Starting phenix.real_space_refine (version: dev) on Mon Dec 12 02:50:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/12_2022/7t6b_25712_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/12_2022/7t6b_25712.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/12_2022/7t6b_25712_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/12_2022/7t6b_25712_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/12_2022/7t6b_25712_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/12_2022/7t6b_25712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/12_2022/7t6b_25712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/12_2022/7t6b_25712_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6b_25712/12_2022/7t6b_25712_updated.pdb" } resolution = 3.19 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= 0.002 sd= 0.109 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 79": "OD1" <-> "OD2" Residue "R ARG 147": "NH1" <-> "NH2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "R TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 256": "OD1" <-> "OD2" Residue "R PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8755 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1849 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1848 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 225, 1848 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 2 bond proxies already assigned to first conformer: 1874 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2063 Unusual residues: {'S1P': 1} Classifications: {'peptide': 264, 'undetermined': 1} Link IDs: {'PTRANS': 7, 'TRANS': 256, None: 1} Not linked: pdbres="TRP R 290 " pdbres="S1P R 401 " Chain breaks: 2 Time building chain proxies: 5.86, per 1000 atoms: 0.67 Number of scatterers: 8755 At special positions: 0 Unit cell: (99.356, 121.248, 114.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 1 15.00 O 1631 8.00 N 1497 7.00 C 5571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 172 " - pdb=" SG CYS R 179 " distance=2.03 Simple disulfide: pdb=" SG CYS R 259 " - pdb=" SG CYS R 264 " distance=2.03 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: 3.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 16 sheets defined 30.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 7 through 28 Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 320 through 333 removed outlier: 4.742A pdb=" N LYS A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 373 removed outlier: 4.239A pdb=" N LYS A 372 " --> pdb=" O HIS A 368 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 removed outlier: 3.824A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 14 through 21 removed outlier: 3.917A pdb=" N THR R 21 " --> pdb=" O HIS R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 60 removed outlier: 4.124A pdb=" N ALA R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE R 39 " --> pdb=" O VAL R 35 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE R 40 " --> pdb=" O ALA R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 93 removed outlier: 3.705A pdb=" N ASN R 74 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE R 86 " --> pdb=" O ALA R 82 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 135 removed outlier: 3.826A pdb=" N THR R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER R 119 " --> pdb=" O THR R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 164 Processing helix chain 'R' and resid 190 through 218 Processing helix chain 'R' and resid 229 through 258 removed outlier: 3.709A pdb=" N LYS R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL R 238 " --> pdb=" O THR R 234 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU R 239 " --> pdb=" O VAL R 235 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLY R 240 " --> pdb=" O THR R 236 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 267 through 287 removed outlier: 4.986A pdb=" N HIS R 271 " --> pdb=" O TYR R 268 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN R 280 " --> pdb=" O SER R 277 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN R 284 " --> pdb=" O SER R 281 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 48 through 53 removed outlier: 7.613A pdb=" N ILE A 51 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS A 219 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A 53 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 221 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 244 through 248 removed outlier: 6.302A pdb=" N ILE A 287 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 247 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE A 289 " --> pdb=" O VAL A 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 100 through 103 removed outlier: 7.011A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.942A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 190 through 192 removed outlier: 4.469A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 294 through 298 removed outlier: 3.546A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 327 through 330 removed outlier: 3.645A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.005A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 78 through 82 removed outlier: 3.526A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.568A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 250 through 254 removed outlier: 3.828A pdb=" N LEU C 252 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= M, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.578A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 95 through 99 removed outlier: 3.564A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.597A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 155 through 159 removed outlier: 3.559A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 945 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: 2.48 