm) REVERT: J2 137 ASP cc_start: 0.8028 (t70) cc_final: 0.7312 (t0) REVERT: M2 165 TYR cc_start: 0.6916 (m-80) cc_final: 0.6584 (m-80) REVERT: O2 159 MET cc_start: 0.7727 (tpp) cc_final: 0.7427 (tpp) REVERT: L2 150 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6835 (mt-10) outliers start: 9 outliers final: 7 residues processed: 131 average time/residue: 0.5024 time to fit residues: 91.3448 Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 153 SER Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 109 SER Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9041 Z= 0.258 Angle : 0.513 5.608 12223 Z= 0.283 Chirality : 0.037 0.149 1486 Planarity : 0.003 0.039 1518 Dihedral : 4.208 22.415 1264 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.02 % Allowed : 13.18 % Favored : 84.80 % 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: 1.18 (0.26), residues: 1174 helix: 1.52 (0.18), residues: 901 sheet: -2.21 (0.49), residues: 94 loop : -1.09 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 PHE 0.013 0.001 PHEI2 121 TYR 0.007 0.001 TYRg2 199 ARG 0.002 0.000 ARGg2 165 *********************** 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 146 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6307 (tpp) cc_final: 0.5918 (tpp) REVERT: g2 164 LYS cc_start: 0.8201 (tptt) cc_final: 0.7763 (tptt) REVERT: I2 146 MET cc_start: 0.7510 (mmm) cc_final: 0.6909 (tmm) REVERT: J2 137 ASP cc_start: 0.8002 (t70) cc_final: 0.7488 (t0) REVERT: M2 165 TYR cc_start: 0.6959 (m-80) cc_final: 0.6605 (m-80) REVERT: O2 159 MET cc_start: 0.7857 (tpp) cc_final: 0.7606 (tpp) REVERT: L2 150 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6894 (mt-10) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 0.5003 time to fit residues: 95.5148 Evaluate side-chains 129 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 13 GLN Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 153 SER Chi-restraints excluded: chain g2 residue 196 MET Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 76 MET Chi-restraints excluded: chain d2 residue 109 SER Chi-restraints excluded: chain H2 residue 137 ASP Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain P2 residue 155 ILE 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: 0.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9041 Z= 0.274 Angle : 0.525 5.189 12223 Z= 0.290 Chirality : 0.037 0.148 1486 Planarity : 0.003 0.041 1518 Dihedral : 4.222 22.648 1264 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.34 % Allowed : 13.39 % Favored : 84.27 % 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: 1.31 (0.26), residues: 1174 helix: 1.60 (0.18), residues: 901 sheet: -2.17 (0.49), residues: 94 loop : -0.96 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 PHE 0.014 0.001 PHEI2 121 TYR 0.007 0.001 TYRg2 199 ARG 0.005 0.000 ARGd2 63 *********************** 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 147 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6355 (tpp) cc_final: 0.6052 (tpp) REVERT: g2 164 LYS cc_start: 0.8245 (tptt) cc_final: 0.7812 (tptt) REVERT: g2 258 MET cc_start: 0.7854 (tpt) cc_final: 0.7176 (tpt) REVERT: I2 146 MET cc_start: 0.7563 (mmm) cc_final: 0.6963 (tmm) REVERT: J2 137 ASP cc_start: 0.8009 (t70) cc_final: 0.7289 (t0) REVERT: N2 131 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8495 (t0) REVERT: O2 146 MET cc_start: 0.7956 (mmm) cc_final: 0.7693 (mmm) REVERT: P2 137 ASP cc_start: 0.7831 (t0) cc_final: 0.7205 (t70) REVERT: L2 150 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6906 (mt-10) outliers start: 22 outliers final: 13 residues processed: 141 average time/residue: 0.4386 time to fit residues: 87.4384 Evaluate side-chains 135 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 212 THR Chi-restraints excluded: chain g2 residue 253 THR Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 109 SER Chi-restraints excluded: chain H2 residue 137 ASP Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain I2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain N2 residue 131 ASN Chi-restraints excluded: chain P2 residue 155 ILE 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: 