Starting phenix.real_space_refine (version: dev) on Thu Sep 1 14:25:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djk_27460/09_2022/8djk_27460_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djk_27460/09_2022/8djk_27460.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djk_27460/09_2022/8djk_27460_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djk_27460/09_2022/8djk_27460_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djk_27460/09_2022/8djk_27460_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djk_27460/09_2022/8djk_27460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djk_27460/09_2022/8djk_27460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djk_27460/09_2022/8djk_27460_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8djk_27460/09_2022/8djk_27460_updated.pdb" } resolution = 3.33 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= 0.003 sd= 0.080 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 TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C ASP 316": "OD1" <-> "OD2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 101": "OD1" <-> "OD2" Residue "L TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ASP 121": "OD1" <-> "OD2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 7091 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1930 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain breaks: 2 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: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 249 Unusual residues: {'AJP': 1, 'Y01': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'AJP': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 19 Time building chain proxies: 4.61, per 1000 atoms: 0.65 Number of scatterers: 7091 At special positions: 0 Unit cell: (111.986, 101.04, 103.566, 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 1295 8.00 N 1123 7.00 C 4637 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: 2.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 5 sheets defined 60.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 3.751A pdb=" N LEU A 5 " --> pdb=" O LYS A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 34 Processing helix chain 'A' and resid 61 through 80 Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.697A pdb=" N PHE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.546A pdb=" N LEU A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 184 Proline residue: A 166 - end of helix removed outlier: 3.567A pdb=" N THR A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 210 Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 236 through 246 removed outlier: 6.213A pdb=" N GLU A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 273 removed outlier: 3.580A pdb=" N ARG A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 52 removed outlier: 4.256A pdb=" N ALA B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 76 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 81 through 106 removed outlier: 4.284A pdb=" N TYR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 152 Processing helix chain 'B' and resid 157 through 166 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 181 through 207 removed outlier: 4.560A pdb=" N ALA B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 185 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY B 186 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 188 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 189 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 194 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY B 195 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Proline residue: B 196 - end of helix removed outlier: 3.566A pdb=" N MET B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 204 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 205 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 219 through 235 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 Processing helix chain 'B' and resid 281 through 298 removed outlier: 4.261A pdb=" N LEU B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 3.630A pdb=" N THR B 289 " --> pdb=" O PRO B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 310 through 329 Processing helix chain 'C' and resid 265 through 284 Processing helix chain 'C' and resid 289 through 307 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: 4.063A pdb=" N ARG C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 70 No H-bonds generated for 'chain 'L' and resid 68 through 70' 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 29 through 31 removed outlier: 6.580A pdb=" N LYS L 122 " --> pdb=" O LEU L 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'L' and