Starting phenix.real_space_refine (version: dev) on Fri Feb 17 15:22:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/02_2023/7uwj_26833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/02_2023/7uwj_26833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/02_2023/7uwj_26833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/02_2023/7uwj_26833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/02_2023/7uwj_26833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/02_2023/7uwj_26833.pdb" } resolution = 3.2 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 771 Classifications: {'peptide': 94} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 86} Chain breaks: 1 Chain: "C" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1844 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 771 Classifications: {'peptide': 94} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 86} Chain breaks: 1 Chain: "D" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1844 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.71, per 1000 atoms: 0.70 Number of scatterers: 5314 At special positions: 0 Unit cell: (93.731, 95.4352, 107.365, 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 50 16.00 O 998 8.00 N 928 7.00 C 3338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 102 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 187 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 257 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 102 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 187 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 261 " 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 NAG-ASN " NAG C 301 " - " ASN C 103 " " NAG C 302 " - " ASN C 156 " " NAG C 303 " - " ASN C 197 " " NAG D 301 " - " ASN D 103 " " NAG D 302 " - " ASN D 156 " " NAG D 303 " - " ASN D 197 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 799.7 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1252 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 15 sheets defined 3.9% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 31 through 36 removed outlier: 4.060A pdb=" N MET C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 36 " --> pdb=" O PRO C 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 36' Processing helix chain 'C' and resid 170 through 177 removed outlier: 3.616A pdb=" N LYS C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 36 removed outlier: 3.913A pdb=" N MET D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 36' Processing helix chain 'D' and resid 170 through 175 removed outlier: 4.322A pdb=" N LYS D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 96 removed outlier: 3.533A pdb=" N HIS A 107 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 95 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 105 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.278A pdb=" N ALA A 167 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N HIS A 135 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER A 165 " --> pdb=" O HIS A 135 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN A 137 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG A 163 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 139 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU A 161 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR A 141 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG A 159 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.266A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS D 264 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 250 " --> pdb=" O HIS D 264 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR D 247 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 211 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 217 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.266A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS D 264 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 250 " --> pdb=" O HIS D 264 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR D 247 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 24 removed outlier: 4.467A pdb=" N GLN C 23 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 83 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 141 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 157 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 136 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.877A pdb=" N VAL C 53 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 65 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 55 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER C 63 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE C 64 " --> pdb=" O PRO C 127 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET C 66 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AA8, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.596A pdb=" N VAL C 222 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 216 through 219 removed outlier: 3.563A pdb=" N ILE C 217 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 211 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 247 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG C 263 " --> pdb=" O MET B 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 96 Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 101 removed outlier: 3.600A pdb=" N LEU B 101 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE B 140 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASN B 129 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS B 170 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU B 131 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N CYS B 168 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 133 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 135 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 139 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.522A pdb=" N SER D 69 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER D 63 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE D 64 " --> pdb=" O PRO D 127 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N MET D 66 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY D 125 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 121 " --> pdb=" O TRP D 