Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 12:39:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/04_2023/7u7n_26382.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/04_2023/7u7n_26382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/04_2023/7u7n_26382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/04_2023/7u7n_26382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/04_2023/7u7n_26382.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/04_2023/7u7n_26382.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4646 2.51 5 N 1221 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7284 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1548 Classifications: {'peptide': 195} Link IDs: {'PCIS': 4, 'PTRANS': 17, 'TRANS': 173} Chain: "B" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2385 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 281} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1582 Classifications: {'peptide': 200} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 177} Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.27, per 1000 atoms: 0.59 Number of scatterers: 7284 At special positions: 0 Unit cell: (96.485, 123.333, 114.943, 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 31 16.00 O 1386 8.00 N 1221 7.00 C 4646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 89 " 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 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 301 " - " ASN A 51 " " NAG A 302 " - " ASN A 76 " " NAG B 401 " - " ASN B 131 " " NAG B 402 " - " ASN B 157 " " NAG E 1 " - " ASN B 43 " " NAG F 1 " - " ASN B 83 " " NAG G 1 " - " ASN B 61 " " NAG H 1 " - " ASN C 105 " Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.0 seconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 17 sheets defined 21.3% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 215 through 220 removed outlier: 4.104A pdb=" N VAL B 220 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.854A pdb=" N LYS B 250 " --> pdb=" O PRO B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'D' and resid 43 through 73 removed outlier: 3.724A pdb=" N VAL D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 50 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.897A pdb=" N LEU D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 100 removed outlier: 3.672A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 114 Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.588A pdb=" N THR D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 159 removed outlier: 3.502A pdb=" N GLY D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 179 Processing helix chain 'D' and resid 196 through 226 removed outlier: 3.546A pdb=" N LYS D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 removed outlier: 3.505A pdb=" N LEU A 66 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 69 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 82 removed outlier: 3.505A pdb=" N LEU A 66 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 69 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 139 removed outlier: 7.037A pdb=" N GLY A 134 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA A 152 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP A 136 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A 150 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA6, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.521A pdb=" N VAL B 47 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE B 44 " --> pdb=" O PHE B 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.531A pdb=" N VAL B 38 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 123 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N CYS B 103 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY B 117 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU B 101 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR B 119 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 99 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 145 Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.739A pdb=" N GLU B 163 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 200 " --> pdb=" O VAL B 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.739A pdb=" N GLU B 163 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 226 through 232 removed outlier: 4.030A pdb=" N LEU B 228 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR B 243 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 230 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS B 241 " --> pdb=" O VAL B 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.627A pdb=" N ARG B 300 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 32 through 39 removed outlier: 4.715A pdb=" N SER C 38 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA C 43 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.706A pdb=" N SER C 61 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 133 through 141 removed outlier: 5.761A pdb=" N GLY C 134 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU C 150 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 178 through 183 removed outlier: 5.638A pdb=" N ARG C 179 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR C 169 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY C 181 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE C 167 " --> pdb=" O GLY C 181 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP C 166 " --> pdb=" O ALA C 204 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 747 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: 1.95 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2308 1.34 - 1.46: 1793 1.46 - 1.58: 3342 1.58 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 7486 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.77e+00 bond pdb=" C5 MAN F 4 " pdb=" O5 