Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 00:58:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/04_2023/7yk6_33888_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/04_2023/7yk6_33888.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/04_2023/7yk6_33888_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/04_2023/7yk6_33888_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/04_2023/7yk6_33888_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/04_2023/7yk6_33888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/04_2023/7yk6_33888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/04_2023/7yk6_33888_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk6_33888/04_2023/7yk6_33888_updated.pdb" } resolution = 3.03 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= 0.023 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 55 5.16 5 Cl 1 4.86 5 C 5575 2.51 5 N 1497 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 8": "OE1" <-> "OE2" Residue "R ARG 194": "NH1" <-> "NH2" Residue "R PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8736 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1694 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 208} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2220 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "T" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'IYF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.54 Number of scatterers: 8736 At special positions: 0 Unit cell: (91.035, 118.881, 131.733, 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) Cl 1 17.00 S 55 16.00 O 1608 8.00 N 1497 7.00 C 5575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 2.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 34.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'I' and resid 7 through 29 Processing helix chain 'I' and resid 46 through 52 Processing helix chain 'I' and resid 209 through 216 removed outlier: 4.172A pdb=" N HIS I 214 " --> pdb=" O LYS I 210 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N CYS I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE I 216 " --> pdb=" O TRP I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 256 Processing helix chain 'I' and resid 272 through 281 removed outlier: 3.913A pdb=" N GLU I 277 " --> pdb=" O ASP I 273 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR I 280 " --> pdb=" O GLU I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 286 No H-bonds generated for 'chain 'I' and resid 284 through 286' Processing helix chain 'I' and resid 300 through 311 Processing helix chain 'I' and resid 332 through 352 removed outlier: 3.744A pdb=" N VAL I 336 " --> pdb=" O ASN I 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 63 Processing helix chain 'R' and resid 75 through 102 removed outlier: 4.381A pdb=" N PHE R 79 " --> pdb=" O PRO R 75 " (cutoff:3.500A) Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 111 through 143 removed outlier: 4.266A pdb=" N LYS R 115 " --> pdb=" O GLY R 111 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N MET R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 179 Proline residue: R 175 - end of helix Processing helix chain 'R' and resid 203 through 211 Processing helix chain 'R' and resid 214 through 233 removed outlier: 3.662A pdb=" N ARG R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 274 removed outlier: 3.876A pdb=" N ARG R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL R 243 " --> pdb=" O GLN R 239 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL R 244 " --> pdb=" O ASP R 240 " (cutoff:3.500A) Proline residue: R 261 - end of helix Processing helix chain 'R' and resid 283 through 310 Proline residue: R 292 - end of helix removed outlier: 3.626A pdb=" N SER R 300 " --> pdb=" O CYS R 296 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN R 301 " --> pdb=" O LEU R 297 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N CYS R 303 " --> pdb=" O HIS R 299 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 314 through 319 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'T' and resid 4 through 24 Processing helix chain 'T' and resid 30 through 36 removed outlier: 4.999A pdb=" N ASN T 36 " --> pdb=" O GLN T 32 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 320 through 324 removed outlier: 6.916A pdb=" N ILE I 265 " --> pdb=" O TYR I 321 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS I 323 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU I 267 " --> pdb=" O HIS I 323 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA I 221 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS I 225 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS I 196 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU I 36 " --> pdb=" O HIS I 196 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS I 198 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU I 38 " --> pdb=" O LYS I 198 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE I 200 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.573A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU S 20 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'S' and resid 95 through 99 removed outlier: 3.623A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.552A pdb=" N ILE S 216 " --> pdb=" O VAL S 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.423A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.688A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'T' and resid 58 through 63 removed outlier: 6.957A pdb=" N ALA T 73 " --> pdb=" O TYR T 59 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET T 61 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL T 71 " --> pdb=" O MET T 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP T 63 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU T 