Starting phenix.real_space_refine on Wed Sep 17 13:43:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgs_60089/09_2025/8zgs_60089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgs_60089/09_2025/8zgs_60089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zgs_60089/09_2025/8zgs_60089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgs_60089/09_2025/8zgs_60089.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgs_60089/09_2025/8zgs_60089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgs_60089/09_2025/8zgs_60089.cif" } resolution = 3.04 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= 0.000 sd= 0.034 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 40 5.16 5 C 5713 2.51 5 N 1483 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s 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: 8915 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1729 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain: "B" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1227 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 1, 'TRANS': 156} Chain: "C" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2602 Classifications: {'peptide': 320} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 300} Chain: "F" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2571 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 295} Chain: "G" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 274 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.36, per 1000 atoms: 0.26 Number of scatterers: 8915 At special positions: 0 Unit cell: (80.75, 103.55, 170.05, 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 40 16.00 O 1679 8.00 N 1483 7.00 C 5713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 91 " distance=2.04 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 171 " distance=2.04 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS G 25 " distance=2.03 Simple disulfide: pdb=" SG CYS E 112 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 184 " distance=2.03 Simple disulfide: pdb=" SG CYS E 230 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 334 " - pdb=" SG CYS E 396 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 184 " distance=2.03 Simple disulfide: pdb=" SG CYS F 230 " - pdb=" SG CYS F 289 " distance=2.03 Simple disulfide: pdb=" SG CYS F 334 " - pdb=" SG CYS F 396 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 301 " - " ASN A 158 " " NAG A 302 " - " ASN A 167 " " NAG D 1 " - " ASN E 265 " " NAG E 501 " - " ASN E 240 " " NAG E 502 " - " ASN E 170 " " NAG F 501 " - " ASN F 170 " " NAG H 1 " - " ASN F 265 " " NAG T 1 " - " ASN A 65 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 286.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 22 sheets defined 28.6% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.518A pdb=" N SER A 86 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.644A pdb=" N SER A 169 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 236 removed outlier: 3.777A pdb=" N ILE A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 83 removed outlier: 4.048A pdb=" N LYS B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.593A pdb=" N PHE B 88 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.737A pdb=" N LEU B 107 " --> pdb=" O TRP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 161 removed outlier: 3.623A pdb=" N VAL B 136 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 205 removed outlier: 3.814A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 58 Processing helix chain 'E' and resid 173 through 178 Processing helix chain 'E' and resid 216 through 222 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.609A pdb=" N GLY E 284 " --> pdb=" O ASP E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'F' and resid 173 through 178 Processing helix chain 'F' and resid 204 through 208 Processing helix chain 'F' and resid 216 through 222 Processing helix chain 'F' and resid 277 through 284 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 385 through 389 Processing helix chain 'G' and resid 25 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 121 removed outlier: 4.171A pdb=" N TYR A 177 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS A 140 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 151 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS A 145 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA6, first strand: chain 'E' and resid 104 through 109 removed outlier: 5.359A pdb=" N ALA E 163 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR E 166 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU E 155 " --> pdb=" O TYR E 166 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG E 168 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASN E 153 " --> pdb=" O ARG E 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AA8, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AA9, first strand: chain 'E' and resid 209 through 213 removed outlier: 3.668A pdb=" N THR E 229 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP E 234 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR E 268 " --> pdb=" O ASP E 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 242 through 246 Processing sheet with id=AB2, first strand: chain 'E' and resid 315 through 319 removed outlier: 4.125A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 315 through 319 removed outlier: 4.125A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 374 " --> pdb=" O TYR E 368 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB5, first strand: chain 'F' and resid 104 through 109 removed outlier: 3.527A pdb=" N TYR F 128 " --> pdb=" O THR F 104 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA F 163 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU F 158 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER F 164 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 104 through 109 removed outlier: 3.527A pdb=" N TYR F 128 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 144 through 145 Processing sheet with id=AB8, first strand: chain 'F' and resid 144 through 145 Processing sheet with id=AB9, first strand: chain 'F' and resid 209 through 213 removed outlier: 3.812A pdb=" N ASP F 234 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR F 268 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 242 through 246 removed outlier: 3.605A pdb=" N ARG F 302 " --> pdb=" O CYS F 289 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 315 through 319 removed outlier: 4.007A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 315 through 319 removed outlier: 4.007A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 366 " --> pdb=" O PHE F 376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 345 through 350 472 hydrogen bonds defined for protein. 1260 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: 1.60 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.21: 8 1.21 - 1.36: 2813 1.36 - 1.51: 2830 1.51 - 1.67: 3420 1.67 - 1.82: 50 Bond restraints: 9121 Sorted by residual: bond pdb=" CG PRO E 114 " pdb=" CD PRO E 114 " ideal model delta sigma weight residual 1.503 1.053 0.450 3.40e-02 8.65e+02 1.76e+02 bond pdb=" C LEU A 111 " pdb=" O LEU A 111 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.14e-02 7.69e+03 4.12e+01 bond pdb=" N PRO E 114 " pdb=" CD PRO E 114 " ideal model delta sigma weight residual 1.473 1.563 -0.090 1.40e-02 5.10e+03 4.09e+01 bond pdb=" C MET A 107 " pdb=" O MET A 107 " ideal model delta sigma weight residual 1.234 1.164 0.070 1.29e-02 6.01e+03 2.96e+01 bond pdb=" CBE Y01 B 601 " pdb=" CBI Y01 B 601 " ideal model delta sigma weight residual 1.550 1.452 0.098 2.00e-02 2.50e+03 2.38e+01 ... (remaining 9116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 12328 4.28 - 8.56: 43 8.56 - 12.84: 9 12.84 - 17.11: 2 17.11 - 21.39: 1 Bond angle restraints: 12383 Sorted by residual: angle pdb=" N PRO E 114 " pdb=" CD PRO E 114 " pdb=" CG PRO E 114 " ideal model delta sigma weight residual 103.20 81.81 21.39 1.50e+00 4.44e-01 2.03e+02 angle pdb=" CA PRO E 114 " pdb=" N PRO E 114 " pdb=" CD PRO E 114 " ideal model delta sigma weight residual 112.00 95.99 16.01 1.40e+00 5.10e-01 1.31e+02 angle pdb=" CA PRO E 114 " pdb=" CB PRO E 114 " pdb=" CG PRO E 114 " ideal model delta sigma weight residual 104.50 90.24 14.26 1.90e+00 2.77e-01 5.63e+01 angle pdb=" N PRO E 114 " pdb=" CA PRO E 114 " pdb=" CB PRO E 114 " ideal model delta sigma weight residual 103.26 96.22 7.04 1.14e+00 7.69e-01 3.82e+01 angle pdb=" N MET A 107 " pdb=" CA MET A 107 " pdb=" C MET A 107 " ideal model delta sigma weight residual 109.14 117.53 -8.39 1.49e+00 4.50e-01 3.17e+01 ... (remaining 12378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 5074 21.92 - 43.83: 519 43.83 - 65.75: 85 65.75 - 87.67: 30 87.67 - 109.59: 8 Dihedral angle restraints: 5716 sinusoidal: 2532 harmonic: 3184 Sorted by residual: dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N PRO A 34 " pdb=" CA PRO A 34 " ideal model delta harmonic sigma weight residual 180.00 118.69 61.31 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CB CYS C 25 " pdb=" SG CYS C 25 " pdb=" SG CYS G 25 " pdb=" CB CYS G 25 " ideal model delta sinusoidal sigma weight residual 93.00 136.14 -43.14 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CA ILE A 198 " pdb=" C ILE A 198 " pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1401 0.110 - 0.220: 45 0.220 - 0.330: 3 0.330 - 0.440: 3 0.440 - 0.550: 1 Chirality restraints: 1453 Sorted by residual: chirality pdb=" CBG Y01 B 601 " pdb=" CAQ Y01 B 601 " pdb=" CBD Y01 B 601 " pdb=" CBI Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.88 0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" CBI Y01 B 601 " pdb=" CAU Y01 B 601 " pdb=" CBE Y01 B 601 " pdb=" CBG Y01 B 601 " both_signs ideal model delta sigma weight residual False 2.94 2.56 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CBH Y01 B 601 " pdb=" CAT Y01 B 601 " pdb=" CAZ Y01 B 601 " pdb=" CBF Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.48 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 