Starting phenix.real_space_refine on Tue Feb 13 18:33:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/02_2024/7u7n_26382.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/02_2024/7u7n_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_26382/02_2024/7u7n_26382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/02_2024/7u7n_26382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/02_2024/7u7n_26382.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u7n_26382/02_2024/7u7n_26382.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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-dev-5238/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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.77, per 1000 atoms: 0.65 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: 2.98 Conformation dependent library (CDL) restraints added in 1.3 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: 0.86 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: 1.89 Time building geometry restraints manager: 3.08 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 - 23.94: 4233 23.94 - 47.87: 374 47.87 - 71.80: 52 71.80 - 95.74: 32 95.74 - 119.67: 13 Dihedral angle restraints: 4704 sinusoidal: 2120 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=" C2 MAN F 4 " pdb=" C1 MAN F 4 " pdb=" O5 MAN F 4 " pdb=" C5 MAN F 4 " ideal model delta sinusoidal sigma weight residual -57.62 62.05 -119.67 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 4701 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: 0.910 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: 3.780 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.170 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.940 ------------------------------------------------------------------------------- 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 : 19.360 119.673 3002 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 % Allowed : 27.90 % Favored : 71.21 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 115 HIS 0.002 0.001 HIS D 150 PHE 0.019 0.001 PHE D 153 TYR 0.016 0.001 TYR C 40 ARG 0.006 0.000 ARG D 55 *********************** 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 : 0.813 Fit side-chains revert: symmetry clash REVERT: B 30 TYR cc_start: 0.8282 (p90) cc_final: 0.8081 (p90) REVERT: B 116 TYR cc_start: 0.8433 (t80) cc_final: 0.8091 (t80) outliers start: 7 outliers final: 5 residues processed: 200 average time/residue: 0.2434 time to fit residues: 60.7698 Evaluate side-chains 202 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain C residue 99 MET 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: 0.9980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7471 moved from start: 0.0751 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= 0.222 Angle : 0.636 8.219 10214 Z= 0.307 Chirality : 0.044 0.165 1174 Planarity : 0.005 0.053 1283 Dihedral : 11.993 92.122 1298 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.08 % Allowed : 24.46 % Favored : 71.46 % 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: 2.47 (0.42), residues: 158 sheet: 1.08 (0.30), residues: 285 loop : -0.24 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 155 HIS 0.004 0.001 HIS A 167 PHE 0.012 0.001 PHE B 158 TYR 0.015 0.002 TYR C 40 ARG 0.005 0.000 ARG D 55 *********************** 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 230 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 THR cc_start: 0.8181 (m) cc_final: 0.7951 (p) REVERT: B 54 CYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7213 (t) REVERT: B 105 ILE cc_start: 0.8576 (pt) cc_final: 0.8369 (pt) REVERT: D 43 LEU cc_start: 0.8574 (mt) cc_final: 0.8119 (mp) REVERT: D 154 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7894 (mt0) outliers start: 32 outliers final: 20 residues processed: 207 average time/residue: 0.2398 time to fit residues: 62.9898 Evaluate side-chains 218 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.8342 ------------------------------------------------------------------------------- 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: 0.7480 moved from start: 0.1012 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= 0.221 Angle : 0.620 9.065 10214 Z= 0.295 Chirality : 0.044 0.177 1174 Planarity : 0.005 0.054 1283 Dihedral : 8.395 70.442 1286 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.33 % Allowed : 24.33 % Favored : 71.34 % 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: 2.53 (0.42), residues: 158 sheet: 1.12 (0.30), residues: 284 loop : -0.30 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 155 HIS 0.005 0.001 HIS B 167 PHE 0.015 0.001 PHE C 62 TYR 0.017 0.002 TYR B 116 ARG 0.004 0.000 ARG B 150 *********************** 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 238 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 204 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7958 (p90) cc_final: 0.7652 (p90) REVERT: B 45 THR cc_start: 0.8223 (m) cc_final: 0.7943 (p) REVERT: B 54 CYS cc_start: 0.7488 (t) cc_final: 0.7258 (t) REVERT: B 116 TYR cc_start: 0.8457 (t80) cc_final: 0.8040 (t80) REVERT: B 219 LYS cc_start: 0.5629 (tptt) cc_final: 0.5414 (tptt) REVERT: C 62 PHE cc_start: 0.8213 (m-80) cc_final: 0.7834 (m-10) REVERT: C 115 SER cc_start: 0.8603 (t) cc_final: 0.8328 (m) REVERT: D 43 LEU cc_start: 0.8543 (mt) cc_final: 0.8073 (mp) REVERT: D 154 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7893 (mt0) outliers start: 34 outliers final: 26 residues processed: 213 average time/residue: 0.2314 time to fit residues: 62.6547 Evaluate side-chains 229 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 37 optimal weight: 10.0000 chunk 53 optimal weight: 0.0010 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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: 0.7458 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7486 Z= 0.174 Angle : 0.581 8.881 10214 Z= 0.277 Chirality : 0.043 0.166 1174 Planarity : 0.005 0.054 1283 Dihedral : 6.589 59.698 1286 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.95 % Allowed : 25.61 % Favored : 70.45 % 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: 1.09 (0.29), residues: 874 helix: 2.63 (0.42), residues: 158 sheet: 1.08 (0.30), residues: 285 loop : -0.23 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 115 HIS 0.005 0.001 HIS B 167 PHE 0.013 0.001 PHE D 153 TYR 0.017 0.002 TYR B 30 ARG 0.005 0.000 ARG B 150 *********************** 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 235 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7943 (p90) cc_final: 0.7684 (p90) REVERT: A 183 LEU cc_start: 0.8310 (mm) cc_final: 0.7960 (mp) REVERT: B 45 THR cc_start: 0.8097 (m) cc_final: 0.7860 (p) REVERT: B 54 CYS cc_start: 0.7498 (t) cc_final: 0.7251 (t) REVERT: B 64 TYR cc_start: 0.8336 (m-80) cc_final: 0.7927 (m-80) REVERT: B 116 TYR cc_start: 0.8469 (t80) cc_final: 0.8042 (t80) REVERT: C 62 PHE cc_start: 0.8199 (m-80) cc_final: 0.7916 (m-10) REVERT: C 209 THR cc_start: 0.8347 (p) cc_final: 0.8061 (p) REVERT: D 43 LEU cc_start: 0.8521 (mt) cc_final: 0.8029 (mp) REVERT: D 91 SER cc_start: 0.8901 (m) cc_final: 0.8694 (m) REVERT: D 154 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7814 (mt0) outliers start: 31 outliers final: 25 residues processed: 214 average time/residue: 0.2373 time to fit residues: 64.2793 Evaluate side-chains 228 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN 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: 1.9990 chunk 34 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1298 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= 0.257 Angle : 0.601 9.583 10214 Z= 0.291 Chirality : 0.044 0.180 1174 Planarity : 0.005 0.053 1283 Dihedral : 5.865 49.590 1286 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.48 % Allowed : 25.10 % Favored : 69.43 % 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: 2.50 (0.42), residues: 158 sheet: 1.20 (0.30), residues: 281 loop : -0.27 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 