69 " --> pdb=" O TRP T 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER T 74 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS T 91 " --> pdb=" O ILE T 81 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP T 83 " --> pdb=" O LYS T 89 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LYS T 89 " --> pdb=" O ASP T 83 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'T' and resid 100 through 105 removed outlier: 6.829A pdb=" N GLY T 115 " --> pdb=" O MET T 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS T 103 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA T 113 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR T 105 " --> pdb=" O TYR T 111 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR T 111 " --> pdb=" O TYR T 105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG T 137 " --> pdb=" O ILE T 123 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN T 125 " --> pdb=" O VAL T 135 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL T 135 " --> pdb=" O ASN T 125 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 146 through 151 removed outlier: 6.760A pdb=" N SER T 160 " --> pdb=" O SER T 147 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS T 149 " --> pdb=" O VAL T 158 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL T 158 " --> pdb=" O CYS T 149 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N PHE T 151 " --> pdb=" O GLN T 156 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN T 156 " --> pdb=" O PHE T 151 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE T 157 " --> pdb=" O TRP T 169 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR T 165 " --> pdb=" O SER T 161 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR T 178 " --> pdb=" O LEU T 168 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP T 170 " --> pdb=" O GLN T 176 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN T 176 " --> pdb=" O ASP T 170 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 220 through 223 removed outlier: 3.761A pdb=" N GLN T 220 " --> pdb=" O LEU T 210 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER T 207 " --> pdb=" O ALA T 203 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY T 202 " --> pdb=" O SER T 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 229 through 234 removed outlier: 6.576A pdb=" N GLY T 244 " --> pdb=" O ASN T 230 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE T 232 " --> pdb=" O ALA T 242 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA T 242 " --> pdb=" O ILE T 232 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE T 234 " --> pdb=" O ALA T 240 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA T 240 " --> pdb=" O PHE T 234 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR T 249 " --> pdb=" O SER T 245 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET T 262 " --> pdb=" O LEU T 252 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP T 254 " --> pdb=" O GLU T 260 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU T 260 " --> pdb=" O ASP T 254 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 276 through 278 Processing sheet with id= M, first strand: chain 'T' and resid 46 through 52 removed outlier: 3.630A pdb=" N ARG T 46 " --> pdb=" O ASN T 340 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN T 340 " --> pdb=" O ARG T 46 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE T 338 " --> pdb=" O ARG T 48 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR T 50 " --> pdb=" O LEU T 336 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU T 336 " --> pdb=" O THR T 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE T 335 " --> pdb=" O SER T 331 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER T 331 " --> pdb=" O PHE T 335 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1062 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: 2.46 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2811 1.34 - 1.46: 2135 1.46 - 1.58: 3902 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8927 Sorted by residual: bond pdb=" C10 IYF R 601 " pdb=" N11 IYF R 601 " ideal model delta sigma weight residual 1.267 1.475 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C27 IYF R 601 " pdb=" N26 IYF R 601 " ideal model delta sigma weight residual 1.372 1.503 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" C25 IYF R 601 " pdb=" C9 IYF R 601 " ideal model delta sigma weight residual 1.378 1.271 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C27 IYF R 601 " pdb=" C8 IYF R 601 " ideal model delta sigma weight residual 1.372 1.476 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C7 IYF R 601 " pdb=" C8 IYF R 601 " ideal model delta sigma weight residual 1.403 1.361 0.042 2.00e-02 2.50e+03 4.37e+00 ... (remaining 8922 not shown) Histogram of bond angle deviations from ideal: 98.26 - 106.95: 211 106.95 - 115.64: 5488 115.64 - 124.33: 6233 124.33 - 133.02: 151 133.02 - 141.71: 26 Bond angle restraints: 12109 Sorted by residual: angle pdb=" N PHE R 324 " pdb=" CA PHE R 324 " pdb=" C PHE R 324 " ideal model delta sigma weight residual 112.23 104.25 7.98 1.26e+00 6.30e-01 4.01e+01 angle pdb=" C25 IYF R 601 " pdb=" C9 IYF R 601 " pdb=" C8 IYF R 601 " ideal model delta sigma weight residual 107.94 125.02 -17.08 3.00e+00 1.11e-01 3.24e+01 angle pdb=" C10 IYF R 601 " pdb=" C9 IYF R 601 " pdb=" C8 IYF R 601 " ideal model delta sigma weight residual 133.12 117.58 15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C2 IYF R 601 " pdb=" C3 IYF R 601 " pdb=" C4 IYF R 601 " ideal model delta sigma weight residual 105.67 120.45 -14.78 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C2 IYF R 601 " pdb=" C3 IYF R 601 " pdb=" C27 IYF R 601 " ideal model delta sigma weight residual 133.82 119.19 14.63 3.00e+00 1.11e-01 2.38e+01 ... (remaining 