Starting phenix.real_space_refine (version: dev) on Thu Sep 1 14:19:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2022/8djm_27461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2022/8djm_27461.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2022/8djm_27461_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2022/8djm_27461_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2022/8djm_27461_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2022/8djm_27461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2022/8djm_27461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2022/8djm_27461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djm_27461/09_2022/8djm_27461_updated.pdb" } resolution = 3.23 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= 0.081 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 7": "NH1" <-> "NH2" Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B ASP 123": "OD1" <-> "OD2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C ASP 340": "OD1" <-> "OD2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 101": "OD1" <-> "OD2" Residue "L PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H GLU 120": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4709/modules/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1871 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 7, 'TRANS': 229} Chain breaks: 3 Chain: "B" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2152 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain breaks: 2 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 944 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "A" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 214 Unusual residues: {'AJP': 1, 'Y01': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'AJP': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 19 Time building chain proxies: 4.67, per 1000 atoms: 0.66 Number of scatterers: 7032 At special positions: 0 Unit cell: (113.67, 101.04, 106.934, 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 36 16.00 O 1281 8.00 N 1114 7.00 C 4601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " 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: 2.67 Conformation dependent library (CDL) restraints added in 939.5 milliseconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 4 sheets defined 60.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 17 through 32 Processing helix chain 'A' and resid 62 through 86 removed outlier: 3.734A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 112 removed outlier: 3.630A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.700A pdb=" N LEU A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.508A pdb=" N ALA A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 184 removed outlier: 4.468A pdb=" N ARG A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Proline residue: A 166 - end of helix removed outlier: 3.568A pdb=" N ASP A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 222 removed outlier: 3.572A pdb=" N CYS A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 236 through 246 removed outlier: 4.716A pdb=" N VAL A 241 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 272 removed outlier: 3.759A pdb=" N MET A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 46 No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 49 through 52 removed outlier: 3.979A pdb=" N ALA B 52 " --> pdb=" O TYR B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 57 through 76 removed outlier: 4.615A pdb=" N THR B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 81 through 107 removed outlier: 3.560A pdb=" N VAL B 85 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 152 removed outlier: 4.052A pdb=" N VAL B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 171 through 174 No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 183 through 207 removed outlier: 3.852A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 213 through 216 No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 219 through 235 removed outlier: 3.539A pdb=" N GLU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 243 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 254 through 278 Proline residue: B 268 - end of helix removed outlier: 3.527A pdb=" N THR B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 298 Proline residue: B 286 - end of helix removed outlier: 3.657A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.694A pdb=" N PHE B 294 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 329 Processing helix chain 'C' and resid 265 through 285 Processing helix chain 'C' and resid 289 through 308 removed outlier: 3.941A pdb=" N THR C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 314 No H-bonds generated for 'chain 'C' and resid 312 through 314' Processing helix chain 'C' and