MAN F 4 " ideal model delta sigma weight residual 1.418 1.461 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" CB PRO A 93 " pdb=" CG PRO A 93 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.81e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 ... (remaining 7481 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.74: 334 106.74 - 113.56: 4196 113.56 - 120.37: 2492 120.37 - 127.18: 3055 127.18 - 134.00: 137 Bond angle restraints: 10214 Sorted by residual: angle pdb=" CA LYS B 219 " pdb=" CB LYS B 219 " pdb=" CG LYS B 219 " ideal model delta sigma weight residual 114.10 126.92 -12.82 2.00e+00 2.50e-01 4.11e+01 angle pdb=" N ASN B 83 " pdb=" CA ASN B 83 " pdb=" CB ASN B 83 " ideal model delta sigma weight residual 111.65 105.69 5.96 1.40e+00 5.10e-01 1.81e+01 angle pdb=" C ASN B 83 " pdb=" CA ASN B 83 " pdb=" CB ASN B 83 " ideal model delta sigma weight residual 111.35 117.43 -6.08 1.72e+00 3.38e-01 1.25e+01 angle pdb=" CB LYS B 219 " pdb=" CG LYS B 219 " pdb=" CD LYS B 219 " ideal model delta sigma weight residual 111.30 119.26 -7.96 2.30e+00 1.89e-01 1.20e+01 angle pdb=" N LYS B 219 " pdb=" CA LYS B 219 " pdb=" CB LYS B 219 " ideal model delta sigma weight residual 111.01 105.97 5.04 1.56e+00 4.11e-01 1.04e+01 ... (remaining 10209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 3698 17.13 - 34.27: 510 34.27 - 51.40: 119 51.40 - 68.53: 35 68.53 - 85.67: 14 Dihedral angle restraints: 4376 sinusoidal: 1792 harmonic: 2584 Sorted by residual: dihedral pdb=" CA TYR B 218 " pdb=" C TYR B 218 " pdb=" N LYS B 219 " pdb=" CA LYS B 219 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ILE B 82 " pdb=" C ILE B 82 " pdb=" N ASN B 83 " pdb=" CA ASN B 83 " ideal model delta harmonic sigma weight residual 180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASP C 93 " pdb=" CB ASP C 93 " pdb=" CG ASP C 93 " pdb=" OD1 ASP C 93 " ideal model delta sinusoidal sigma weight residual -30.00 -88.00 58.00 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 4373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 973 0.055 - 0.111: 164 0.111 - 0.166: 33 0.166 - 0.222: 0 0.222 - 0.277: 4 Chirality restraints: 1174 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1171 not shown) Planarity restraints: 1291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 92 " -0.055 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 93 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 83 " 0.025 2.00e-02 2.50e+03 2.26e-02 6.39e+00 pdb=" CG ASN B 83 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 83 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 83 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 26 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO B 27 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.029 5.00e-02 4.00e+02 ... (remaining 1288 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 249 2.71 - 3.26: 6841 3.26 - 3.81: 11632 3.81 - 4.35: 13347 4.35 - 4.90: 22640 Nonbonded interactions: 54709 Sorted by model distance: nonbonded pdb=" O LEU B 124 " pdb=" OG1 THR B 152 " model vdw 2.164 2.440 nonbonded pdb=" O THR C 83 " pdb=" OG SER C 86 " model vdw 2.228 2.440 nonbonded pdb=" O TYR B 261 " pdb=" OG SER B 270 " model vdw 2.255 2.440 nonbonded pdb=" OD1 ASN B 61 " pdb=" N ALA B 62 " model vdw 2.265 2.520 nonbonded pdb=" OG SER B 229 " pdb=" OG1 THR B 243 " model vdw 2.286 2.440 ... (remaining 54704 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 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.000 Extract box with map and model: 4.010 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.780 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.004 0.084 7486 Z= 0.264 Angle : 0.687 12.824 10214 Z= 0.327 Chirality : 0.047 0.277 1174 Planarity : 0.005 0.081 1283 Dihedral : 17.191 85.666 2674 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.04 (0.29), residues: 874 helix: 2.48 (0.42), residues: 155 sheet: 1.04 (0.32), residues: 273 loop : -0.14 (0.30), residues: 446 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 0.794 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 200 average time/residue: 0.2560 time to fit residues: 63.7740 Evaluate side-chains 202 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0942 time to fit residues: 1.9499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7486 Z= 0.183 Angle : 0.600 8.242 10214 Z= 0.294 Chirality : 0.043 0.157 1174 Planarity : 0.005 0.054 1283 Dihedral : 3.982 23.695 955 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.08 (0.29), residues: 874 helix: 2.55 (0.42), residues: 158 sheet: 1.08 (0.30), residues: 290 loop : -0.23 (0.31), residues: 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 207 average time/residue: 0.2289 time to fit residues: 60.3382 Evaluate side-chains 212 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0734 time to fit residues: 3.4134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 7486 Z= 0.305 Angle : 0.636 9.033 10214 Z= 0.311 Chirality : 0.045 0.164 1174 Planarity : 0.005 0.053 1283 Dihedral : 4.208 22.160 955 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 0.99 (0.29), residues: 874 helix: 2.36 (0.42), residues: 158 sheet: 1.19 (0.30), residues: 283 loop : -0.34 (0.30), residues: 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 0.795 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 211 average time/residue: 0.2399 time to fit residues: 64.2017 Evaluate side-chains 212 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 204 time to evaluate : 0.810 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1550 time to fit residues: 2.8447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7486 Z= 0.196 Angle : 0.597 9.015 10214 Z= 0.289 Chirality : 0.043 0.164 1174 Planarity : 0.005 0.053 1283 Dihedral : 4.097 20.666 955 