155 HIS 0.006 0.001 HIS B 167 PHE 0.014 0.002 PHE C 121 TYR 0.017 0.002 TYR C 40 ARG 0.004 0.000 ARG D 216 *********************** 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 249 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7974 (p90) cc_final: 0.7692 (p90) REVERT: B 45 THR cc_start: 0.8148 (m) cc_final: 0.7894 (p) REVERT: B 54 CYS cc_start: 0.7554 (t) cc_final: 0.7317 (t) REVERT: B 64 TYR cc_start: 0.8394 (m-80) cc_final: 0.8133 (m-80) REVERT: B 146 TRP cc_start: 0.6784 (p90) cc_final: 0.6368 (p90) REVERT: C 118 PHE cc_start: 0.8009 (m-80) cc_final: 0.7611 (m-80) REVERT: D 43 LEU cc_start: 0.8542 (mt) cc_final: 0.8055 (mp) REVERT: D 91 SER cc_start: 0.8899 (m) cc_final: 0.8678 (m) REVERT: D 154 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7866 (mt0) outliers start: 43 outliers final: 31 residues processed: 225 average time/residue: 0.2310 time to fit residues: 65.8033 Evaluate side-chains 237 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.0570 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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: 0.7479 moved from start: 0.1387 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= 0.208 Angle : 0.591 9.578 10214 Z= 0.285 Chirality : 0.043 0.176 1174 Planarity : 0.004 0.053 1283 Dihedral : 5.364 45.465 1283 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.10 % Allowed : 25.22 % Favored : 69.68 % 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: 1.11 (0.29), residues: 874 helix: 2.58 (0.42), residues: 158 sheet: 1.20 (0.30), residues: 283 loop : -0.26 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 155 HIS 0.005 0.001 HIS B 167 PHE 0.022 0.001 PHE C 62 TYR 0.016 0.002 TYR C 40 ARG 0.005 0.000 ARG D 105 *********************** 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 254 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 214 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 THR cc_start: 0.8397 (m) cc_final: 0.8182 (p) REVERT: A 168 TYR cc_start: 0.7936 (p90) cc_final: 0.7626 (p90) REVERT: A 179 LEU cc_start: 0.8341 (mt) cc_final: 0.8012 (mp) REVERT: A 183 LEU cc_start: 0.8346 (mm) cc_final: 0.8007 (mp) REVERT: B 45 THR cc_start: 0.8142 (m) cc_final: 0.7876 (p) REVERT: B 54 CYS cc_start: 0.7548 (t) cc_final: 0.7309 (t) REVERT: B 64 TYR cc_start: 0.8364 (m-80) cc_final: 0.8047 (m-80) REVERT: B 116 TYR cc_start: 0.8464 (t80) cc_final: 0.8088 (t80) REVERT: C 62 PHE cc_start: 0.8124 (m-80) cc_final: 0.7917 (m-10) REVERT: D 43 LEU cc_start: 0.8529 (mt) cc_final: 0.8046 (mp) REVERT: D 91 SER cc_start: 0.8900 (m) cc_final: 0.8668 (m) REVERT: D 154 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7855 (mt0) outliers start: 40 outliers final: 35 residues processed: 227 average time/residue: 0.2284 time to fit residues: 66.0332 Evaluate side-chains 246 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.1980 chunk 47 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.0050 chunk 25 optimal weight: 3.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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: 0.7481 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7486 Z= 0.207 Angle : 0.589 9.448 10214 Z= 0.285 Chirality : 0.043 0.174 1174 Planarity : 0.004 0.053 1283 Dihedral : 5.157 44.220 1283 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.10 % Allowed : 26.37 % Favored : 68.54 % 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: 1.10 (0.29), residues: 874 helix: 2.57 (0.42), residues: 158 sheet: 1.17 (0.30), residues: 283 loop : -0.26 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 155 HIS 0.004 0.001 HIS B 167 PHE 0.020 0.001 PHE C 62 TYR 0.016 0.002 TYR C 40 ARG 0.005 0.000 ARG D 105 *********************** 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 245 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 205 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7728 (mtpp) REVERT: A 155 THR cc_start: 0.8399 (m) cc_final: 0.8185 (p) REVERT: A 179 LEU cc_start: 0.8368 (mt) cc_final: 