Starting phenix.real_space_refine on Thu Mar 14 13:23:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykd_33891/03_2024/7ykd_33891_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykd_33891/03_2024/7ykd_33891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykd_33891/03_2024/7ykd_33891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykd_33891/03_2024/7ykd_33891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykd_33891/03_2024/7ykd_33891_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ykd_33891/03_2024/7ykd_33891_updated.pdb" } resolution = 2.81 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5778 2.51 5 N 1496 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 137": "NH1" <-> "NH2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "S GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8965 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "A" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2250 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain breaks: 1 Chain: "C" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1716 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2580 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.16, per 1000 atoms: 0.58 Number of scatterers: 8965 At special positions: 0 Unit cell: (87.98, 121.18, 121.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1623 8.00 N 1496 7.00 C 5778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 34.5% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 35 through 67 Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.675A pdb=" N TRP A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 109 through 142 removed outlier: 3.987A pdb=" N LEU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 153 through 176 Proline residue: A 173 - end of helix removed outlier: 3.680A pdb=" N VAL A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 249 removed outlier: 6.143A pdb=" N VAL A 231 " --> pdb=" O CYS A 227 " (cutoff:3.500A) Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 257 through 282 Proline residue: A 275 - end of helix Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 291 through 316 Proline residue: A 299 - end of helix Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'C' and resid 7 through 30 Processing helix chain 'C' and resid 46 through 52 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 310 removed outlier: 4.193A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' 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 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 180 through 183 removed outlier: 3.721A pdb=" N LEU A 183 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 322 through 324 removed outlier: 3.564A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS C 195 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU C 36 " --> pdb=" O HIS C 195 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LYS C 197 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 38 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE C 199 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLY C 40 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.760A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.968A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.501A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.651A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.400A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.453A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.616A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 5 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 115 through 117 removed outlier: 5.571A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.445A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.577A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1179 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: 2.59 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1438 1.32 - 1.44: 2502 1.44 - 1.56: 5131 1.56 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 9170 Sorted by residual: bond pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.34e-02 5.57e+03 3.68e+01 bond pdb=" CA LYS B 337 " pdb=" C LYS B 337 " ideal model delta sigma weight residual 1.521 1.471 0.050 1.24e-02 6.50e+03 1.61e+01 bond pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.23e-02 6.61e+03 1.36e+01 bond pdb=" CA PHE B 335 " pdb=" C PHE B 335 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.20e-02 6.94e+03 1.30e+01 bond pdb=" C LYS B 337 " pdb=" O LYS B 337 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.22e-02 6.72e+03 1.02e+01 ... (remaining 9165 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.52: 154 105.52 - 112.68: 4901 112.68 - 119.85: 3024 119.85 - 127.01: 4267 127.01 - 134.17: 103 Bond angle restraints: 12449 Sorted by residual: angle pdb=" N VAL S 2 " pdb=" CA VAL S 2 " pdb=" C VAL S 2 " ideal model delta sigma weight residual 112.43 104.83 7.60 9.20e-01 1.18e+00 6.82e+01 angle pdb=" N LEU B 336 " pdb=" CA LEU B 336 " pdb=" C LEU B 336 " ideal model delta sigma weight residual 109.40 102.00 7.40 1.63e+00 3.76e-01 2.06e+01 angle pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" O ASP B 291 " ideal model delta sigma weight residual 120.51 114.44 6.07 1.43e+00 4.89e-01 1.80e+01 angle pdb=" N VAL A 141 " pdb=" CA VAL A 141 " pdb=" C VAL A 141 " ideal model delta sigma weight residual 111.90 108.60 3.30 8.10e-01 1.52e+00 1.66e+01 angle pdb=" CA LEU A 143 " pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 117.73 121.77 -4.04 1.04e+00 9.25e-01 1.51e+01 ... (remaining 12444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 