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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 (0.29), residues: 874 helix: 2.42 (0.42), residues: 158 sheet: 1.14 (0.30), residues: 283 loop : -0.35 (0.30), residues: 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 208 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 214 average time/residue: 0.2348 time to fit residues: 63.6978 Evaluate side-chains 218 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0713 time to fit residues: 3.1067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 7486 Z= 0.265 Angle : 0.622 9.956 10214 Z= 0.302 Chirality : 0.044 0.167 1174 Planarity : 0.005 0.049 1283 Dihedral : 4.233 21.366 955 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.01 (0.29), residues: 874 helix: 2.60 (0.42), residues: 152 sheet: 1.14 (0.30), residues: 284 loop : -0.34 (0.30), residues: 438 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 212 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 218 average time/residue: 0.2425 time to fit residues: 66.8064 Evaluate side-chains 215 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 208 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0802 time to fit residues: 2.1528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 44 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7486 Z= 0.207 Angle : 0.603 9.456 10214 Z= 0.293 Chirality : 0.043 0.166 1174 Planarity : 0.005 0.050 1283 Dihedral : 4.145 21.578 955 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 0.96 (0.29), residues: 874 helix: 2.41 (0.42), residues: 158 sheet: 1.13 (0.30), residues: 283 loop : -0.37 (0.30), residues: 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 207 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 211 average time/residue: 0.2400 time to fit residues: 64.3876 Evaluate side-chains 211 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0734 time to fit residues: 2.5164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.0050 chunk 25 optimal weight: 0.7980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7486 Z= 0.228 Angle : 0.621 9.403 10214 Z= 0.300 Chirality : 0.044 0.172 1174 Planarity : 0.005 0.048 1283 Dihedral : 4.158 22.587 955 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.02 (0.29), residues: 874 helix: 2.70 (0.42), residues: 152 sheet: 1.11 (0.30), residues: 283 loop : -0.34 (0.30), residues: 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 202 average time/residue: 0.2432 time to fit residues: 62.0164 Evaluate side-chains 206 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 200 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0743 time to fit residues: 1.8887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 chunk 57 optimal weight: 0.0980 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 0.0470 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 80 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.1094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 7486 Z= 0.161 Angle : 0.591 8.935 10214 Z= 0.287 Chirality : 0.042 0.184 1174 Planarity : 0.004 0.048 1283 Dihedral : 3.879 19.020 955 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.03 (0.29), residues: 874 helix: 2.86 (0.42), residues: 152 sheet: 0.98 (0.30), residues: 285 loop : -0.29 (0.31), residues: 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 200 average time/residue: 0.2466 time to fit residues: 62.4685 Evaluate side-chains 201 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 195 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0694 time to fit residues: 1.8180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 0.0370 chunk 82 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 167 HIS C 125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7486 Z= 0.188 Angle : 0.601 9.196 10214 Z= 0.291 Chirality : 0.043 0.171 1174 Planarity : 0.004 0.048 1283 Dihedral : 3.922 18.327 955 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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 (0.29), residues: 874 helix: 2.88 (0.42), residues: 152 sheet: 0.96 (0.30), residues: 285 loop : -0.24 (0.30), residues: 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 199 average time/residue: 0.2442 time to fit residues: 61.6236 Evaluate side-chains 201 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0793 time to fit residues: 1.7841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 10 optimal weight: 6.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7486 Z= 0.214 Angle : 0.630 11.168 10214 Z= 0.301 Chirality : 0.043 0.156 1174 Planarity : 0.005 0.048 1283 Dihedral : 4.035 19.108 955 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.04 (0.29), residues: 874 helix: 2.80 (0.42), residues: 152 sheet: 1.01 (0.30), residues: 283 loop : -0.27 (0.30), residues: 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 199 average time/residue: 0.2566 time to fit residues: 64.5419 Evaluate side-chains 198 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0672 time to fit residues: 1.4192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.155607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120190 restraints weight = 11942.009| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.23 r_work: 0.3313 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7486 Z= 0.245 Angle : 0.644 11.030 10214 Z= 0.311 Chirality : 0.044 0.225 1174 Planarity : 0.005 0.048 1283 Dihedral : 4.085 18.684 955 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.29 % 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: 1.04 (0.29), residues: 874 helix: 2.78 (0.42), residues: 152 sheet: 1.04 (0.30), residues: 282 loop : -0.28 (0.30), residues: 440 =============================================================================== Job complete usr+sys time: 2098.22 seconds wall clock time: 38 minutes 26.99 seconds (2306.99 seconds total)