resid 104 through 109 removed outlier: 3.597A pdb=" N ILE L 67 " --> pdb=" O TRP L 54 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN L 56 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU L 65 " --> pdb=" O GLN L 56 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 81 through 86 removed outlier: 3.619A pdb=" N SER L 86 " --> pdb=" O ASP L 89 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP L 89 " --> pdb=" O SER L 86 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 22 through 25 Processing sheet with id= E, first strand: chain 'H' and resid 112 through 116 removed outlier: 3.756A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1071 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: 2.04 Time building geometry restraints manager: 3.02 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: 2795 1.40 - 1.60: 4326 1.60 - 1.80: 101 1.80 - 2.01: 32 Bond restraints: 7266 Sorted by residual: bond pdb=" C08 AJP A 406 " pdb=" O09 AJP A 406 " ideal model delta sigma weight residual 1.566 0.996 0.570 2.00e-02 2.50e+03 8.11e+02 bond pdb=" C08 AJP B 401 " pdb=" O09 AJP B 401 " ideal model delta sigma weight residual 1.566 1.006 0.560 2.00e-02 2.50e+03 7.85e+02 bond pdb=" C12 AJP A 406 " pdb=" C13 AJP A 406 " ideal model delta sigma weight residual 1.069 1.442 -0.373 2.00e-02 2.50e+03 3.48e+02 bond pdb=" C05 AJP B 401 " pdb=" O09 AJP B 401 " ideal model delta sigma weight residual 1.429 1.798 -0.369 2.00e-02 2.50e+03 3.41e+02 bond pdb=" C05 AJP B 401 " pdb=" O84 AJP B 401 " ideal model delta sigma weight residual 1.415 1.048 0.367 2.00e-02 2.50e+03 3.37e+02 ... (remaining 7261 not shown) Histogram of bond angle deviations from ideal: 95.65 - 105.05: 162 105.05 - 114.44: 4261 114.44 - 123.84: 5297 123.84 - 133.24: 180 133.24 - 142.63: 14 Bond angle restraints: 9914 Sorted by residual: angle pdb=" C SER L 26 " pdb=" N PRO L 27 " pdb=" CA PRO L 27 " ideal model delta sigma weight residual 120.25 106.53 13.72 1.35e+00 5.49e-01 1.03e+02 angle pdb=" CA TRP L 113 " pdb=" C TRP L 113 " pdb=" N PRO L 114 " ideal model delta sigma weight residual 118.85 109.55 9.30 9.50e-01 1.11e+00 9.59e+01 angle pdb=" C06 AJP B 401 " pdb=" C07 AJP B 401 " pdb=" C12 AJP B 401 " ideal model delta sigma weight residual 111.04 136.31 -25.27 3.00e+00 1.11e-01 7.10e+01 angle pdb=" C06 AJP A 406 " pdb=" C07 AJP A 406 " pdb=" C12 AJP A 406 " ideal model delta sigma weight residual 111.04 134.55 -23.51 3.00e+00 1.11e-01 6.14e+01 angle pdb=" N SER L 26 " pdb=" CA SER L 26 " pdb=" C SER L 26 " ideal model delta sigma weight residual 109.81 126.67 -16.86 2.21e+00 2.05e-01 5.82e+01 ... (remaining 9909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.48: 3833 19.48 - 38.97: 264 38.97 - 58.45: 74 58.45 - 77.93: 9 77.93 - 97.42: 6 Dihedral angle restraints: 4186 sinusoidal: 1670 harmonic: 2516 Sorted by residual: dihedral pdb=" CA SER L 26 " pdb=" C SER L 26 " pdb=" N PRO L 27 " pdb=" CA PRO L 27 " ideal model delta harmonic sigma weight residual 180.00 148.65 31.35 0 5.00e+00 4.00e-02 3.93e+01 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 122.80 134.83 -12.03 0 2.50e+00 1.60e-01 2.32e+01 dihedral pdb=" CA TRP L 113 " pdb=" C TRP L 113 " pdb=" N PRO L 114 " pdb=" CA PRO L 114 " ideal model delta harmonic sigma weight residual 0.00 22.81 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 4183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.115: 1134 1.115 - 2.230: 0 2.230 - 3.344: 0 3.344 - 4.459: 4 4.459 - 5.574: 47 Chirality restraints: 1185 Sorted by residual: chirality pdb=" C20 AJP B 401 " pdb=" C15 AJP B 401 " pdb=" C19 AJP B 401 " pdb=" C21 AJP B 401 " both_signs ideal model delta sigma weight residual False 2.75 -2.83 5.57 2.00e-01 2.50e+01 7.77e+02 chirality pdb=" C20 AJP A 406 " pdb=" C15 AJP A 406 " pdb=" C19 AJP A 406 " pdb=" C21 AJP A 406 " both_signs ideal model delta sigma weight residual False 2.75 -2.78 5.52 2.00e-01 2.50e+01 7.63e+02 chirality pdb=" C16 AJP B 401 " pdb=" C11 AJP B 401 " pdb=" C15 AJP B 401 " pdb=" C17 AJP B 401 " both_signs ideal model delta sigma weight residual False -2.73 2.77 -5.50 2.00e-01 2.50e+01 7.56e+02 ... (remaining 1182 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP L 113 " 0.023 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" C TRP L 113 " -0.083 2.00e-02 2.50e+03 pdb=" O TRP L 113 " 0.033 2.00e-02 2.50e+03 pdb=" N PRO L 114 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP L 113 " -0.076 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO L 114 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO L 114 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO L 114 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 380 