Starting phenix.real_space_refine (version: dev) on Sat Feb 18 07:30:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31087/02_2023/7efo_31087_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31087/02_2023/7efo_31087.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31087/02_2023/7efo_31087_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31087/02_2023/7efo_31087_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31087/02_2023/7efo_31087_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31087/02_2023/7efo_31087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31087/02_2023/7efo_31087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31087/02_2023/7efo_31087_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efo_31087/02_2023/7efo_31087_updated.pdb" } resolution = 3.85 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= -0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7306 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1833 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain: "B" Number of atoms: 1840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1840 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 228} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1699 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "G" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1734 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 200 Unusual residues: {'JSG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.56, per 1000 atoms: 0.62 Number of scatterers: 7306 At special positions: 0 Unit cell: (68.64, 100.88, 101.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 4 15.00 O 1319 8.00 N 1220 7.00 C 4725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 55.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 95 through 105 removed outlier: 4.179A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.770A pdb=" N ASP A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.605A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.665A pdb=" N GLU A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 72 through 78 Don't know bonding for helix class unknown. No H-bonds generated for 'chain 'B' and resid 72 through 78' Processing helix chain 'B' and resid 95 through 103 removed outlier: 4.398A pdb=" N MET B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.657A pdb=" N ALA B 118 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 140 through 152 removed outlier: 3.673A pdb=" N ARG B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.886A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.628A pdb=" N VAL B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 40 removed outlier: 3.739A pdb=" N ALA F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.159A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 95 through 118 removed outlier: 4.738A pdb=" N PHE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.862A pdb=" N GLU F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 283 removed outlier: 4.447A pdb=" N VAL F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 274 " --> pdb=" O PHE F 270 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 316 Proline residue: F 301 - end of helix Processing helix chain 'F' and resid 331 through 346 removed outlier: 3.573A pdb=" N LEU F 345 " --> pdb=" O LEU F 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 40 removed outlier: 3.705A pdb=" N ASP G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 64 removed outlier: 4.384A pdb=" N TYR G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) Proline residue: G 61 - end of helix removed outlier: 4.243A pdb=" N ILE G 64 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 85 removed outlier: 3.739A pdb=" N LEU G 74 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 78 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY G 81 " --> pdb=" O LEU G 77 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 94 Processing helix chain 'G' and resid 99 through 118 removed outlier: 3.655A pdb=" N ALA G 103 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 3.594A pdb=" N LEU G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 133 Processing helix chain 'G' and resid 271 through 279 Processing helix chain 'G' and resid 281 through 297 Processing helix chain 'G' and resid 305 through 324 removed outlier: 3.568A pdb=" N TYR G 320 " --> pdb=" O GLY G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 333 removed outlier: 4.746A pdb=" N LEU G 331 " --> pdb=" O GLY G 327 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL G 332 " --> pdb=" O PRO G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 353 Proline residue: G 344 - end of helix removed outlier: 3.634A pdb=" N PHE G 348 " --> pdb=" O SER G 345 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 353 " --> pdb=" O LEU G 350 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 32 through 36 removed outlier: 7.389A pdb=" N ARG A 206 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU A 35 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR A 208 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER A 211 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 80 through 83 removed outlier: 6.705A pdb=" N PHE A 158 