12104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 4993 26.07 - 52.15: 231 52.15 - 78.22: 17 78.22 - 104.30: 5 104.30 - 130.37: 1 Dihedral angle restraints: 5247 sinusoidal: 2018 harmonic: 3229 Sorted by residual: dihedral pdb=" CA TRP R 200 " pdb=" C TRP R 200 " pdb=" N LEU R 201 " pdb=" CA LEU R 201 " ideal model delta harmonic sigma weight residual -180.00 -152.18 -27.82 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA LEU R 193 " pdb=" C LEU R 193 " pdb=" N ARG R 194 " pdb=" CA ARG R 194 " ideal model delta harmonic sigma weight residual 180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ARG R 198 " pdb=" C ARG R 198 " pdb=" N TYR R 199 " pdb=" CA TYR R 199 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1210 0.072 - 0.144: 160 0.144 - 0.216: 3 0.216 - 0.288: 0 0.288 - 0.360: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA THR R 323 " pdb=" N THR R 323 " pdb=" C THR R 323 " pdb=" CB THR R 323 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA PHE R 324 " pdb=" N PHE R 324 " pdb=" C PHE R 324 " pdb=" CB PHE R 324 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA ARG I 32 " pdb=" N ARG I 32 " pdb=" C ARG I 32 " pdb=" CB ARG I 32 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1371 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 IYF R 601 " -0.127 2.00e-02 2.50e+03 3.79e-01 2.15e+03 pdb=" C16 IYF R 601 " 0.554 2.00e-02 2.50e+03 pdb=" N11 IYF R 601 " 0.318 2.00e-02 2.50e+03 pdb=" N12 IYF R 601 " -0.318 2.00e-02 2.50e+03 pdb=" N14 IYF R 601 " 0.136 2.00e-02 2.50e+03 pdb=" N15 IYF R 601 " -0.563 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IYF R 601 " 0.259 2.00e-02 2.50e+03 2.69e-01 7.23e+02 pdb=" C9 IYF R 601 " -0.255 2.00e-02 2.50e+03 pdb=" N11 IYF R 601 " 0.278 2.00e-02 2.50e+03 pdb=" N12 IYF R 601 " -0.282 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.077 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO S 148 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.061 5.00e-02 4.00e+02 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 193 2.68 - 3.24: 8570 3.24 - 3.79: 13496 3.79 - 4.35: 17765 4.35 - 4.90: 29840 Nonbonded interactions: 69864 Sorted by model distance: nonbonded pdb=" O THR R 282 " pdb=" OG1 THR R 285 " model vdw 2.130 2.440 nonbonded pdb=" OG SER T 245 " pdb=" OD1 ASP T 247 " model vdw 2.158 2.440 nonbonded pdb=" OG SER T 161 " pdb=" OD1 ASP T 163 " model vdw 2.166 2.440 nonbonded pdb=" OG SER T 331 " pdb=" OD1 ASP T 333 " model vdw 2.182 2.440 nonbonded pdb=" OD1 ASP T 153 " pdb=" N ASP T 154 " model vdw 2.207 2.520 ... (remaining 69859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.010 Extract box with map and model: 4.170 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.670 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 0.006 0.208 8927 Z= 0.352 Angle : 0.744 17.078 12109 Z= 0.382 Chirality : 0.046 0.360 1374 Planarity : 0.013 0.379 1528 Dihedral : 14.186 130.370 3157 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.44 % Rotamer Outliers : 0.21 % 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: -0.18 (0.26), residues: 1098 helix: 1.79 (0.28), residues: 358 sheet: -0.56 (0.32), residues: 297 loop : -1.38 (0.28), residues: 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 1.024 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 197 average time/residue: 0.2513 time to fit residues: 64.8111 Evaluate side-chains 178 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0827 time to fit residues: 1.5798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8927 Z= 0.206 Angle : 0.634 21.987 12109 Z= 0.308 Chirality : 0.043 0.149 1374 Planarity : 0.005 0.076 1528 Dihedral : 6.832 127.316 1213 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % 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: 0.13 (0.26), residues: 1098 helix: 2.03 (0.28), residues: 352 sheet: -0.12 (0.32), residues: 290 loop : -1.35 (0.28), residues: 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 224 time to evaluate : 1.006 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 227 average time/residue: 0.2728 time to fit residues: 79.9547 Evaluate side-chains 211 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0918 time to fit residues: 2.7567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8927 Z= 0.256 Angle : 0.597 14.917 12109 Z= 0.300 Chirality : 0.043 0.153 1374 Planarity : 0.005 0.062 1528 Dihedral : 6.048 103.138 1213 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.26 % Rotamer Outliers : 1.39 % 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: 0.19 (0.26), residues: 1098 helix: 2.04 (0.28), residues: 352 sheet: 0.06 (0.33), residues: 284 loop : -1.37 (0.28), residues: 462 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 210 average time/residue: 0.2452 time to fit residues: 68.6899 Evaluate side-chains 215 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 207 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1655 time to fit residues: 3.3794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 0.0070 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 GLN ** T 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8927 Z= 0.162 Angle : 0.533 9.486 12109 Z= 0.271 Chirality : 0.041 0.152 1374 Planarity : 0.004 0.055 1528 Dihedral : 5.623 86.891 1213 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 1.28 % 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: 0.33 (0.27), residues: 1098 helix: 2.20 (0.28), residues: 351 sheet: 0.09 (0.33), residues: 289 loop : -1.30 (0.29), residues: 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 218 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 225 average time/residue: 0.2554 time to fit residues: 75.7374 Evaluate side-chains 215 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1474 time to fit residues: 