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2834 1.35 - 1.48: 2215 1.48 - 1.60: 3795 1.60 - 1.73: 1 1.73 - 1.86: 78 Bond restraints: 8923 Sorted by residual: bond pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " ideal model delta sigma weight residual 1.661 1.858 -0.197 2.00e-02 2.50e+03 9.72e+01 bond pdb=" C1 S1P R 401 " pdb=" C2 S1P R 401 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1 S1P R 401 " pdb=" O1 S1P R 401 " ideal model delta sigma weight residual 1.411 1.355 0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C5 S1P R 401 " pdb=" C6 S1P R 401 " ideal model delta sigma weight residual 1.558 1.509 0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" C2 S1P R 401 " pdb=" C3 S1P R 401 " ideal model delta sigma weight residual 1.531 1.568 -0.037 2.00e-02 2.50e+03 3.43e+00 ... (remaining 8918 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 129 105.81 - 112.87: 4799 112.87 - 119.93: 3034 119.93 - 126.99: 4025 126.99 - 134.06: 96 Bond angle restraints: 12083 Sorted by residual: angle pdb=" N VAL A 302 " pdb=" CA VAL A 302 " pdb=" C VAL A 302 " ideal model delta sigma weight residual 113.53 110.61 2.92 9.80e-01 1.04e+00 8.87e+00 angle pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " pdb=" O23 S1P R 401 " ideal model delta sigma weight residual 109.47 100.64 8.83 3.00e+00 1.11e-01 8.67e+00 angle pdb=" CA GLY C 115 " pdb=" C GLY C 115 " pdb=" N GLY C 116 " ideal model delta sigma weight residual 114.58 117.09 -2.51 8.60e-01 1.35e+00 8.55e+00 angle pdb=" CA LEU A 54 " pdb=" CB LEU A 54 " pdb=" CG LEU A 54 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.52e+00 angle pdb=" N SER C 275 " pdb=" CA SER C 275 " pdb=" C SER C 275 " ideal model delta sigma weight residual 108.32 112.94 -4.62 1.64e+00 3.72e-01 7.93e+00 ... (remaining 12078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4753 18.01 - 36.01: 462 36.01 - 54.02: 82 54.02 - 72.03: 12 72.03 - 90.03: 5 Dihedral angle restraints: 5314 sinusoidal: 2071 harmonic: 3243 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CA VAL R 238 " pdb=" C VAL R 238 " pdb=" N LEU R 239 " pdb=" CA LEU R 239 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALA A 349 " pdb=" C ALA A 349 " pdb=" N ILE A 350 " pdb=" CA ILE A 350 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 841 0.036 - 0.072: 393 0.072 - 0.108: 120 0.108 - 0.144: 35 0.144 - 0.181: 8 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA VAL C 327 " pdb=" N VAL C 327 " pdb=" C VAL C 327 " pdb=" CB VAL C 327 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" C2 S1P R 401 " pdb=" C1 S1P R 401 " pdb=" C3 S1P R 401 " pdb=" N2 S1P R 401 " both_signs ideal model delta sigma weight residual False -2.61 -2.77 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA PRO E 41 " pdb=" N PRO E 41 " pdb=" C PRO E 41 " pdb=" CB PRO E 41 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1394 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 48 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO D 49 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO C 236 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 165 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO R 166 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 166 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 166 " 0.029 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 658 2.74 - 3.28: 8459 3.28 - 3.82: 13692 3.82 - 4.36: 16731 4.36 - 4.90: 29407 Nonbonded interactions: 68947 Sorted by model distance: nonbonded pdb=" O THR R 278 " pdb=" OG SER R 281 " model vdw 2.195 2.440 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.245 2.440 nonbonded pdb=" O LEU R 162 " pdb=" OH TYR R 190 " model vdw 2.254 2.440 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.258 2.440 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.296 2.440 ... (remaining 68942 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 55 5.16 5 C 5571 2.51 5 N 1497 2.21 5 O 1631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.860 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: 5.780 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 25.210 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.005 0.197 8923 Z= 0.310 Angle : 0.802 10.217 12083 Z= 0.422 Chirality : 0.047 0.181 1397 Planarity : 0.005 0.054 1519 Dihedral : 14.393 90.032 3206 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.82 (0.21), residues: 1099 helix: -1.34 (0.24), residues: 362 sheet: -2.95 (0.27), residues: 277 loop : -3.16 (0.23), residues: 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.2286 time to fit residues: 39.9356 Evaluate side-chains 98 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN C 6 GLN C 91 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 232 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8923 Z= 0.252 Angle : 0.583 6.782 12083 Z= 0.305 Chirality : 0.042 0.150 1397 Planarity : 0.004 0.045 1519 Dihedral : 5.160 28.996 1221 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.64 (0.23), residues: 1099 helix: 0.14 (0.27), residues: 363 sheet: -2.56 (0.28), residues: 277 loop : -2.74 (0.24), residues: 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.958 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 111 average time/residue: 0.2292 time to fit residues: 34.6851 Evaluate side-chains 103 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0791 time to fit residues: 2.3599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 0.0270 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8923 Z= 0.197 Angle : 0.539 8.560 12083 Z= 0.281 Chirality : 0.041 0.139 1397 Planarity : 0.004 0.040 1519 Dihedral : 4.843 27.695 1221 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.24), residues: 1099 helix: 0.75 (0.28), residues: 365 sheet: -2.20 (0.28), residues: 287 loop : -2.42 (0.26), residues: 447 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.102 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 