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 83 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A 160 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLY A 189 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 161 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU A 191 " --> pdb=" O LEU A 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 24 through 27 Processing sheet with id= E, first strand: chain 'B' and resid 214 through 217 removed outlier: 6.445A pdb=" N ILE B 209 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 190 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU B 34 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 192 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 159 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY B 81 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.349A pdb=" N TYR B 13 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 933 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: 1.89 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1157 1.30 - 1.43: 1738 1.43 - 1.56: 4462 1.56 - 1.69: 7 1.69 - 1.82: 71 Bond restraints: 7435 Sorted by residual: bond pdb=" C7 JSG F 401 " pdb=" N2 JSG F 401 " ideal model delta sigma weight residual 1.621 1.344 0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" CDO JSG F 401 " pdb=" NAO JSG F 401 " ideal model delta sigma weight residual 1.505 1.342 0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" C LEU G 23 " pdb=" O LEU G 23 " ideal model delta sigma weight residual 1.236 1.169 0.068 1.15e-02 7.56e+03 3.50e+01 bond pdb=" CEE JSG F 401 " pdb=" OAQ JSG F 401 " ideal model delta sigma weight residual 1.469 1.356 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" CAN JSG F 401 " pdb=" NAO JSG F 401 " ideal model delta sigma weight residual 1.577 1.471 0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 7430 not shown) Histogram of bond angle deviations from ideal: 98.20 - 105.43: 188 105.43 - 112.66: 4049 112.66 - 119.88: 2715 119.88 - 127.11: 3050 127.11 - 134.34: 67 Bond angle restraints: 10069 Sorted by residual: angle pdb=" N ARG B 131 " pdb=" CA ARG B 131 " pdb=" C ARG B 131 " ideal model delta sigma weight residual 110.97 123.88 -12.91 1.09e+00 8.42e-01 1.40e+02 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 112.94 98.20 14.74 1.41e+00 5.03e-01 1.09e+02 angle pdb=" N GLN G 65 " pdb=" CA GLN G 65 " pdb=" C GLN G 65 " ideal model delta sigma weight residual 112.90 101.10 11.80 1.31e+00 5.83e-01 8.11e+01 angle pdb=" N ASP G 63 " pdb=" CA ASP G 63 " pdb=" C ASP G 63 " ideal model delta sigma weight residual 111.14 120.26 -9.12 1.08e+00 8.57e-01 7.14e+01 angle pdb=" N TRP F 332 " pdb=" CA TRP F 332 " pdb=" C TRP F 332 " ideal model delta sigma weight residual 113.23 104.83 8.40 1.24e+00 6.50e-01 4.59e+01 ... (remaining 10064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3784 17.11 - 34.21: 447 34.21 - 51.32: 157 51.32 - 68.43: 38 68.43 - 85.54: 7 Dihedral angle restraints: 4433 sinusoidal: 1810 harmonic: 2623 Sorted by residual: dihedral pdb=" C ASP A 194 " pdb=" N ASP A 194 " pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " ideal model delta harmonic sigma weight residual -122.60 -110.40 -12.20 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" N ASP A 194 " pdb=" C ASP A 194 " pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " ideal model delta harmonic sigma weight residual 122.80 112.89 9.91 0 2.50e+00 1.60e-01 1.57e+01 dihedral pdb=" CA LEU G 300 " pdb=" C LEU G 300 " pdb=" N ARG G 301 " pdb=" CA ARG G 301 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 4430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.930: 1209 0.930 - 1.860: 0 1.860 - 2.790: 0 2.790 - 3.721: 0 3.721 - 4.651: 1 Chirality restraints: 1210 Sorted by residual: chirality pdb=" CCB JSG F 401 " pdb=" CCC JSG F 401 " pdb=" OBF JSG F 401 " pdb=" OCL JSG F 401 " both_signs ideal model delta sigma weight residual False 2.42 -2.24 4.65 2.00e-01 2.50e+01 5.41e+02 chirality pdb=" CA ILE G 313 " pdb=" N ILE G 313 " pdb=" C ILE G 313 " pdb=" CB ILE G 313 " both_signs ideal model delta sigma weight residual False 2.43 2.83 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CBP JSG F 401 " pdb=" CBM JSG F 401 " pdb=" CBQ JSG F 401 " pdb=" OBW JSG F 401 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 1207 not shown) Planarity restraints: 1238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 325 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C ILE G 325 " 0.074 2.00e-02 2.50e+03 pdb=" O ILE G 325 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE G 326 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 86 " 0.020 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C GLU B 86 " -0.072 2.00e-02 2.50e+03 pdb=" O GLU B 86 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA B 87 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 36 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C GLY A 36 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY A 36 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO A 37 " -0.023 2.00e-02 2.50e+03 ... (remaining 1235 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 201 2.64 - 3.20: 7488 3.20 - 3.77: 11761 3.77 - 4.33: 16694 4.33 - 4.90: 25341 Nonbonded interactions: 