1450 not shown) Planarity restraints: 1527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 113 " 0.108 5.00e-02 4.00e+02 1.48e-01 3.52e+01 pdb=" N PRO E 114 " -0.256 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 198 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.97e+00 pdb=" C ILE A 198 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE A 198 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 199 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 33 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" CG ASP A 33 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP A 33 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 33 " -0.014 2.00e-02 2.50e+03 ... (remaining 1524 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 985 2.75 - 3.29: 8033 3.29 - 3.83: 13743 3.83 - 4.36: 16075 4.36 - 4.90: 29102 Nonbonded interactions: 67938 Sorted by model distance: nonbonded pdb=" O VAL B 78 " pdb=" OG1 THR B 82 " model vdw 2.217 3.040 nonbonded pdb=" O THR E 225 " pdb=" OG1 THR E 225 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 132 " pdb=" O TRP A 136 " model vdw 2.243 3.040 nonbonded pdb=" O LEU F 387 " pdb=" NZ LYS F 392 " model vdw 2.243 3.120 nonbonded pdb=" NH2 ARG E 380 " pdb=" OE1 GLU E 382 " model vdw 2.252 3.120 ... (remaining 67933 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 'C' and resid 24 through 57) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 101 through 416 or resid 502)) selection = chain 'F' } 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.230 Find NCS groups from input model: 0.120 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.007 0.450 9145 Z= 0.304 Angle : 0.763 21.393 12444 Z= 0.383 Chirality : 0.050 0.550 1453 Planarity : 0.005 0.148 1519 Dihedral : 18.157 109.587 3613 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.61 % Allowed : 23.51 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.87 (0.26), residues: 1065 helix: 1.99 (0.31), residues: 271 sheet: 0.91 (0.29), residues: 354 loop : -0.58 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 259 TYR 0.008 0.001 TYR F 166 PHE 0.010 0.001 PHE A 150 TRP 0.019 0.001 TRP A 110 HIS 0.002 0.000 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00714 ( 9121) covalent geometry : angle 0.74574 (12383) SS BOND : bond 0.00340 ( 11) SS BOND : angle 0.74892 ( 22) hydrogen bonds : bond 0.20753 ( 419) hydrogen bonds : angle 7.06356 ( 1260) link_BETA1-4 : bond 0.00331 ( 5) link_BETA1-4 : angle 1.86539 ( 15) link_NAG-ASN : bond 0.00685 ( 8) link_NAG-ASN : angle 3.48315 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.339 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.1025 time to fit residues: 11.6896 Evaluate side-chains 82 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 412 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.172321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130146 restraints weight = 10160.929| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.70 r_work: 0.3187 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9145 Z= 0.133 Angle : 0.605 13.648 12444 Z= 0.308 Chirality : 0.045 0.204 1453 Planarity : 0.004 0.066 1519 Dihedral : 10.391 74.683 1512 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.23 % Allowed : 22.40 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.14 (0.26), residues: 1065 helix: 2.43 (0.31), residues: 270 sheet: 1.08 (0.29), residues: 343 loop : -0.54 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 247 TYR 0.014 0.001 TYR A 172 PHE 0.011 0.001 PHE E 339 TRP 0.013 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9121) covalent geometry : angle 0.57568 (12383) SS BOND : bond 0.00505 ( 11) SS BOND : angle 1.05491 ( 22) hydrogen bonds : bond 0.04815 ( 419) hydrogen bonds : angle 4.91003 ( 1260) link_BETA1-4 : bond 0.00510 ( 5) link_BETA1-4 : angle 2.21906 ( 15) link_NAG-ASN : bond 0.00572 ( 8) link_NAG-ASN : angle 3.82613 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 68 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 182 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.6607 (tp30) REVERT: E 238 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: E 405 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: F 384 THR cc_start: 0.8091 (t) cc_final: 0.7858 (p) outliers start: 32 outliers final: 16 residues processed: 111 average time/residue: 0.0945 time to fit residues: 14.8573 Evaluate side-chains 104 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.173837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122179 restraints weight = 10223.609| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.74 r_work: 0.3130 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9145 Z= 0.212 Angle : 0.679 13.455 12444 Z= 0.339 Chirality : 0.048 0.164 1453 Planarity : 0.005 0.063 1519 Dihedral : 9.877 70.743 1506 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 4.24 % Allowed : 22.20 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.02 (0.26), residues: 1065 helix: 2.28 (0.30), residues: 271 sheet: 