Starting phenix.real_space_refine on Wed Sep 17 05:37:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uwj_26833/09_2025/7uwj_26833.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uwj_26833/09_2025/7uwj_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 { model { file = "/net/cci-nas-00/data/ceres_data/7uwj_26833/09_2025/7uwj_26833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uwj_26833/09_2025/7uwj_26833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uwj_26833/09_2025/7uwj_26833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uwj_26833/09_2025/7uwj_26833.map" } 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 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= 0.001 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 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. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.46, per 1000 atoms: 0.27 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 - 3.00 Amino acid : True - 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: 0.40 Conformation dependent library (CDL) restraints added in 195.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.19 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: 0.68 Time building geometry restraints manager: 0.55 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=" C1 NAG D 303 " pdb=" O5 NAG D 303 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 5429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 7117 1.94 - 3.88: 229 3.88 - 5.82: 23 5.82 - 7.76: 4 7.76 - 9.71: 5 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: 3088 17.85 - 35.70: 255 35.70 - 53.55: 49 53.55 - 71.40: 14 71.40 - 89.26: 2 Dihedral angle restraints: 3408 sinusoidal: 1476 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 3405 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 3.040 nonbonded pdb=" N SER A 77 " pdb=" O SER A 84 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLN A 119 " pdb=" NH1 ARG B 127 " model vdw 2.284 3.120 nonbonded pdb=" OE1 GLN C 249 " pdb=" NH1 ARG C 263 " model vdw 2.287 3.120 nonbonded pdb=" OD1 ASP D 47 " pdb=" NH1 ARG D 49 " model vdw 2.290 3.120 ... (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 Time spend for trying shortcut: 0.00 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.350 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 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 5456 Z= 0.206 Angle : 0.828 10.968 7428 Z= 0.468 Chirality : 0.051 0.561 846 Planarity : 0.009 0.109 940 Dihedral : 13.198 70.187 2108 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 232 TYR 0.017 0.001 TYR A 162 PHE 0.010 0.001 PHE C 108 TRP 0.007 0.001 TRP D 70 HIS 0.004 0.001 HIS D 213 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 5434) covalent geometry : angle 0.79478 ( 7378) SS BOND : bond 0.00374 ( 16) SS BOND : angle 1.19003 ( 32) hydrogen bonds : bond 0.30494 ( 109) hydrogen bonds : angle 12.18102 ( 312) link_NAG-ASN : bond 0.00652 ( 6) link_NAG-ASN : angle 4.61717 ( 18) *********************** 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 to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 LYS cc_start: 0.7764 (mtpt) cc_final: 0.7419 (mtpt) REVERT: D 35 MET cc_start: 0.5671 (mmm) cc_final: 0.5456 (mmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1000 time to fit residues: 13.9332 Evaluate side-chains 106 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 0.0370 chunk 17 optimal weight: 0.8980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 ASN B 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.218809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.192597 restraints weight = 7920.645| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 3.14 r_work: 0.4336 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5456 Z= 0.119 Angle : 0.659 11.996 7428 Z= 0.321 Chirality : 0.043 0.164 846 Planarity : 0.006 0.075 940 Dihedral : 6.191 49.806 848 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.34 % Allowed : 6.86 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.31), residues: 640 helix: -2.54 (1.03), residues: 16 sheet: -1.01 (0.31), residues: 268 loop : -1.48 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 232 TYR 0.014 0.001 TYR C 253 PHE 0.012 0.001 PHE C 157 TRP 0.014 0.002 TRP D 70 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5434) covalent geometry : angle 0.62062 ( 7378) SS BOND : bond 0.00224 ( 16) SS BOND : angle 0.96325 ( 32) hydrogen bonds : bond 0.04040 ( 109) hydrogen bonds : angle 8.32641 ( 312) link_NAG-ASN : bond 0.00640 ( 6) link_NAG-ASN : angle 4.43321 ( 18) *********************** 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 105 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7421 (mtpt) REVERT: D 35 MET cc_start: 0.6016 (mmm) cc_final: 0.5714 (mmm) outliers start: 8 outliers final: 6 residues processed: 100 average time/residue: 0.1028 time to fit residues: 12.8261 Evaluate side-chains 100 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.216639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.190443 restraints weight = 7797.640| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 3.13 r_work: 0.4306 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5456 Z= 0.133 Angle : 0.645 11.616 7428 Z= 0.318 Chirality : 0.043 0.157 846 Planarity : 0.006 0.057 940 Dihedral : 6.059 50.794 848 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.01 % Allowed : 7.69 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.31), residues: 640 helix: -2.35 (1.07), residues: 16 sheet: -0.95 (0.31), residues: 266 loop : -1.52 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.013 0.001 TYR C 169 PHE 0.013 0.001 PHE D 198 TRP 0.017 0.002 TRP D 70 HIS 0.004 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5434) covalent geometry : angle 0.61126 ( 7378) SS BOND : bond 0.00283 ( 16) SS BOND : angle 0.99400 ( 32) hydrogen bonds : bond 0.04159 ( 109) hydrogen bonds : angle 7.38212 ( 312) link_NAG-ASN : bond 0.00525 ( 6) link_NAG-ASN : angle 4.11853 ( 18) *********************** 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 111 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 265 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7530 (mtpt) REVERT: D 35 MET cc_start: 0.6049 (mmm) cc_final: 0.5745 (mmm) REVERT: D 49 ARG cc_start: 0.2530 (mmm160) cc_final: 0.2215 (mmm160) outliers start: 12 outliers final: 9 residues processed: 104 average time/residue: 0.0978 time to fit residues: 12.5966 Evaluate side-chains 106 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 63 optimal weight: 0.0000 chunk 61 optimal weight: 0.0370 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4262 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.217620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.191466 restraints weight = 7815.266| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 3.15 r_work: 0.4323 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5456 Z= 0.114 Angle : 0.611 11.169 7428 Z= 0.300 Chirality : 0.042 0.159 846 Planarity : 0.005 0.051 940 Dihedral : 5.758 54.370 848 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.84 % Allowed : 9.70 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.31), residues: 640 helix: -2.45 (1.06), residues: 16 sheet: -0.91 (0.32), residues: 252 loop : -1.49 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 232 TYR 0.013 0.001 TYR C 253 PHE 0.011 0.001 PHE D 198 TRP 0.015 0.002 TRP D 70 HIS 0.003 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5434) covalent geometry : angle 0.57922 ( 7378) SS BOND : bond 0.00228 ( 16) SS BOND : angle 0.72508 ( 32) hydrogen bonds : bond 0.03366 ( 109) hydrogen bonds : angle 6.83125 ( 312) link_NAG-ASN : bond 0.00533 ( 6) link_NAG-ASN : angle 3.97888 ( 18) *********************** 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 107 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7616 (mtm180) REVERT: D 35 MET cc_start: 0.6033 (mmm) cc_final: 0.5748 (mmm) REVERT: D 49 ARG cc_start: 0.2018 (mmm160) cc_final: 0.1652 (mmm160) outliers start: 11 outliers final: 10 residues processed: 99 average time/residue: 0.0981 time to fit residues: 12.0772 Evaluate side-chains 105 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 60 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 48 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: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.214178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.187546 restraints weight = 7890.273| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 3.19 r_work: 0.4280 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5456 Z= 0.164 Angle : 0.667 10.824 7428 Z= 0.329 Chirality : 0.044 0.163 846 Planarity : 0.006 0.056 940 Dihedral : 6.259 54.408 848 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.68 % Allowed : 8.86 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.31), residues: 640 helix: -2.50 (1.05), residues: 16 sheet: -1.02 (0.32), residues: 252 loop : -1.55 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 232 TYR 0.015 0.001 TYR C 253 PHE 0.015 0.001 PHE D 198 TRP 0.020 0.003 TRP D 70 HIS 0.006 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5434) covalent geometry : angle 0.63715 ( 7378) SS BOND : bond 0.00395 ( 16) SS BOND : angle 1.01638 ( 32) hydrogen bonds : bond 0.04065 ( 109) hydrogen bonds : angle 6.88410 ( 312) link_NAG-ASN : bond 0.00476 ( 6) link_NAG-ASN : angle 3.89447 ( 18) *********************** 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 117 