0.8043 (mp) REVERT: A 183 LEU cc_start: 0.8356 (mm) cc_final: 0.8007 (mp) REVERT: A 214 GLU cc_start: 0.7040 (pp20) cc_final: 0.6524 (pp20) REVERT: B 45 THR cc_start: 0.8151 (m) cc_final: 0.7871 (p) REVERT: B 54 CYS cc_start: 0.7549 (t) cc_final: 0.7288 (t) REVERT: B 64 TYR cc_start: 0.8359 (m-80) cc_final: 0.8074 (m-80) REVERT: B 65 ILE cc_start: 0.8973 (mm) cc_final: 0.8731 (mm) REVERT: B 116 TYR cc_start: 0.8452 (t80) cc_final: 0.8085 (t80) REVERT: B 219 LYS cc_start: 0.6312 (tptp) cc_final: 0.5942 (tptt) REVERT: C 62 PHE cc_start: 0.8176 (m-80) cc_final: 0.7956 (m-10) REVERT: D 43 LEU cc_start: 0.8525 (mt) cc_final: 0.8038 (mp) REVERT: D 91 SER cc_start: 0.8881 (m) cc_final: 0.8651 (m) REVERT: D 154 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7846 (mt0) outliers start: 40 outliers final: 36 residues processed: 219 average time/residue: 0.2481 time to fit residues: 68.8870 Evaluate side-chains 241 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7495 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7486 Z= 0.248 Angle : 0.614 9.578 10214 Z= 0.297 Chirality : 0.044 0.173 1174 Planarity : 0.005 0.053 1283 Dihedral : 5.106 43.333 1283 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.10 % Allowed : 26.24 % Favored : 68.66 % 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: 1.11 (0.29), residues: 874 helix: 2.80 (0.42), residues: 152 sheet: 1.17 (0.30), residues: 283 loop : -0.29 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.004 0.001 HIS B 167 PHE 0.022 0.002 PHE A 166 TYR 0.026 0.002 TYR A 205 ARG 0.004 0.000 ARG D 105 *********************** 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 249 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7677 (mtpp) REVERT: A 123 GLU cc_start: 0.7496 (tt0) cc_final: 0.7272 (tt0) REVERT: A 155 THR cc_start: 0.8414 (m) cc_final: 0.8190 (p) REVERT: A 179 LEU cc_start: 0.8377 (mt) cc_final: 0.8153 (mp) REVERT: A 183 LEU cc_start: 0.8385 (mm) cc_final: 0.8044 (mp) REVERT: A 214 GLU cc_start: 0.7034 (pp20) cc_final: 0.6490 (pp20) REVERT: B 45 THR cc_start: 0.8158 (m) cc_final: 0.7865 (p) REVERT: B 54 CYS cc_start: 0.7553 (t) cc_final: 0.7307 (t) REVERT: B 64 TYR cc_start: 0.8381 (m-80) cc_final: 0.8068 (m-80) REVERT: B 116 TYR cc_start: 0.8460 (t80) cc_final: 0.8114 (t80) REVERT: B 146 TRP cc_start: 0.6804 (p90) cc_final: 0.6389 (p90) REVERT: B 219 LYS cc_start: 0.6352 (tptp) cc_final: 0.5921 (tptt) REVERT: B 249 ILE cc_start: 0.5898 (OUTLIER) cc_final: 0.5556 (mt) REVERT: C 62 PHE cc_start: 0.8183 (m-80) cc_final: 0.7947 (m-10) REVERT: C 118 PHE cc_start: 0.8004 (m-80) cc_final: 0.7600 (m-80) REVERT: D 43 LEU cc_start: 0.8567 (mt) cc_final: 0.8072 (mp) REVERT: D 91 SER cc_start: 0.8896 (m) cc_final: 0.8568 (p) REVERT: D 154 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7846 (mt0) outliers start: 40 outliers final: 37 residues processed: 223 average time/residue: 0.2282 time to fit residues: 64.7470 Evaluate side-chains 246 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 207 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 89 CYS Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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: 0.7472 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7486 Z= 0.184 Angle : 0.591 9.253 10214 Z= 0.283 Chirality : 0.043 0.178 1174 Planarity : 0.004 0.053 1283 Dihedral : 4.956 41.973 1283 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.46 % Allowed : 27.13 % Favored : 68.41 % 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: 1.18 (0.29), residues: 874 helix: 2.93 (0.42), residues: 152 sheet: 1.18 (0.30), residues: 283 loop : -0.25 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.003 0.001 HIS B 167 PHE 0.021 0.001 PHE A 166 TYR 0.023 0.002 TYR A 205 ARG 0.004 0.000 ARG D 105 *********************** 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 245 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 210 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7737 (mtpp) REVERT: A 155 THR