resid 322 through 345 Processing helix chain 'C' and resid 351 through 366 Processing helix chain 'C' and resid 368 through 382 removed outlier: 4.023A pdb=" N SER C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 382 " --> pdb=" O THR C 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 101 No H-bonds generated for 'chain 'L' and resid 99 through 101' Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing sheet with id= A, first strand: chain 'L' and resid 104 through 108 removed outlier: 3.611A pdb=" N ILE L 67 " --> pdb=" O TRP L 54 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLN L 56 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEU L 65 " --> pdb=" O GLN L 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 82 through 84 Processing sheet with id= C, first strand: chain 'H' and resid 22 through 25 Processing sheet with id= D, first strand: chain 'H' and resid 111 through 116 removed outlier: 3.709A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N SER H 59 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU H 64 " --> pdb=" O SER H 59 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1023 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: 1.72 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.20: 12 1.20 - 1.40: 2776 1.40 - 1.60: 4287 1.60 - 1.81: 110 1.81 - 2.01: 21 Bond restraints: 7206 Sorted by residual: bond pdb=" C08 AJP A 405 " pdb=" O09 AJP A 405 " ideal model delta sigma weight residual 1.566 0.996 0.570 2.00e-02 2.50e+03 8.13e+02 bond pdb=" C08 AJP B 402 " pdb=" O09 AJP B 402 " ideal model delta sigma weight residual 1.566 0.997 0.569 2.00e-02 2.50e+03 8.08e+02 bond pdb=" C05 AJP A 405 " pdb=" O09 AJP A 405 " ideal model delta sigma weight residual 1.429 1.804 -0.375 2.00e-02 2.50e+03 3.52e+02 bond pdb=" C05 AJP B 402 " pdb=" O09 AJP B 402 " ideal model delta sigma weight residual 1.429 1.803 -0.374 2.00e-02 2.50e+03 3.49e+02 bond pdb=" C12 AJP A 405 " pdb=" C13 AJP A 405 " ideal model delta sigma weight residual 1.069 1.442 -0.373 2.00e-02 2.50e+03 3.49e+02 ... (remaining 7201 not shown) Histogram of bond angle deviations from ideal: 85.50 - 97.56: 3 97.56 - 109.62: 884 109.62 - 121.68: 6988 121.68 - 133.74: 1942 133.74 - 145.80: 15 Bond angle restraints: 9832 Sorted by residual: angle pdb=" C TRP L 113 " pdb=" CA TRP L 113 " pdb=" CB TRP L 113 " ideal model delta sigma weight residual 108.68 85.50 23.18 1.39e+00 5.18e-01 2.78e+02 angle pdb=" C SER L 26 " pdb=" N PRO L 27 " pdb=" CA PRO L 27 " ideal model delta sigma weight residual 120.51 104.02 16.49 1.26e+00 6.30e-01 1.71e+02 angle pdb=" N SER L 26 " pdb=" CA SER L 26 " pdb=" C SER L 26 " ideal model delta sigma weight residual 109.81 128.99 -19.18 2.21e+00 2.05e-01 7.53e+01 angle pdb=" C06 AJP B 402 " pdb=" C07 AJP B 402 " pdb=" C12 AJP B 402 " ideal model delta sigma weight residual 111.04 134.89 -23.85 3.00e+00 1.11e-01 6.32e+01 angle pdb=" C06 AJP A 405 " pdb=" C07 AJP A 405 " pdb=" C12 AJP A 405 " ideal model delta sigma weight residual 111.04 134.73 -23.69 3.00e+00 1.11e-01 6.23e+01 ... (remaining 9827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 3852 22.07 - 44.14: 231 44.14 - 66.21: 52 66.21 - 88.29: 5 88.29 - 110.36: 8 Dihedral angle restraints: 4148 sinusoidal: 1655 harmonic: 2493 Sorted by residual: dihedral pdb=" C TRP L 113 " pdb=" N TRP L 113 " pdb=" CA TRP L 113 " pdb=" CB TRP L 113 " ideal model delta harmonic sigma weight residual -122.60 -95.39 -27.21 0 2.50e+00 1.60e-01 1.18e+02 dihedral pdb=" N SER L 26 " pdb=" C SER L 26 " pdb=" CA SER L 26 " pdb=" CB SER L 26 " ideal model delta harmonic sigma weight residual 122.80 138.69 -15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" C SER L 26 " pdb=" N SER L 26 " pdb=" CA SER L 26 " pdb=" CB SER L 26 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 4145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.120: 1124 1.120 - 2.239: 0 2.239 - 3.359: 0 3.359 - 4.478: 5 4.478 - 5.598: 46 Chirality restraints: 1175 Sorted by residual: chirality pdb=" C16 AJP A 405 " pdb=" C11 AJP A 405 " pdb=" C15 AJP A 405 " pdb=" C17 AJP A 405 " both_signs ideal model delta sigma weight residual False -2.73 2.87 -5.60 2.00e-01 2.50e+01 7.83e+02 chirality pdb=" C20 AJP A 405 " pdb=" C15 AJP A 405 " pdb=" C19 AJP A 405 " pdb=" C21 AJP A 405 " both_signs ideal model delta sigma weight residual False 2.75 -2.78 5.53 2.00e-01 2.50e+01 7.65e+02 chirality pdb=" C20 AJP B 402 " pdb=" C15 AJP B 402 " pdb=" C19 AJP B 402 " pdb=" C21 AJP B 402 " both_signs ideal model delta sigma weight residual False 2.75 -2.76 5.51 2.00e-01 2.50e+01 7.60e+02 ... (remaining 1172 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP L 113 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C TRP L 113 " 0.044 2.00e-02 2.50e+03 pdb=" O TRP L 113 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO L 114 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 367 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C TYR C 367 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR C 367 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE C 368 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO L 27 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C PRO L 27 " -0.028 2.00e-02 2.50e+03 pdb=" O PRO L 27 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA L 28 " 0.010 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 8 2.45 - 3.07: 3863 3.07 - 3.68: 10480 3.68 - 4.29: 14760 4.29 - 4.90: 25478 Nonbonded interactions: 54589 Sorted by model distance: nonbonded pdb=" N PRO B 309 " pdb=" O VAL C 383 " model vdw 1.844 3.120 nonbonded pdb=" CA PRO B 309 " pdb=" O VAL C 383 " model vdw 2.320 3.470 nonbonded pdb=" C04 AJP A 405 " pdb=" C85 AJP A 405 " model vdw 2.408 3.072 nonbonded pdb=" C04 AJP B 402 " pdb=" C85 AJP B 402 " model vdw 2.416 3.072 nonbonded pdb=" C03 AJP B 402 " pdb=" O84 AJP B 402 " model vdw 2.440 2.752 ... (remaining 54584 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4601 2.51 5 N 1114 2.21 5 O 1281 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=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: 1.200 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: 7.530 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.050 Process input model: 21.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.030 0.570 7206 Z= 1.869 Angle : 1.552 23.854 9832 Z= 0.880 Chirality : 1.029 5.598 1175 Planarity : 0.004 0.038 1172 Dihedral : 15.726 110.357 2536 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 3.23 % 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: -2.26 (0.25), residues: 842 helix: -0.85 (0.19), residues: 501 sheet: -3.36 (0.36), residues: 110 loop : -1.49 (0.40), residues: 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.764 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 0.2294 time to fit residues: 29.7285 Evaluate side-chains 81 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0598 time to fit residues: 1.3955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 79 GLN B 95 HIS B 316 ASN C 272 ASN C 277 ASN C 279 ASN C 337 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN L 25 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7206 Z= 0.207 Angle : 1.181 28.853 9832 Z= 0.438 Chirality : 0.122 1.956 1175 Planarity : 0.004 0.034 1172 Dihedral : 9.482 104.960 1013 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.29), residues: 842 helix: 1.35 (0.23), residues: 499 sheet: -2.28 (0.40), residues: 126 loop : -1.26 (0.42), residues: 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 95 average time/residue: 0.1819 time to fit residues: 23.7657 Evaluate side-chains 88 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0638 time to fit residues: 1.9963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.0050 chunk 23 optimal weight: 0.0670 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN C 277 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7206 Z= 0.163 Angle : 1.105 26.933 9832 Z= 0.405 Chirality : 0.123 1.989 1175 Planarity : 0.004 0.033 1172 Dihedral : 9.050 111.072 1013 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.91 (0.30), residues: 842 helix: 1.91 (0.23), residues: 499 sheet: -1.79 (0.44), residues: 122 loop : -0.94 (0.42), residues: 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.756 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 86 average time/residue: 0.1888 time to fit residues: 22.2541 Evaluate side-chains 81 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN C 277 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7206 Z= 0.186 Angle : 1.104 27.259 9832 Z= 0.405 Chirality : 0.122 1.986 1175 Planarity : 0.004 0.032 1172 Dihedral : 8.867 110.449 1013 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.05 (0.30), residues: 842 helix: 1.95 (0.23), residues: 499 sheet: -1.50 (0.45), residues: 122 loop : -0.81 (0.42), residues: 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 90 average time/residue: 0.1711 time to fit residues: 21.8384 Evaluate side-chains 86 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0683 time to fit residues: 1.4871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 72 optimal weight: 0.0170 chunk 20 optimal weight: 3.