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 96 through 100 removed outlier: 3.667A pdb=" N GLY D 90 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 83 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS D 139 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D 136 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D 155 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA D 138 " --> pdb=" O MET D 153 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET D 153 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 132 through 133 removed outlier: 4.088A pdb=" N THR D 132 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 185 through 187 removed outlier: 3.966A pdb=" N PHE D 198 " --> pdb=" O ALA D 233 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 312 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: 1.54 Time building geometry restraints manager: 2.15 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: 1719 1.34 - 1.46: 1238 1.46 - 1.58: 2411 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 5434 Sorted by residual: bond pdb=" C VAL C 22 " pdb=" N GLN C 23 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.34e-02 5.57e+03 1.24e+01 bond pdb=" N VAL C 100 " pdb=" CA VAL C 100 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.24e+00 bond pdb=" N ARG C 101 " pdb=" CA ARG C 101 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.33e+00 bond pdb=" N GLY C 25 " pdb=" CA GLY C 25 " ideal model delta sigma weight residual 1.449 1.483 -0.034 1.45e-02 4.76e+03 5.51e+00 bond pdb=" N ASN C 103 " pdb=" CA ASN C 103 " ideal model delta sigma weight residual 1.453 1.480 -0.026 1.22e-02 6.72e+03 4.69e+00 ... (remaining 5429 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.71: 178 105.71 - 112.78: 2942 112.78 - 119.85: 1667 119.85 - 126.92: 2518 126.92 - 133.99: 73 Bond angle restraints: 7378 Sorted by residual: angle pdb=" CA VAL C 22 " pdb=" C VAL C 22 " pdb=" N GLN C 23 " ideal model delta sigma weight residual 116.34 108.39 7.95 1.28e+00 6.10e-01 3.86e+01 angle pdb=" O VAL C 22 " pdb=" C VAL C 22 " pdb=" N GLN C 23 " ideal model delta sigma weight residual 123.10 129.18 -6.08 1.17e+00 7.31e-01 2.70e+01 angle pdb=" CA ASN C 103 " pdb=" CB ASN C 103 " pdb=" CG ASN C 103 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" C TYR C 104 " pdb=" CA TYR C 104 " pdb=" CB TYR C 104 " ideal model delta sigma weight residual 109.38 117.94 -8.56 1.80e+00 3.09e-01 2.26e+01 angle pdb=" CA ASN C 103 " pdb=" C ASN C 103 " pdb=" O ASN C 103 " ideal model delta sigma weight residual 121.89 116.84 5.05 1.17e+00 7.31e-01 1.86e+01 ... (remaining 7373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3020 17.85 - 35.70: 243 35.70 - 53.55: 39 53.55 - 71.40: 14 71.40 - 89.26: 2 Dihedral angle restraints: 3318 sinusoidal: 1386 harmonic: 1932 Sorted by residual: dihedral pdb=" CB CYS C 162 " pdb=" SG CYS C 162 " pdb=" SG CYS C 173 " pdb=" CB CYS C 173 " ideal model delta sinusoidal sigma weight residual 93.00 -177.74 -89.26 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS D 162 " pdb=" SG CYS D 162 " pdb=" SG CYS D 173 " pdb=" CB CYS D 173 " ideal model delta sinusoidal sigma weight residual 93.00 162.08 -69.08 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CB CYS A 115 " pdb=" SG CYS A 115 " pdb=" SG CYS A 170 " pdb=" CB CYS A 170 " ideal model delta sinusoidal sigma weight residual 93.00 149.03 -56.03 1 1.00e+01 1.00e-02 4.24e+01 ... (remaining 3315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 830 0.112 - 0.224: 14 0.224 - 0.337: 0 0.337 - 0.449: 0 0.449 - 0.561: 2 Chirality restraints: 846 Sorted by residual: chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 103 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA GLN C 23 " pdb=" N GLN C 23 " pdb=" C GLN C 23 " pdb=" CB GLN C 23 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CA VAL C 100 " pdb=" N VAL C 100 " pdb=" C VAL C 100 " pdb=" CB VAL C 100 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 843 not shown) Planarity restraints: 946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 41 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO C 42 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO C 42 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 42 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 80 " 0.066 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO B 81 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 181 " 0.065 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO D 182 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 182 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 182 " 0.052 5.00e-02 4.00e+02 ... (remaining 943 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 321 2.73 - 3.27: 4823 3.27 - 3.82: 7946 3.82 - 4.36: 9021 4.36 - 4.90: 15828 Nonbonded interactions: 37939 Sorted by model distance: nonbonded pdb=" O ALA D 138 " pdb=" OG SER D 152 " model vdw 2.189 2.440 nonbonded pdb=" N SER A 77 " pdb=" O SER A 84 " model vdw 2.203 2.520 nonbonded pdb=" OE1 GLN A 119 " pdb=" NH1 ARG B 127 " model vdw 2.284 2.520 nonbonded pdb=" OE1 GLN C 249 " pdb=" NH1 ARG C 263 " model vdw 2.287 2.520 nonbonded pdb=" OD1 ASP D 47 " pdb=" NH1 ARG D 49 " model vdw 2.290 2.520 ... (remaining 37934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 3338 2.51 5 N 928 2.21 5 O 998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 4.150 Check model and map are aligned: 0.080 Process input model: 18.200 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 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 0.079 5434 Z= 0.216 Angle : 0.777 9.705 7378 Z= 0.459 Chirality : 0.050 0.561 846 Planarity : 0.009 0.109 940 Dihedral : 12.972 70.187 2018 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.31), residues: 640 helix: -3.23 (0.93), residues: 12 sheet: -1.09 (0.31), residues: 266 loop : -1.60 (0.29), residues: 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2127 time to fit residues: 29.7370 Evaluate side-chains 106 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.0030 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN C 147 ASN B 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5434 Z= 0.160 Angle : 0.588 9.514 7378 Z= 0.297 Chirality : 0.043 0.166 846 Planarity : 0.006 0.074 940 Dihedral : 4.656 20.350 758 