0.5980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4475 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= 0.229 Angle : 0.506 5.943 12223 Z= 0.276 Chirality : 0.036 0.141 1486 Planarity : 0.003 0.038 1518 Dihedral : 4.141 22.727 1264 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 14.67 % Favored : 83.74 % 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: 1.52 (0.26), residues: 1174 helix: 1.75 (0.18), residues: 902 sheet: -2.13 (0.49), residues: 94 loop : -0.90 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 PHE 0.013 0.001 PHEI2 121 TYR 0.006 0.001 TYRg2 249 ARG 0.002 0.000 ARGd2 63 *********************** 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 140 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6388 (tpp) cc_final: 0.6050 (tpp) REVERT: g2 164 LYS cc_start: 0.8253 (tptt) cc_final: 0.7812 (tptt) REVERT: g2 258 MET cc_start: 0.7836 (tpt) cc_final: 0.7184 (tpt) REVERT: J2 137 ASP cc_start: 0.8025 (t70) cc_final: 0.7285 (t0) REVERT: K2 165 TYR cc_start: 0.7193 (m-10) cc_final: 0.6762 (m-10) REVERT: N2 131 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8412 (t0) REVERT: P2 137 ASP cc_start: 0.7778 (t0) cc_final: 0.7131 (t70) REVERT: Q2 146 MET cc_start: 0.7838 (mmm) cc_final: 0.6581 (tmm) REVERT: L2 150 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6858 (mt-10) outliers start: 15 outliers final: 11 residues processed: 137 average time/residue: 0.4249 time to fit residues: 83.5826 Evaluate side-chains 140 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 97 VAL Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 109 SER Chi-restraints excluded: chain H2 residue 137 ASP Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain N2 residue 131 ASN Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9041 Z= 0.273 Angle : 0.524 5.297 12223 Z= 0.289 Chirality : 0.037 0.148 1486 Planarity : 0.003 0.040 1518 Dihedral : 4.189 22.915 1264 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.81 % Allowed : 14.35 % Favored : 83.85 % 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: 1.44 (0.26), residues: 1174 helix: 1.72 (0.18), residues: 903 sheet: -2.17 (0.49), residues: 94 loop : -1.04 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 PHE 0.013 0.001 PHEI2 121 TYR 0.007 0.001 TYRg2 199 ARG 0.002 0.000 ARGd2 63 *********************** 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 149 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6453 (tpp) cc_final: 0.6064 (tpp) REVERT: g2 164 LYS cc_start: 0.8321 (tptt) cc_final: 0.7868 (tptm) REVERT: g2 258 MET cc_start: 0.7871 (tpt) cc_final: 0.7218 (tpt) REVERT: I2 146 MET cc_start: 0.7579 (mmm) cc_final: 0.6859 (tmm) REVERT: J2 137 ASP cc_start: 0.8038 (t70) cc_final: 0.7305 (t0) REVERT: K2 165 TYR cc_start: 0.7162 (m-10) cc_final: 0.6713 (m-10) REVERT: O2 146 MET cc_start: 0.7973 (mmm) cc_final: 0.7660 (mmm) REVERT: Q2 146 MET cc_start: 0.7940 (mmm) cc_final: 0.6662 (tmm) REVERT: L2 150 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6868 (mt-10) outliers start: 17 outliers final: 14 residues processed: 145 average time/residue: 0.4370 time to fit residues: 88.9010 Evaluate side-chains 140 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 97 VAL Chi-restraints excluded: chain g2 residue 212 THR Chi-restraints excluded: chain g2 residue 253 THR Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 109 SER Chi-restraints excluded: chain H2 residue 137 ASP Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain I2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9041 Z= 0.216 Angle : 0.494 5.006 12223 Z= 0.270 Chirality : 0.036 0.144 1486 Planarity : 0.003 0.039 1518 Dihedral : 4.091 22.912 1264 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.81 % Allowed : 14.24 % Favored : 83.95 % 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: 1.65 (0.26), residues: 1174 helix: 1.88 (0.18), residues: 903 sheet: -2.17 (0.49), residues: 94 loop : -0.98 (0.49), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 PHE 0.011 0.001 PHEI2 121 TYR 0.006 0.001 TYRg2 249 ARG 0.002 0.000 ARGd2 63 *********************** 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 