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7206 Z= 0.176 Angle : 1.097 27.043 9832 Z= 0.401 Chirality : 0.122 1.980 1175 Planarity : 0.003 0.033 1172 Dihedral : 8.692 110.863 1013 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.20 (0.30), residues: 842 helix: 2.03 (0.23), residues: 499 sheet: -1.31 (0.46), residues: 122 loop : -0.73 (0.42), residues: 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.800 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 91 average time/residue: 0.1723 time to fit residues: 22.1091 Evaluate side-chains 91 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0721 time to fit residues: 1.8603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 26 optimal weight: 0.0020 chunk 42 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7206 Z= 0.169 Angle : 1.091 27.064 9832 Z= 0.398 Chirality : 0.122 1.978 1175 Planarity : 0.003 0.033 1172 Dihedral : 8.581 111.485 1013 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.35 (0.30), residues: 842 helix: 2.09 (0.23), residues: 499 sheet: -1.09 (0.47), residues: 122 loop : -0.66 (0.42), residues: 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.749 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 0.1703 time to fit residues: 21.3405 Evaluate side-chains 88 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 59 optimal weight: 0.0170 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7206 Z= 0.129 Angle : 1.074 27.141 9832 Z= 0.388 Chirality : 0.121 1.966 1175 Planarity : 0.003 0.033 1172 Dihedral : 8.345 112.431 1013 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.30), residues: 842 helix: 2.34 (0.23), residues: 499 sheet: -0.85 (0.48), residues: 122 loop : -0.62 (0.42), residues: 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.758 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 93 average time/residue: 0.1722 time to fit residues: 22.5978 Evaluate side-chains 85 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0646 time to fit residues: 1.2202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN C 277 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 7206 Z= 0.276 Angle : 1.127 26.923 9832 Z= 0.419 Chirality : 0.122 1.985 1175 Planarity : 0.004 0.034 1172 Dihedral : 8.564 111.533 1013 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.29 (0.30), residues: 842 helix: 1.94 (0.23), residues: 498 sheet: -0.91 (0.48), residues: 122 loop : -0.52 (0.43), residues: 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.791 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 86 average time/residue: 0.1930 time to fit residues: 22.7264 Evaluate side-chains 83 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0720 time to fit residues: 1.2393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 0.0370 chunk 48 optimal weight: 0.7980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 7206 Z= 0.147 Angle : 1.083 27.097 9832 Z= 0.395 Chirality : 0.122 1.969 1175 Planarity : 0.003 0.035 1172 Dihedral : 8.445 112.926 1013 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.30), residues: 842 helix: 2.15 (0.23), residues: 498 sheet: -0.81 (0.48), residues: 122 loop : -0.49 (0.43), residues: 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.834 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1815 time to fit residues: 20.9039 Evaluate side-chains 83 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 20 optimal weight: 0.0670 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 HIS B 99 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7206 Z= 0.226 Angle : 1.119 27.013 9832 Z= 0.413 Chirality : 0.122 1.977 1175 Planarity : 0.004 0.034 1172 Dihedral : 8.537 111.968 1013 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.30), residues: 842 helix: 2.01 (0.23), residues: 497 sheet: -0.87 (0.48), residues: 122 loop : -0.45 (0.43), residues: 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.776 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1863 time to fit residues: 21.5769 Evaluate side-chains 82 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.754 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.196036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140160 restraints weight = 7705.640| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.51 r_work: 0.3548 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.3500 rms_B_bonded: 2.36 restraints_weight: 0.1250 r_work: 0.3473 rms_B_bonded: 2.55 restraints_weight: 0.0625 r_work: 0.3443 rms_B_bonded: 2.84 restraints_weight: 0.0312 r_work: 0.3407 rms_B_bonded: 3.24 restraints_weight: 0.0156 r_work: 0.3364 rms_B_bonded: 3.80 restraints_weight: 0.0078 r_work: 0.3309 rms_B_bonded: 4.58 restraints_weight: 0.0039 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7206 Z= 0.189 Angle : 1.105 26.996 9832 Z= 0.405 Chirality : 0.122 1.970 1175 Planarity : 0.003 0.034 1172 Dihedral : 8.533 112.930 1013 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.46 (0.30), residues: 842 helix: 2.10 (0.23), residues: 491 sheet: -0.88 (0.47), residues: 122 loop : -0.38 (0.42), residues: 229 =============================================================================== Job complete usr+sys time: 1585.16 seconds wall clock time: 29 minutes 32.66 seconds (1772.66 seconds total)