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.98 (0.31), residues: 640 helix: -2.48 (1.05), residues: 16 sheet: -0.96 (0.31), residues: 266 loop : -1.52 (0.29), residues: 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.2195 time to fit residues: 26.8021 Evaluate side-chains 100 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0652 time to fit residues: 1.6371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5434 Z= 0.197 Angle : 0.598 10.405 7378 Z= 0.307 Chirality : 0.043 0.157 846 Planarity : 0.006 0.056 940 Dihedral : 4.694 19.114 758 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.31), residues: 640 helix: -2.40 (1.08), residues: 16 sheet: -0.97 (0.31), residues: 266 loop : -1.55 (0.29), residues: 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 102 average time/residue: 0.2422 time to fit residues: 30.7203 Evaluate side-chains 98 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0544 time to fit residues: 1.8846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5434 Z= 0.237 Angle : 0.635 11.142 7378 Z= 0.326 Chirality : 0.043 0.161 846 Planarity : 0.006 0.056 940 Dihedral : 4.920 20.603 758 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.30), residues: 640 helix: -2.53 (1.05), residues: 16 sheet: -1.00 (0.31), residues: 266 loop : -1.63 (0.29), residues: 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.2324 time to fit residues: 28.7416 Evaluate side-chains 101 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0559 time to fit residues: 1.8646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5434 Z= 0.223 Angle : 0.621 11.172 7378 Z= 0.317 Chirality : 0.043 0.158 846 Planarity : 0.005 0.056 940 Dihedral : 4.853 20.501 758 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.30), residues: 640 helix: -2.59 (1.05), residues: 16 sheet: -1.05 (0.31), residues: 256 loop : -1.69 (0.29), residues: 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 95 average time/residue: 0.2399 time to fit residues: 28.2519 Evaluate side-chains 90 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0519 time to fit residues: 1.1007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.0070 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 5434 Z= 0.153 Angle : 0.551 10.222 7378 Z= 0.280 Chirality : 0.042 0.161 846 Planarity : 0.005 0.046 940 Dihedral : 4.481 21.538 758 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.31), residues: 640 helix: -2.56 (1.06), residues: 16 sheet: -0.98 (0.32), residues: 252 loop : -1.52 (0.29), residues: 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 93 average time/residue: 0.2304 time to fit residues: 26.7675 Evaluate side-chains 97 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0518 time to fit residues: 1.6643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.0010 chunk 18 optimal weight: 0.4980 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5434 Z= 0.167 Angle : 0.554 10.227 7378 Z= 0.281 Chirality : 0.042 0.157 846 Planarity : 0.005 0.060 940 Dihedral : 4.411 20.682 758 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.95 (0.31), residues: 640 helix: -2.53 (1.07), residues: 16 sheet: -0.95 (0.32), residues: 252 loop : -1.48 (0.29), residues: 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 92 average time/residue: 0.2276 time to fit residues: 25.8362 Evaluate side-chains 93 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0583 time to fit residues: 1.1055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 0.0870 chunk 53 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 5434 Z= 0.168 Angle : 0.560 10.172 7378 Z= 0.282 Chirality : 0.042 0.159 846 Planarity : 0.005 0.045 940 Dihedral : 4.373 20.102 758 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.94 (0.31), residues: 640 helix: -2.49 (1.08), residues: 16 sheet: -0.94 (0.32), residues: 252 loop : -1.47 (0.29), residues: 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 93 average time/residue: 0.2531 time to fit residues: 29.0467 Evaluate side-chains 96 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.626 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1497 time to fit residues: 1.9548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.0470 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 overall best weight: 0.3090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 5434 Z= 0.155 Angle : 0.548 9.740 7378 Z= 0.275 Chirality : 0.042 0.158 846 Planarity : 0.004 0.044 940 Dihedral : 4.232 19.952 758 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.89 (0.31), residues: 640 helix: -2.46 (1.09), residues: 16 sheet: -0.91 (0.32), residues: 252 loop : -1.43 (0.29), residues: 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.2500 time to fit residues: 28.9199 Evaluate side-chains 93 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0596 time to fit residues: 1.1571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.0470 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 5434 Z= 0.159 Angle : 0.551 9.775 7378 Z= 0.277 Chirality : 0.042 0.156 846 Planarity : 0.004 0.042 940 Dihedral : 4.191 19.424 758 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.87 (0.31), residues: 640 helix: -2.33 (1.11), residues: 16 sheet: -0.80 (0.32), residues: 258 loop : -1.52 (0.29), residues: 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.2322 time to fit residues: 26.5873 Evaluate side-chains 91 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 2 optimal weight: 0.0870 chunk 36 optimal weight: 0.0980 chunk 58 optimal weight: 0.9980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.217967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.191734 restraints weight = 7840.478| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 3.13 r_work: 0.4320 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 5434 Z= 0.168 Angle : 0.564 9.854 7378 Z= 0.282 Chirality : 0.042 0.154 846 Planarity : 0.004 0.042 940 Dihedral : 4.248 18.598 758 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.88 (0.31), residues: 640 helix: -2.25 (1.10), residues: 16 sheet: -0.81 (0.32), residues: 258 loop : -1.52 (0.29), residues: 366 =============================================================================== Job complete usr+sys time: 1646.36 seconds wall clock time: 30 minutes 31.03 seconds (1831.03 seconds total)