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 ARG cc_start: 0.7238 (mpt90) cc_final: 0.6030 (mpt90) REVERT: D 35 MET cc_start: 0.6042 (mmm) cc_final: 0.5770 (mmm) outliers start: 22 outliers final: 15 residues processed: 106 average time/residue: 0.0930 time to fit residues: 12.1454 Evaluate side-chains 109 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 0.0000 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.4702 r_free = 0.4702 target = 0.215541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.188568 restraints weight = 7874.873| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 3.29 r_work: 0.4299 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5456 Z= 0.129 Angle : 0.630 10.434 7428 Z= 0.310 Chirality : 0.043 0.157 846 Planarity : 0.005 0.054 940 Dihedral : 5.792 43.836 848 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.84 % Allowed : 11.04 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.31), residues: 640 helix: -2.65 (1.02), residues: 16 sheet: -0.97 (0.32), residues: 252 loop : -1.51 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 232 TYR 0.015 0.001 TYR C 253 PHE 0.012 0.001 PHE D 198 TRP 0.017 0.002 TRP D 70 HIS 0.004 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5434) covalent geometry : angle 0.60196 ( 7378) SS BOND : bond 0.00272 ( 16) SS BOND : angle 0.87284 ( 32) hydrogen bonds : bond 0.03532 ( 109) hydrogen bonds : angle 6.53562 ( 312) link_NAG-ASN : bond 0.00458 ( 6) link_NAG-ASN : angle 3.74608 ( 18) *********************** 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 109 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 134 TYR cc_start: 0.7828 (m-80) cc_final: 0.7581 (m-80) REVERT: B 109 ARG cc_start: 0.7243 (mpt90) cc_final: 0.5899 (mpt90) REVERT: D 35 MET cc_start: 0.6066 (mmm) cc_final: 0.5774 (mmm) outliers start: 17 outliers final: 14 residues processed: 101 average time/residue: 0.0951 time to fit residues: 12.0018 Evaluate side-chains 104 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.214820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.188013 restraints weight = 7860.342| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 3.24 r_work: 0.4286 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5456 Z= 0.158 Angle : 0.662 10.787 7428 Z= 0.327 Chirality : 0.044 0.167 846 Planarity : 0.005 0.056 940 Dihedral : 6.216 49.571 848 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.51 % Allowed : 10.54 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.31), residues: 640 helix: -2.61 (1.01), residues: 16 sheet: -1.04 (0.32), residues: 254 loop : -1.55 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 232 TYR 0.016 0.001 TYR C 169 PHE 0.015 0.001 PHE D 198 TRP 0.020 0.003 TRP D 70 HIS 0.005 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5434) covalent geometry : angle 0.63430 ( 7378) SS BOND : bond 0.00354 ( 16) SS BOND : angle 1.13842 ( 32) hydrogen bonds : bond 0.03924 ( 109) hydrogen bonds : angle 6.59917 ( 312) link_NAG-ASN : bond 0.00425 ( 6) link_NAG-ASN : angle 3.67560 ( 18) *********************** 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 116 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 134 TYR cc_start: 0.7760 (m-80) cc_final: 0.7541 (m-80) REVERT: B 109 ARG cc_start: 0.7244 (mpt90) cc_final: 0.6020 (mpt90) REVERT: D 35 MET cc_start: 0.6048 (mmm) cc_final: 0.5782 (mmm) REVERT: D 66 MET cc_start: 0.6798 (ptp) cc_final: 0.5746 (pmm) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.0977 time to fit residues: 12.5637 Evaluate side-chains 111 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 59 optimal weight: 0.0270 chunk 37 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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** B 123 HIS D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.214815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.188387 restraints weight = 7709.949| |-----------------------------------------------------------------------------| r_work (start): 0.4418 rms_B_bonded: 3.17 r_work: 0.4299 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5456 Z= 0.132 Angle : 0.627 10.528 7428 Z= 0.309 Chirality : 0.043 0.157 846 Planarity : 0.005 0.057 940 Dihedral : 5.813 40.666 848 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.01 % Allowed : 12.21 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.31), residues: 640 helix: -2.60 (1.00), residues: 16 sheet: -1.02 (0.32), residues: 254 loop : -1.54 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 232 TYR 0.015 0.001 TYR C 169 PHE 0.012 0.001 PHE D 198 TRP 0.017 0.002 TRP D 70 HIS 0.004 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5434) covalent geometry : angle 0.60304 ( 7378) SS BOND : bond 0.00288 ( 16) SS BOND : angle 0.87888 ( 32) hydrogen bonds : bond 