cc_start: 0.8394 (m) cc_final: 0.8181 (p) REVERT: A 183 LEU cc_start: 0.8369 (mm) cc_final: 0.8010 (mp) REVERT: A 214 GLU cc_start: 0.7040 (pp20) cc_final: 0.6459 (pp20) REVERT: B 45 THR cc_start: 0.8146 (m) cc_final: 0.7857 (p) REVERT: B 54 CYS cc_start: 0.7531 (t) cc_final: 0.7275 (t) REVERT: B 64 TYR cc_start: 0.8315 (m-80) cc_final: 0.7902 (m-80) REVERT: B 65 ILE cc_start: 0.8981 (mm) cc_final: 0.8693 (mm) REVERT: B 116 TYR cc_start: 0.8484 (t80) cc_final: 0.8086 (t80) REVERT: B 219 LYS cc_start: 0.6179 (tptp) cc_final: 0.5790 (tptt) REVERT: B 249 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5500 (mt) REVERT: C 62 PHE cc_start: 0.8173 (m-80) cc_final: 0.7919 (m-10) REVERT: C 118 PHE cc_start: 0.7977 (m-80) cc_final: 0.7583 (m-80) REVERT: C 209 THR cc_start: 0.8312 (p) cc_final: 0.8075 (p) REVERT: D 43 LEU cc_start: 0.8509 (mt) cc_final: 0.7995 (mp) REVERT: D 91 SER cc_start: 0.8856 (m) cc_final: 0.8629 (m) REVERT: D 154 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7848 (mt0) outliers start: 35 outliers final: 28 residues processed: 223 average time/residue: 0.2335 time to fit residues: 66.1035 Evaluate side-chains 237 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 207 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 154 GLN 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: 2.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7487 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7486 Z= 0.230 Angle : 0.608 9.356 10214 Z= 0.293 Chirality : 0.044 0.170 1174 Planarity : 0.005 0.053 1283 Dihedral : 4.967 41.346 1283 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.08 % Allowed : 27.77 % Favored : 68.15 % 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: 1.13 (0.29), residues: 874 helix: 2.80 (0.41), residues: 152 sheet: 1.19 (0.30), residues: 283 loop : -0.28 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 97 HIS 0.003 0.001 HIS A 167 PHE 0.028 0.002 PHE A 166 TYR 0.025 0.002 TYR A 205 ARG 0.005 0.000 ARG D 105 ********************** 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 239 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7746 (mtpp) REVERT: A 155 THR cc_start: 0.8412 (m) cc_final: 0.8192 (p) REVERT: A 183 LEU cc_start: 0.8382 (mm) cc_final: 0.8047 (mp) REVERT: A 214 GLU cc_start: 0.7066 (pp20) cc_final: 0.6469 (pp20) REVERT: B 45 THR cc_start: 0.8164 (m) cc_final: 0.7850 (p) REVERT: B 54 CYS cc_start: 0.7545 (t) cc_final: 0.7299 (t) REVERT: B 64 TYR cc_start: 0.8342 (m-80) cc_final: 0.7912 (m-80) REVERT: B 116 TYR cc_start: 0.8465 (t80) cc_final: 0.8072 (t80) REVERT: B 219 LYS cc_start: 0.6214 (tptp) cc_final: 0.5771 (tptt) REVERT: C 62 PHE cc_start: 0.8192 (m-80) cc_final: 0.7925 (m-10) REVERT: D 43 LEU cc_start: 0.8545 (mt) cc_final: 0.8048 (mp) REVERT: D 91 SER cc_start: 0.8870 (m) cc_final: 0.8535 (p) REVERT: D 154 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7877 (mt0) outliers start: 32 outliers final: 30 residues processed: 217 average time/residue: 0.2372 time to fit residues: 64.7547 Evaluate side-chains 238 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 0.0000 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121465 restraints weight = 12025.079| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.28 r_work: 0.3323 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7486 Z= 0.172 Angle : 0.584 9.117 10214 Z= 0.281 Chirality : 0.043 0.176 1174 Planarity : 0.004 0.053 1283 Dihedral : 4.810 39.583 1283 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.57 % Allowed : 28.15 % Favored : 68.28 % 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: 1.13 (0.29), residues: 874 helix: 2.93 (0.42), residues: 152 sheet: 1.05 (0.31), residues: 286 loop : -0.22 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 97 HIS 0.003 0.001 HIS B 167 PHE 0.016 0.001 PHE C 62 TYR 0.017 0.002 TYR A 205 ARG 0.004 0.000 ARG D 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.62 seconds wall clock time: 40 minutes 56.39 seconds (2456.39 seconds total)