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C GLN C 380 " -0.038 2.00e-02 2.50e+03 pdb=" O GLN C 380 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS C 381 " 0.013 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 221 2.76 - 3.47: 10408 3.47 - 4.19: 15542 4.19 - 4.90: 28936 Nonbonded interactions: 55108 Sorted by model distance: nonbonded pdb=" N PRO B 309 " pdb=" O VAL C 383 " model vdw 1.327 3.120 nonbonded pdb=" CD PRO B 309 " pdb=" O VAL C 383 " model vdw 2.286 3.440 nonbonded pdb=" CA PRO B 309 " pdb=" O VAL C 383 " model vdw 2.296 3.470 nonbonded pdb=" O GLY A 180 " pdb=" OG1 THR A 183 " model vdw 2.346 2.440 nonbonded pdb=" N PRO B 309 " pdb=" C VAL C 383 " model vdw 2.371 3.350 ... (remaining 55103 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 4637 2.51 5 N 1123 2.21 5 O 1295 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: 1.160 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: 7.460 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.050 Process input model: 22.490 Find NCS groups from input model: 0.220 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.029 0.570 7266 Z= 1.915 Angle : 1.559 25.270 9914 Z= 0.872 Chirality : 1.021 5.574 1185 Planarity : 0.005 0.118 1183 Dihedral : 15.066 97.416 2560 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.84 (0.26), residues: 852 helix: -0.12 (0.20), residues: 520 sheet: -3.05 (0.39), residues: 117 loop : -2.55 (0.35), residues: 215 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.709 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 86 average time/residue: 0.2031 time to fit residues: 23.4538 Evaluate side-chains 71 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0628 time to fit residues: 1.2219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN B 95 HIS C 291 GLN L 25 GLN L 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7266 Z= 0.258 Angle : 1.206 32.762 9914 Z= 0.455 Chirality : 0.128 2.172 1185 Planarity : 0.005 0.041 1183 Dihedral : 9.041 59.818 1022 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.90 % 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: -0.18 (0.29), residues: 852 helix: 1.21 (0.23), residues: 525 sheet: -2.43 (0.40), residues: 123 loop : -1.98 (0.39), residues: 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.791 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 87 average time/residue: 0.1968 time to fit residues: 23.2321 Evaluate side-chains 80 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1285 time to fit residues: 2.3669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 64 optimal weight: 0.0980 chunk 52 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 95 HIS B 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7266 Z= 0.183 Angle : 1.118 29.184 9914 Z= 0.415 Chirality : 0.125 2.106 1185 Planarity : 0.004 0.037 1183 Dihedral : 8.127 59.356 1022 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 1.36 % 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: 0.46 (0.29), residues: 852 helix: 1.64 (0.23), residues: 525 sheet: -1.91 (0.45), residues: 117 loop : -1.73 (0.38), residues: 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.796 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 84 average time/residue: 0.1767 time to fit residues: 20.9241 Evaluate side-chains 82 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1550 time to fit residues: 2.1532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7266 Z= 0.176 Angle : 1.105 28.168 9914 Z= 0.408 Chirality : 0.124 2.091 1185 Planarity : 0.004 0.041 1183 Dihedral : 7.867 63.258 1022 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.22 % 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: 0.69 (0.30), residues: 852 helix: 1.74 (0.23), residues: 526 sheet: -1.53 (0.48), residues: 118 loop : -1.62 (0.38), residues: 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.1592 time to fit residues: 20.1696 Evaluate side-chains 83 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0659 time to fit residues: 1.6748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 chunk 20 optimal weight: 6.9990 chunk 27 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: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7266 Z= 0.275 Angle : 1.135 27.684 9914 Z= 0.426 Chirality : 0.124 2.090 1185 Planarity : 0.004 0.037 1183 Dihedral : 7.894 63.383 1022 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.54 % 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: 0.61 (0.29), residues: 852 helix: 1.59 (0.23), residues: 526 sheet: -1.37 (0.49), residues: 117 loop : -1.54 (0.39), residues: 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.1859 time to fit residues: 21.7798 