0.03492 ( 109) hydrogen bonds : angle 6.34042 ( 312) link_NAG-ASN : bond 0.00436 ( 6) link_NAG-ASN : angle 3.45345 ( 18) *********************** 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 111 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 ARG cc_start: 0.7248 (mpt90) cc_final: 0.5977 (mpt90) REVERT: D 35 MET cc_start: 0.6011 (mmm) cc_final: 0.5746 (mmm) outliers start: 18 outliers final: 17 residues processed: 102 average time/residue: 0.0985 time to fit residues: 12.4064 Evaluate side-chains 107 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.213306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.186093 restraints weight = 7767.965| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 3.32 r_work: 0.4272 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5456 Z= 0.173 Angle : 0.682 10.850 7428 Z= 0.339 Chirality : 0.045 0.212 846 Planarity : 0.006 0.058 940 Dihedral : 6.610 54.297 848 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.84 % Allowed : 12.37 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.31), residues: 640 helix: -2.51 (1.00), residues: 16 sheet: -1.15 (0.32), residues: 258 loop : -1.58 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 232 TYR 0.014 0.002 TYR C 169 PHE 0.014 0.001 PHE D 198 TRP 0.021 0.003 TRP D 70 HIS 0.006 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 5434) covalent geometry : angle 0.65877 ( 7378) SS BOND : bond 0.00361 ( 16) SS BOND : angle 1.13329 ( 32) hydrogen bonds : bond 0.04131 ( 109) hydrogen bonds : angle 6.55098 ( 312) link_NAG-ASN : bond 0.00318 ( 6) link_NAG-ASN : angle 3.44640 ( 18) *********************** 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 116 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 35 MET cc_start: 0.6009 (mmm) cc_final: 0.5773 (mmm) outliers start: 17 outliers final: 16 residues processed: 106 average time/residue: 0.1005 time to fit residues: 13.0860 Evaluate side-chains 115 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** B 123 HIS D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.214337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.187780 restraints weight = 7753.395| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 3.19 r_work: 0.4281 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5456 Z= 0.157 Angle : 0.662 10.702 7428 Z= 0.329 Chirality : 0.044 0.171 846 Planarity : 0.006 0.058 940 Dihedral : 6.454 49.231 848 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.68 % Allowed : 12.88 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.30), residues: 640 helix: -2.50 (1.00), residues: 16 sheet: -1.12 (0.32), residues: 256 loop : -1.67 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 232 TYR 0.012 0.001 TYR C 169 PHE 0.012 0.001 PHE D 198 TRP 0.018 0.002 TRP D 70 HIS 0.007 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5434) covalent geometry : angle 0.64041 ( 7378) SS BOND : bond 0.00328 ( 16) SS BOND : angle 1.02637 ( 32) hydrogen bonds : bond 0.03825 ( 109) hydrogen bonds : angle 6.42914 ( 312) link_NAG-ASN : bond 0.00286 ( 6) link_NAG-ASN : angle 3.25828 ( 18) ********************** 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 113 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 ARG cc_start: 0.7277 (mpt90) cc_final: 0.5995 (mpt90) outliers start: 16 outliers final: 16 residues processed: 104 average time/residue: 0.1004 time to fit residues: 12.8559 Evaluate side-chains 113 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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** B 123 HIS D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.215250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.188700 restraints weight = 7792.681| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 3.22 r_work: 0.4292 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5456 Z= 0.125 Angle : 0.632 10.485 7428 Z= 0.314 Chirality : 0.043 0.155 846 Planarity : 0.005 0.055 940 Dihedral : 6.139 43.734 848 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.68 % Allowed : 13.38 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.31), residues: 640 helix: -2.61 (0.99), residues: 16 sheet: -1.08 (0.32), residues: 256 loop : -1.62 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 232 TYR 0.014 0.001 TYR C 169 PHE 0.012 0.001 PHE D 198 TRP 0.017 0.002 TRP D 70 HIS 0.007 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5434) covalent geometry : angle 0.61149 ( 7378) SS BOND : bond 0.00266 ( 16) SS BOND : angle 0.87686 ( 32) hydrogen bonds : bond 0.03436 ( 109) hydrogen bonds : angle 6.27426 ( 312) link_NAG-ASN : bond 0.00296 ( 6) link_NAG-ASN : angle 3.19937 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1600.58 seconds wall clock time: 28 minutes 13.86 seconds (1693.86 seconds total)