61485 Sorted by model distance: nonbonded pdb=" O ASP G 63 " pdb=" N PHE G 68 " model vdw 2.071 2.520 nonbonded pdb=" O ILE F 329 " pdb=" CE3 TRP F 330 " model vdw 2.130 3.340 nonbonded pdb=" O ILE F 63 " pdb=" N SER F 67 " model vdw 2.202 2.520 nonbonded pdb=" O LEU F 54 " pdb=" NE2 GLN F 128 " model vdw 2.210 2.520 nonbonded pdb=" OG SER A 94 " pdb=" O ARG A 131 " model vdw 2.218 2.440 ... (remaining 61480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 130 or (resid 131 and (name N or name CA or name \ C or name O or name CB )) or resid 132 through 141 or (resid 142 and (name N or \ name CA or name C or name O or name CB )) or resid 143 through 236)) selection = (chain 'B' and resid 2 through 236) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 38 5.16 5 C 4725 2.51 5 N 1220 2.21 5 O 1319 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 2.240 Check model and map are aligned: 0.120 Process input model: 23.220 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0193 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 : 0.010 0.277 7435 Z= 0.689 Angle : 1.203 14.739 10069 Z= 0.743 Chirality : 0.147 4.651 1210 Planarity : 0.008 0.110 1238 Dihedral : 17.152 85.537 2743 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 58.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.08 % Favored : 92.81 % Rotamer Outliers : 6.18 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.27), residues: 904 helix: -0.97 (0.23), residues: 489 sheet: -1.15 (0.73), residues: 47 loop : -2.10 (0.31), residues: 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 102 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 12 residues processed: 139 average time/residue: 0.2097 time to fit residues: 38.0870 Evaluate side-chains 72 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0772 time to fit residues: 2.7669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 45 optimal weight: 0.0370 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 ASN B 104 GLN B 129 HIS F 313 GLN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0719 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 7435 Z= 0.320 Angle : 0.946 10.481 10069 Z= 0.448 Chirality : 0.049 0.246 1210 Planarity : 0.007 0.054 1238 Dihedral : 9.649 63.979 1060 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 28.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 5.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.26), residues: 904 helix: -0.76 (0.22), residues: 505 sheet: -1.33 (0.70), residues: 48 loop : -1.90 (0.32), residues: 351 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 63 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 100 average time/residue: 0.1976 time to fit residues: 26.8966 Evaluate side-chains 76 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0834 time to fit residues: 4.0337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 72 optimal weight: 0.2980 chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0724 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7435 Z= 0.229 Angle : 0.750 6.630 10069 Z= 0.359 Chirality : 0.044 0.192 1210 Planarity : 0.005 0.067 1238 Dihedral : 9.899 63.704 1060 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.27), residues: 904 helix: -0.60 (0.23), residues: 504 sheet: -1.00 (0.62), residues: 58 loop : -1.73 (0.32), residues: 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.821 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 84 average time/residue: 0.1945 time to fit residues: 22.6223 Evaluate side-chains 68 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0967 time to fit residues: 2.7099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 40.0000 chunk 54 optimal weight: 0.0030 chunk 81 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 71 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN F 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1090 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 7435 Z= 0.307 Angle : 0.925 12.419 10069 Z= 0.445 Chirality : 0.049 0.303 1210 Planarity : 0.006 0.046 1238 Dihedral : 10.652 91.808 1060 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.63 % Favored : 92.26 % Rotamer Outliers : 3.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.27), residues: 904 helix: -0.97 (0.22), residues: 509 sheet: -0.79 (0.62), residues: 58 loop : -1.81 (0.33), residues: 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.671 Fit side-chains outliers start: 27 outliers final: 12 residues processed: 86 average time/residue: 0.1586 time to fit residues: 20.1093 Evaluate side-chains 70 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0772 time to fit residues: 2.