115 average time/residue: 0.2329 time to fit residues: 36.7453 Evaluate side-chains 104 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0812 time to fit residues: 2.2616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8923 Z= 0.269 Angle : 0.561 7.556 12083 Z= 0.295 Chirality : 0.042 0.140 1397 Planarity : 0.004 0.043 1519 Dihedral : 4.923 27.577 1221 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.25), residues: 1099 helix: 1.04 (0.28), residues: 364 sheet: -2.04 (0.29), residues: 283 loop : -2.21 (0.26), residues: 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.039 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 0.2388 time to fit residues: 36.8464 Evaluate side-chains 99 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0818 time to fit residues: 2.3845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 43 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 8923 Z= 0.133 Angle : 0.498 8.492 12083 Z= 0.260 Chirality : 0.040 0.170 1397 Planarity : 0.003 0.040 1519 Dihedral : 4.430 23.995 1221 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1099 helix: 1.33 (0.29), residues: 364 sheet: -1.81 (0.29), residues: 283 loop : -1.94 (0.27), residues: 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.044 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 119 average time/residue: 0.2385 time to fit residues: 38.5179 Evaluate side-chains 107 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0785 time to fit residues: 1.7285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8923 Z= 0.264 Angle : 0.565 9.311 12083 Z= 0.294 Chirality : 0.042 0.143 1397 Planarity : 0.004 0.043 1519 Dihedral : 4.726 26.633 1221 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1099 helix: 1.35 (0.28), residues: 365 sheet: -1.94 (0.28), residues: 291 loop : -1.86 (0.28), residues: 443 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.981 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 0.2424 time to fit residues: 35.8073 Evaluate side-chains 101 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0972 time to fit residues: 2.4828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8923 Z= 0.178 Angle : 0.524 9.013 12083 Z= 0.270 Chirality : 0.041 0.136 1397 Planarity : 0.003 0.041 1519 Dihedral : 4.554 25.327 1221 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.26), residues: 1099 helix: 1.42 (0.28), residues: 368 sheet: -1.72 (0.29), residues: 283 loop : -1.79 (0.28), residues: 448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.985 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 0.2222 time to fit residues: 33.8449 Evaluate side-chains 107 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0876 time to fit residues: 2.6001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.0670 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 95 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8923 Z= 0.133 Angle : 0.497 7.968 12083 Z= 0.257 Chirality : 0.040 0.138 1397 Planarity : 0.003 0.040 1519 Dihedral : 4.287 28.610 1221 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.84 (0.26), residues: 1099 helix: 1.50 (0.28), residues: 373 sheet: -1.47 (0.29), residues: 288 loop : -1.70 (0.28), residues: 438 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.953 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.2262 time to fit residues: 33.9135 Evaluate side-chains 98 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8923 Z= 0.193 Angle : 0.528 9.187 12083 Z= 0.273 Chirality : 0.041 0.132 1397 Planarity : 0.003 0.040 1519 Dihedral : 4.412 25.327 1221 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.84 (0.26), residues: 1099 helix: 1.50 (0.28), residues: 373 sheet: -1.43 (0.29), residues: 287 loop : -1.71 (0.28), residues: 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.881 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 101 average time/residue: 0.2340 time to fit residues: 32.1575 Evaluate side-chains 102 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0880 time to fit residues: 2.0012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8923 Z= 0.227 Angle : 0.546 9.254 12083 Z= 0.284 Chirality : 0.042 0.134 1397 Planarity : 0.004 0.040 1519 Dihedral : 4.502 24.890 1221 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.81 (0.26), residues: 1099 helix: 1.54 (0.28), residues: 368 sheet: -1.50 (0.30), residues: 283 loop : -1.60 (0.28), residues: 448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 1.071 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 96 average time/residue: 0.2303 time to fit residues: 30.8604 Evaluate side-chains 96 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0774 time to fit residues: 1.6381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 0.0770 chunk 76 optimal weight: 0.3980 chunk 4 optimal weight: 0.0050 chunk 62 optimal weight: 0.6980 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** 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 = 0.4079 r_free = 0.4079 target = 0.193918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128304 restraints weight = 8960.867| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.16 r_work: 0.3203 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4079 r_free = 0.4079 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4079 r_free = 0.4079 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8923 Z= 0.132 Angle : 0.501 9.494 12083 Z= 0.258 Chirality : 0.040 0.135 1397 Planarity : 0.003 0.039 1519 Dihedral : 4.209 25.139 1221 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.57 (0.26), residues: 1099 helix: 1.65 (0.29), residues: 368 sheet: -1.24 (0.29), residues: 288 loop : -1.49 (0.28), residues: 443 =============================================================================== Job complete usr+sys time: 2057.20 seconds wall clock time: 37 minutes 58.05 seconds (2278.05 seconds total)