5384 23.97 - 47.94: 217 47.94 - 71.91: 31 71.91 - 95.88: 19 95.88 - 119.85: 1 Dihedral angle restraints: 5652 sinusoidal: 2373 harmonic: 3279 Sorted by residual: dihedral pdb=" CB CYS A 112 " pdb=" SG CYS A 112 " pdb=" SG CYS A 189 " pdb=" CB CYS A 189 " ideal model delta sinusoidal sigma weight residual 93.00 161.98 -68.98 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE A 67 " pdb=" C PHE A 67 " pdb=" N LYS A 68 " pdb=" CA LYS A 68 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1218 0.075 - 0.150: 204 0.150 - 0.226: 5 0.226 - 0.301: 3 0.301 - 0.376: 3 Chirality restraints: 1433 Sorted by residual: chirality pdb=" CA ASP B 312 " pdb=" N ASP B 312 " pdb=" C ASP B 312 " pdb=" CB ASP B 312 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C20 CLR A 403 " pdb=" C17 CLR A 403 " pdb=" C21 CLR A 403 " pdb=" C22 CLR A 403 " both_signs ideal model delta sigma weight residual False 2.59 2.23 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C20 CLR A 405 " pdb=" C17 CLR A 405 " pdb=" C21 CLR A 405 " pdb=" C22 CLR A 405 " both_signs ideal model delta sigma weight residual False 2.59 2.24 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1430 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 23 " 0.033 2.00e-02 2.50e+03 2.02e-02 7.16e+00 pdb=" CG PHE L 23 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE L 23 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE L 23 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE L 23 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE L 23 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE L 23 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO S 75 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 226 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C LEU A 226 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU A 226 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 227 " -0.011 2.00e-02 2.50e+03 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 203 2.67 - 3.23: 8682 3.23 - 3.79: 14305 3.79 - 4.34: 19913 4.34 - 4.90: 33715 Nonbonded interactions: 76818 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.118 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.122 2.440 nonbonded pdb=" C25 CLR A 402 " pdb=" C21 CLR A 403 " model vdw 2.146 3.890 nonbonded pdb=" NZ LYS S 244 " pdb=" OE2 GLU S 246 " model vdw 2.160 2.520 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.175 2.520 ... (remaining 76813 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: 1.320 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: 6.770 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.230 Find NCS groups from input model: 0.260 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.009 0.081 9170 Z= 0.562 Angle : 0.860 9.265 12449 Z= 0.461 Chirality : 0.055 0.376 1433 Planarity : 0.004 0.057 1535 Dihedral : 14.190 119.850 3525 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.10 % Allowed : 0.83 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1111 helix: 0.91 (0.26), residues: 382 sheet: -0.04 (0.32), residues: 288 loop : -1.01 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.006 0.002 HIS A 217 PHE 0.033 0.003 PHE L 23 TYR 0.019 0.002 TYR B 105 ARG 0.009 0.001 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.055 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 33 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7468 (mm-30) REVERT: B 291 ASP cc_start: 0.7436 (m-30) cc_final: 0.7077 (m-30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 1.4278 time to fit residues: 224.9344 Evaluate side-chains 118 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0270 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9170 Z= 0.192 Angle : 0.628 7.538 12449 Z= 0.310 Chirality : 0.045 0.320 1433 Planarity : 0.004 0.048 1535 Dihedral : 7.035 56.958 1539 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.77 % Allowed : 8.85 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1111 helix: 1.57 (0.26), residues: 382 sheet: -0.00 (0.31), residues: 260 loop : -0.79 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS A 184 PHE 0.016 0.001 PHE A 190 TYR 0.014 0.001 TYR A 103 ARG 0.011 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.049 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 33 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7346 (mm-30) REVERT: C 248 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7793 (mmtt) REVERT: B 13 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8501 (pp30) REVERT: B 19 ARG cc_start: 0.7982 (tmm160) cc_final: 0.7694 (ttp-110) outliers start: 17 outliers final: 6 residues processed: 135 average time/residue: 1.2098 time to fit residues: 174.1999 Evaluate side-chains 127 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN C 331 ASN B 75 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9170 Z= 0.190 Angle : 0.593 8.867 12449 Z= 0.292 Chirality : 0.045 0.260 1433 Planarity : 0.003 0.045 1535 Dihedral : 7.421 74.543 1539 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.56 % Allowed : 12.50 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.51 (0.25), residues: 1111 helix: 1.85 (0.26), residues: 383 sheet: 0.02 (0.30), residues: 266 loop : -0.72 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 184 PHE 0.010 0.001 PHE A 124 TYR 0.011 0.001 TYR S 190 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 0.890 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 188 SER cc_start: 0.6074 (OUTLIER) cc_final: 0.5835 (p) REVERT: C 248 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7799 (mmtt) REVERT: B 19 ARG cc_start: 0.8062 (tmm160) cc_final: 0.7649 (ttp-110) REVERT: B 