Evaluate side-chains 80 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0665 time to fit residues: 1.4853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.0170 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7266 Z= 0.198 Angle : 1.107 27.041 9914 Z= 0.410 Chirality : 0.123 2.059 1185 Planarity : 0.004 0.036 1183 Dihedral : 7.712 63.105 1022 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.95 % 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: 0.80 (0.30), residues: 852 helix: 1.72 (0.23), residues: 525 sheet: -1.24 (0.50), residues: 118 loop : -1.40 (0.39), residues: 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.722 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.1690 time to fit residues: 20.6740 Evaluate side-chains 84 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0949 time to fit residues: 2.1923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7266 Z= 0.208 Angle : 1.117 26.872 9914 Z= 0.415 Chirality : 0.123 2.050 1185 Planarity : 0.004 0.036 1183 Dihedral : 7.650 63.911 1022 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.82 % 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: 0.81 (0.30), residues: 852 helix: 1.70 (0.23), residues: 524 sheet: -1.15 (0.50), residues: 117 loop : -1.35 (0.40), residues: 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.735 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 78 average time/residue: 0.1534 time to fit residues: 17.7547 Evaluate side-chains 81 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0758 time to fit residues: 1.9467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 74 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7266 Z= 0.172 Angle : 1.101 26.689 9914 Z= 0.407 Chirality : 0.123 2.032 1185 Planarity : 0.004 0.034 1183 Dihedral : 7.510 64.540 1022 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % 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: 0.97 (0.30), residues: 852 helix: 1.81 (0.23), residues: 524 sheet: -1.07 (0.52), residues: 113 loop : -1.25 (0.40), residues: 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.817 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.1644 time to fit residues: 18.3665 Evaluate side-chains 76 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0636 time to fit residues: 1.2148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 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 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7266 Z= 0.199 Angle : 1.108 26.712 9914 Z= 0.411 Chirality : 0.123 2.028 1185 Planarity : 0.004 0.035 1183 Dihedral : 7.456 64.928 1022 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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: 0.98 (0.30), residues: 852 helix: 1.73 (0.23), residues: 531 sheet: -0.94 (0.52), residues: 112 loop : -1.17 (0.41), residues: 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.767 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1641 time to fit residues: 17.8672 Evaluate side-chains 72 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 7266 Z= 0.275 Angle : 1.132 26.878 9914 Z= 0.427 Chirality : 0.123 2.043 1185 Planarity : 0.004 0.035 1183 Dihedral : 7.599 64.161 1022 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: 0.81 (0.30), residues: 852 helix: 1.63 (0.23), residues: 524 sheet: -1.01 (0.50), residues: 117 loop : -1.24 (0.40), residues: 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.787 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1943 time to fit residues: 22.1482 Evaluate side-chains 77 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.0770 chunk 62 optimal weight: 9.9990 chunk 9 optimal weight: 0.0060 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.0770 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS B 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.231240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.173929 restraints weight = 7928.446| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.42 r_work: 0.4070 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work: 0.3941 rms_B_bonded: 3.91 restraints_weight: 0.1250 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 7266 Z= 0.161 Angle : 1.101 26.883 9914 Z= 0.405 Chirality : 0.122 2.008 1185 Planarity : 0.004 0.034 1183 Dihedral : 7.312 64.219 1022 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: 1.13 (0.30), residues: 852 helix: 1.85 (0.23), residues: 527 sheet: -0.92 (0.51), residues: 113 loop : -1.04 (0.42), residues: 212 =============================================================================== Job complete usr+sys time: 1448.96 seconds wall clock time: 27 minutes 3.72 seconds (1623.72 seconds total)