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 126 HIS B 126 HIS ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0993 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7435 Z= 0.197 Angle : 0.733 11.521 10069 Z= 0.347 Chirality : 0.043 0.227 1210 Planarity : 0.005 0.048 1238 Dihedral : 10.335 80.766 1060 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.27), residues: 904 helix: -0.62 (0.23), residues: 510 sheet: -0.74 (0.59), residues: 68 loop : -1.75 (0.34), residues: 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.785 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 79 average time/residue: 0.1947 time to fit residues: 21.5502 Evaluate side-chains 66 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2037 time to fit residues: 3.8592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.0060 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 0.2980 chunk 71 optimal weight: 0.0980 chunk 39 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 28 optimal weight: 0.0670 chunk 45 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0847 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 7435 Z= 0.161 Angle : 0.673 9.946 10069 Z= 0.311 Chirality : 0.041 0.217 1210 Planarity : 0.004 0.042 1238 Dihedral : 9.881 80.094 1060 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.28), residues: 904 helix: -0.18 (0.23), residues: 504 sheet: -0.62 (0.62), residues: 70 loop : -2.00 (0.33), residues: 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.749 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 78 average time/residue: 0.1824 time to fit residues: 19.9918 Evaluate side-chains 65 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0761 time to fit residues: 1.4513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0957 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7435 Z= 0.179 Angle : 0.688 8.109 10069 Z= 0.323 Chirality : 0.042 0.202 1210 Planarity : 0.004 0.044 1238 Dihedral : 9.867 79.935 1060 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.28), residues: 904 helix: -0.24 (0.23), residues: 509 sheet: -0.48 (0.63), residues: 70 loop : -1.94 (0.33), residues: 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.832 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.1702 time to fit residues: 17.9484 Evaluate side-chains 68 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0705 time to fit residues: 2.1994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0957 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7435 Z= 0.172 Angle : 0.667 7.498 10069 Z= 0.314 Chirality : 0.042 0.200 1210 Planarity : 0.004 0.041 1238 Dihedral : 9.621 83.446 1060 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.28), residues: 904 helix: -0.09 (0.23), residues: 513 sheet: -0.58 (0.59), residues: 77 loop : -1.95 (0.34), residues: 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.808 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.1827 time to fit residues: 17.1705 Evaluate side-chains 63 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0898 time to fit residues: 1.4428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0945 moved from start: 0.7071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 7435 Z= 0.158 Angle : 0.661 8.062 10069 Z= 0.310 Chirality : 0.041 0.199 1210 Planarity : 0.004 0.040 1238 Dihedral : 9.533 84.943 1060 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.28), residues: 904 helix: -0.07 (0.23), residues: 520 sheet: -0.62 (0.63), residues: 72 loop : -1.91 (0.34), residues: 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.732 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 66 average time/residue: 0.1837 time to fit residues: 17.5886 Evaluate side-chains 60 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0725 time to fit residues: 1.3283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 0.0470 chunk 43 optimal weight: 40.0000 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1002 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 7435 Z= 0.171 Angle : 0.692 11.067 10069 Z= 0.323 Chirality : 0.042 0.201 1210 Planarity : 0.004 0.040 1238 Dihedral : 9.472 87.382 1060 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.28), residues: 904 helix: -0.10 (0.23), residues: 517 sheet: -0.42 (0.61), residues: 74 loop : -1.89 (0.34), residues: 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.797 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.1937 time to fit residues: 18.5206 Evaluate side-chains 64 residues out of total 763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0736 time to fit residues: 1.3255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 72 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5550 r_free = 0.5550 target = 0.366829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5422 r_free = 0.5422 target = 0.348945 restraints weight = 15443.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5454 r_free = 0.5454 target = 0.353667 restraints weight = 10643.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5480 r_free = 0.5480 target = 0.357273 restraints weight = 7484.541| |-----------------------------------------------------------------------------| r_work (final): 0.5473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0914 moved from start: 0.7431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 7435 Z= 0.163 Angle : 0.679 9.730 10069 Z= 0.317 Chirality : 0.041 0.195 1210 Planarity : 0.004 0.039 1238 Dihedral : 9.351 88.505 1060 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.28), residues: 904 helix: 0.01 (0.23), residues: 521 sheet: -0.36 (0.61), residues: 74 loop : -1.91 (0.34), residues: 309 =============================================================================== Job complete usr+sys time: 1366.41 seconds wall clock time: 25 minutes 57.29 seconds (1557.29 seconds total)