148 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6423 (tpp) cc_final: 0.6061 (tpp) REVERT: K 172 SER cc_start: 0.7411 (OUTLIER) cc_final: 0.6885 (m) REVERT: g2 164 LYS cc_start: 0.8266 (tptt) cc_final: 0.7840 (tptm) REVERT: g2 258 MET cc_start: 0.7826 (tpt) cc_final: 0.7191 (tpt) REVERT: I2 146 MET cc_start: 0.7490 (mmm) cc_final: 0.6806 (tmm) REVERT: J2 137 ASP cc_start: 0.8009 (t70) cc_final: 0.7448 (t0) REVERT: O2 146 MET cc_start: 0.7893 (mmm) cc_final: 0.7566 (mmm) REVERT: Q2 146 MET cc_start: 0.7899 (mmm) cc_final: 0.6627 (tmm) REVERT: L2 150 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6862 (mt-10) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.4806 time to fit residues: 95.7233 Evaluate side-chains 143 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 97 VAL Chi-restraints excluded: chain g2 residue 253 THR Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 109 SER Chi-restraints excluded: chain H2 residue 137 ASP Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain I2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain L2 residue 154 ILE 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: 0.8980 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9041 Z= 0.281 Angle : 0.527 5.345 12223 Z= 0.292 Chirality : 0.037 0.148 1486 Planarity : 0.003 0.040 1518 Dihedral : 4.173 23.269 1264 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.81 % Allowed : 14.35 % Favored : 83.85 % 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: 1.48 (0.26), residues: 1174 helix: 1.76 (0.18), residues: 909 sheet: -2.24 (0.49), residues: 94 loop : -1.13 (0.49), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 PHE 0.015 0.001 PHEO2 148 TYR 0.007 0.001 TYRg2 199 ARG 0.002 0.000 ARG K 166 ********************** 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 145 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6469 (tpp) cc_final: 0.6082 (tpp) REVERT: K 172 SER cc_start: 0.7333 (OUTLIER) cc_final: 0.6807 (m) REVERT: g2 164 LYS cc_start: 0.8330 (tptt) cc_final: 0.7885 (tptm) REVERT: g2 258 MET cc_start: 0.7860 (tpt) cc_final: 0.7207 (tpt) REVERT: I2 146 MET cc_start: 0.7477 (mmm) cc_final: 0.6956 (tmm) REVERT: J2 137 ASP cc_start: 0.8015 (t70) cc_final: 0.7460 (t0) REVERT: M2 146 MET cc_start: 0.7290 (tpp) cc_final: 0.6759 (tpp) REVERT: Q2 146 MET cc_start: 0.7937 (mmm) cc_final: 0.6592 (tmm) REVERT: L2 150 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6907 (mt-10) outliers start: 17 outliers final: 14 residues processed: 141 average time/residue: 0.4815 time to fit residues: 95.5520 Evaluate side-chains 143 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 97 VAL Chi-restraints excluded: chain g2 residue 212 THR Chi-restraints excluded: chain g2 residue 253 THR Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 109 SER Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain I2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain O2 residue 120 LEU Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain L2 residue 154 ILE 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: 0.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.151507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134468 restraints weight = 28702.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138717 restraints weight = 13856.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141389 restraints weight = 8264.897| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9041 Z= 0.280 Angle : 0.530 5.360 12223 Z= 0.293 Chirality : 0.037 0.145 1486 Planarity : 0.003 0.040 1518 Dihedral : 4.212 23.102 1264 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.59 % Allowed : 14.56 % Favored : 83.85 % 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: 1.44 (0.26), residues: 1174 helix: 1.74 (0.18), residues: 909 sheet: -2.34 (0.48), residues: 94 loop : -1.19 (0.49), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 PHE 0.012 0.001 PHEI2 121 TYR 0.007 0.001 TYRg2 199 ARG 0.002 0.000 ARGd2 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4256.13 seconds wall clock time: 77 minutes 17.64 seconds (4637.64 seconds total)