44 GLN cc_start: 0.8154 (mt0) cc_final: 0.7816 (mm-40) REVERT: B 118 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7892 (p0) outliers start: 15 outliers final: 3 residues processed: 136 average time/residue: 1.2740 time to fit residues: 184.2815 Evaluate side-chains 120 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain S residue 147 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN B 75 GLN B 340 ASN G 59 ASN S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9170 Z= 0.202 Angle : 0.577 8.364 12449 Z= 0.288 Chirality : 0.044 0.264 1433 Planarity : 0.003 0.044 1535 Dihedral : 6.307 57.428 1539 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.50 % Allowed : 14.17 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1111 helix: 2.00 (0.26), residues: 383 sheet: -0.01 (0.30), residues: 263 loop : -0.72 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 184 PHE 0.014 0.001 PHE A 52 TYR 0.010 0.001 TYR S 190 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.029 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 161 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6241 (mpm) REVERT: B 19 ARG cc_start: 0.8063 (tmm160) cc_final: 0.7598 (ttp-110) REVERT: B 23 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8629 (ttmt) REVERT: B 44 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7826 (mm-40) REVERT: B 100 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8756 (m) REVERT: B 118 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7913 (p0) REVERT: B 217 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7038 (pmm) REVERT: G 42 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6491 (mp0) outliers start: 24 outliers final: 9 residues processed: 129 average time/residue: 1.2622 time to fit residues: 173.5598 Evaluate side-chains 125 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9170 Z= 0.212 Angle : 0.576 9.138 12449 Z= 0.288 Chirality : 0.044 0.268 1433 Planarity : 0.003 0.044 1535 Dihedral : 6.189 59.053 1539 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.60 % Allowed : 14.79 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.66 (0.26), residues: 1111 helix: 2.05 (0.26), residues: 383 sheet: 0.10 (0.30), residues: 267 loop : -0.72 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 184 PHE 0.015 0.001 PHE A 190 TYR 0.011 0.001 TYR B 59 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 0.946 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 161 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6298 (mpm) REVERT: C 33 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: B 19 ARG cc_start: 0.8073 (tmm160) cc_final: 0.7570 (ttp-110) REVERT: B 23 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8632 (ttmt) REVERT: B 44 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7835 (mm-40) REVERT: B 100 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8767 (m) REVERT: B 118 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7914 (p0) REVERT: B 217 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7038 (pmm) REVERT: B 304 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7368 (ttp-110) REVERT: G 21 MET cc_start: 0.8444 (tpp) cc_final: 0.8175 (tpp) outliers start: 25 outliers final: 9 residues processed: 131 average time/residue: 1.2971 time to fit residues: 180.5347 Evaluate side-chains 124 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 103 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9170 Z= 0.179 Angle : 0.563 9.657 12449 Z= 0.282 Chirality : 0.043 0.268 1433 Planarity : 0.003 0.043 1535 Dihedral : 6.057 58.963 1539 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.50 % Allowed : 16.25 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.71 (0.26), residues: 1111 helix: 2.07 (0.26), residues: 383 sheet: 0.18 (0.30), residues: 267 loop : -0.69 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 184 PHE 0.016 0.001 PHE A 52 TYR 0.009 0.001 TYR S 190 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 0.936 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 161 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6181 (mpm) REVERT: C 33 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: B 44 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7814 (mm-40) REVERT: B 100 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8739 (m) REVERT: B 217 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7125 (pmm) REVERT: B 304 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7344 (ttp-110) REVERT: G 21 MET cc_start: 0.8451 (tpp) cc_final: 0.8184 (tpp) outliers start: 24 outliers final: 8 residues processed: 132 average time/residue: 1.1882 time to fit residues: 167.6188 Evaluate side-chains 123 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9170 Z= 0.257 Angle : 0.610 10.363 12449 Z= 0.303 Chirality : 0.044 0.267 1433 Planarity : 0.003 0.044 1535 Dihedral : 6.139 58.264 1539 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.60 % Allowed : 17.50 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.66 (0.26), residues: 1111 helix: 2.01 (0.26), residues: 383 sheet: 0.14 (0.30), residues: 267 loop : -0.70 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.012 0.001 HIS A 184 PHE 0.013 0.001 PHE A 124 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.056 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 161 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6285 (mpm) REVERT: C 33 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: B 19 ARG cc_start: 0.8073 (ttp-110) cc_final: 0.7584 (ttp-110) REVERT: B 44 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7830 (mm-40) REVERT: B 100 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8749 (m) REVERT: B 217 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7122 (pmm) REVERT: G 21 MET cc_start: 0.8455 (tpp) cc_final: 0.8226 (tpp) REVERT: G 42 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6738 (mp0) outliers start: 25 outliers final: 11 residues processed: 127 average time/residue: 1.2250 time to fit residues: 165.9282 Evaluate side-chains 123 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9170 Z= 0.231 Angle : 0.601 11.046 12449 Z= 0.299 Chirality : 0.044 0.265 1433 Planarity : 0.003 0.044 1535 Dihedral : 6.091 59.448 1539 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.71 % Allowed : 18.12 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.67 (0.26), residues: 1111 helix: 2.01 (0.26), residues: 383 sheet: 0.14 (0.30), residues: 267 loop : -0.67 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 77 HIS 0.010 0.001 HIS A 184 PHE 0.026 0.001 PHE C 274 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.013 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 161 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6285 (mpm) REVERT: C 33 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: B 19 ARG cc_start: 0.8077 (ttp-110) cc_final: 0.7678 (ttp-110) REVERT: B 44 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7794 (mm-40) REVERT: B 100 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8719 (m) REVERT: B 217 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7124 (pmm) REVERT: B 304 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7345 (ttp-110) REVERT: G 21 MET cc_start: 0.8459 (tpp) cc_final: 0.8226 (tpp) REVERT: G 42 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6641 (mp0) outliers start: 26 outliers final: 12 residues processed: 124 average time/residue: 1.2700 time to fit residues: 167.6094 Evaluate side-chains 123 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 247 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.0050 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 HIS C 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9170 Z= 0.201 Angle : 0.591 11.084 12449 Z= 0.294 Chirality : 0.044 0.257 1433 Planarity : 0.003 0.044 1535 Dihedral : 5.970 58.190 1539 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.08 % Allowed : 18.54 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.71 (0.26), residues: 1111 helix: 2.02 (0.26), residues: 383 sheet: 0.14 (0.31), residues: 268 loop : -0.61 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.010 0.001 HIS A 184 PHE 0.024 0.001 PHE C 274 TYR 0.009 0.001 TYR S 190 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.971 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 161 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6221 (mpm) REVERT: C 33 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: B 19 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7666 (ttp-110) REVERT: B 44 GLN cc_start: 0.8114 (mt0) cc_final: 0.7763 (mm-40) REVERT: B 100 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8685 (m) REVERT: B 217 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7128 (pmm) REVERT: B 304 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7344 (ttp-110) REVERT: G 21 MET cc_start: 0.8461 (tpp) cc_final: 0.8226 (tpp) REVERT: G 42 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6647 (mp0) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 1.3071 time to fit residues: 179.2442 Evaluate side-chains 125 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9170 Z= 0.222 Angle : 0.611 12.001 12449 Z= 0.303 Chirality : 0.044 0.248 1433 Planarity : 0.003 0.044 1535 Dihedral : 5.934 55.973 1539 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 1.67 % Allowed : 19.90 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.71 (0.26), residues: 1111 helix: 2.01 (0.26), residues: 383 sheet: 0.22 (0.31), residues: 261 loop : -0.65 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.023 0.001 PHE C 274 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.905 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 161 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6233 (mpm) REVERT: C 33 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: B 19 ARG cc_start: 0.8081 (ttp-110) cc_final: 0.7657 (ttp-110) REVERT: B 100 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8729 (m) REVERT: B 217 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7138 (pmm) REVERT: B 304 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7335 (ttp-110) REVERT: G 21 MET cc_start: 0.8487 (tpp) cc_final: 0.8247 (tpp) REVERT: G 42 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6623 (mp0) outliers start: 16 outliers final: 10 residues processed: 125 average time/residue: 1.3121 time to fit residues: 174.2112 Evaluate side-chains 125 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103957 restraints weight = 11339.835| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.37 r_work: 0.3136 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9170 Z= 0.217 Angle : 0.603 12.273 12449 Z= 0.299 Chirality : 0.044 0.236 1433 Planarity : 0.003 0.044 1535 Dihedral : 5.880 54.545 1539 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.08 % Allowed : 19.58 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.75 (0.26), residues: 1111 helix: 2.02 (0.26), residues: 383 sheet: 0.22 (0.31), residues: 261 loop : -0.59 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 77 HIS 0.009 0.001 HIS A 184 PHE 0.024 0.001 PHE C 274 TYR 0.009 0.001 TYR B 59 ARG 0.003 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3662.17 seconds wall clock time: 65 minutes 23.27 seconds (3923.27 seconds total)