2.4857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8927 Z= 0.248 Angle : 0.582 12.891 12109 Z= 0.293 Chirality : 0.043 0.169 1374 Planarity : 0.005 0.060 1528 Dihedral : 5.563 80.463 1213 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 1.49 % 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: 1098 helix: 2.11 (0.28), residues: 355 sheet: 0.09 (0.33), residues: 288 loop : -1.29 (0.29), residues: 455 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 1.028 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 220 average time/residue: 0.2604 time to fit residues: 74.7725 Evaluate side-chains 208 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 203 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1752 time to fit residues: 2.6165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.0030 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 270 ASN ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8927 Z= 0.202 Angle : 0.561 10.960 12109 Z= 0.284 Chirality : 0.042 0.158 1374 Planarity : 0.005 0.061 1528 Dihedral : 5.383 71.660 1213 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.39 % 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: 0.32 (0.26), residues: 1098 helix: 2.09 (0.27), residues: 358 sheet: 0.13 (0.33), residues: 283 loop : -1.29 (0.29), residues: 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 208 average time/residue: 0.2606 time to fit residues: 70.9332 Evaluate side-chains 206 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 200 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1381 time to fit residues: 2.4518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.0170 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 270 ASN ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8927 Z= 0.210 Angle : 0.565 10.303 12109 Z= 0.285 Chirality : 0.043 0.167 1374 Planarity : 0.004 0.063 1528 Dihedral : 5.319 68.303 1213 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.28 % 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: 0.34 (0.26), residues: 1098 helix: 2.07 (0.27), residues: 359 sheet: 0.17 (0.33), residues: 283 loop : -1.27 (0.29), residues: 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 206 time to evaluate : 0.955 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 211 average time/residue: 0.2548 time to fit residues: 70.8546 Evaluate side-chains 210 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1534 time to fit residues: 2.1804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.0570 chunk 72 optimal weight: 0.0970 chunk 52 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 270 ASN ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 8927 Z= 0.150 Angle : 0.546 9.709 12109 Z= 0.276 Chirality : 0.042 0.174 1374 Planarity : 0.004 0.061 1528 Dihedral : 4.998 51.845 1213 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 1.28 % 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: 0.38 (0.26), residues: 1098 helix: 2.16 (0.28), residues: 357 sheet: 0.13 (0.33), residues: 287 loop : -1.24 (0.29), residues: 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 206 time to evaluate : 0.904 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 212 average time/residue: 0.2471 time to fit residues: 69.2731 Evaluate side-chains 207 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 200 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1318 time to fit residues: 2.7952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.0270 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8927 Z= 0.191 Angle : 0.562 9.823 12109 Z= 0.282 Chirality : 0.042 0.189 1374 Planarity : 0.004 0.055 1528 Dihedral : 5.007 52.068 1213 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 0.64 % 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: 0.33 (0.26), residues: 1098 helix: 2.10 (0.27), residues: 357 sheet: 0.10 (0.32), residues: 294 loop : -1.27 (0.29), residues: 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 198 average time/residue: 0.2610 time to fit residues: 67.9534 Evaluate side-chains 198 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1082 time to fit residues: 2.0609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.0070 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8927 Z= 0.175 Angle : 0.561 10.375 12109 Z= 0.282 Chirality : 0.042 0.192 1374 Planarity : 0.004 0.054 1528 Dihedral : 4.974 50.394 1213 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % 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: 0.33 (0.26), residues: 1098 helix: 2.09 (0.27), residues: 357 sheet: 0.14 (0.33), residues: 287 loop : -1.28 (0.29), residues: 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 1.084 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 202 average time/residue: 0.2513 time to fit residues: 67.5716 Evaluate side-chains 201 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0840 time to fit residues: 1.9904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 176 GLN T 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.154303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130992 restraints weight = 13598.467| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.62 r_work: 0.3573 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8927 Z= 0.190 Angle : 0.575 10.204 12109 Z= 0.288 Chirality : 0.042 0.191 1374 Planarity : 0.004 0.055 1528 Dihedral : 4.988 50.732 1213 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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: 0.30 (0.26), residues: 1098 helix: 2.05 (0.27), residues: 357 sheet: 0.13 (0.33), residues: 287 loop : -1.29 (0.29), residues: 454 =============================================================================== Job complete usr+sys time: 2343.92 seconds wall clock time: 43 minutes 1.33 seconds (2581.33 seconds total)