1.12 (0.28), residues: 351 loop : -0.73 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.015 0.002 TYR A 172 PHE 0.021 0.002 PHE E 339 TRP 0.016 0.002 TRP B 103 HIS 0.007 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 9121) covalent geometry : angle 0.64485 (12383) SS BOND : bond 0.00604 ( 11) SS BOND : angle 1.41888 ( 22) hydrogen bonds : bond 0.05020 ( 419) hydrogen bonds : angle 4.65278 ( 1260) link_BETA1-4 : bond 0.00498 ( 5) link_BETA1-4 : angle 2.87509 ( 15) link_NAG-ASN : bond 0.00662 ( 8) link_NAG-ASN : angle 4.17370 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 58 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.5095 (mp) REVERT: B 183 MET cc_start: 0.7836 (mtt) cc_final: 0.7633 (mtt) REVERT: E 238 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7806 (pt0) REVERT: E 405 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: F 121 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7659 (mt) REVERT: F 282 ILE cc_start: 0.7446 (mm) cc_final: 0.7236 (mt) REVERT: F 283 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: F 384 THR cc_start: 0.8194 (t) cc_final: 0.7943 (p) outliers start: 42 outliers final: 28 residues processed: 114 average time/residue: 0.1079 time to fit residues: 16.9184 Evaluate side-chains 115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.176268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124710 restraints weight = 10366.303| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.78 r_work: 0.3162 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9145 Z= 0.129 Angle : 0.592 13.098 12444 Z= 0.296 Chirality : 0.045 0.151 1453 Planarity : 0.004 0.058 1519 Dihedral : 8.713 64.487 1506 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.84 % Allowed : 21.59 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.21 (0.26), residues: 1065 helix: 2.47 (0.30), residues: 272 sheet: 1.21 (0.28), residues: 343 loop : -0.59 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 259 TYR 0.012 0.001 TYR A 144 PHE 0.011 0.001 PHE A 150 TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9121) covalent geometry : angle 0.56022 (12383) SS BOND : bond 0.00515 ( 11) SS BOND : angle 1.03366 ( 22) hydrogen bonds : bond 0.04231 ( 419) hydrogen bonds : angle 4.37344 ( 1260) link_BETA1-4 : bond 0.00462 ( 5) link_BETA1-4 : angle 2.48074 ( 15) link_NAG-ASN : bond 0.00694 ( 8) link_NAG-ASN : angle 3.88468 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6609 (tpp-160) REVERT: B 183 MET cc_start: 0.7786 (mtt) cc_final: 0.7584 (mtt) REVERT: E 238 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7797 (pt0) REVERT: E 398 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8169 (t) REVERT: E 405 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: F 121 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7655 (mt) REVERT: F 282 ILE cc_start: 0.7427 (mm) cc_final: 0.7221 (mt) REVERT: F 283 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: F 384 THR cc_start: 0.8223 (t) cc_final: 0.7991 (p) outliers start: 48 outliers final: 30 residues processed: 130 average time/residue: 0.1040 time to fit residues: 18.6593 Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 104 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN E 122 GLN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.174948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130147 restraints weight = 10325.129| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.94 r_work: 0.3160 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9145 Z= 0.164 Angle : 0.623 11.640 12444 Z= 0.312 Chirality : 0.046 0.158 1453 Planarity : 0.004 0.060 1519 Dihedral : 8.481 66.025 1506 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 4.64 % Allowed : 22.00 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.17 (0.26), residues: 1065 helix: 2.46 (0.30), residues: 272 sheet: 1.23 (0.28), residues: 351 loop : -0.70 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.023 0.002 TYR B 201 PHE 0.015 0.002 PHE E 339 TRP 0.016 0.001 TRP B 103 HIS 0.006 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9121) covalent geometry : angle 0.59408 (12383) SS BOND : bond 0.00545 ( 11) SS BOND : angle 1.19821 ( 22) hydrogen bonds : bond 0.04333 ( 419) hydrogen bonds : angle 4.27585 ( 1260) link_BETA1-4 : bond 0.00448 ( 5) link_BETA1-4 : angle 2.63667 ( 15) link_NAG-ASN : bond 0.00708 ( 8) link_NAG-ASN : angle 3.69136 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 90 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6856 (tpp-160) REVERT: E 238 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: E 398 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8256 (t) REVERT: E 405 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: F 121 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7771 (mt) REVERT: F 282 ILE cc_start: 0.7494 (mm) cc_final: 0.7287 (mt) REVERT: F 283 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: F 374 ARG cc_start: 0.8036 (mtt-85) cc_final: 0.6730 (mtm180) REVERT: F 384 THR cc_start: 0.8296 (t) cc_final: 0.8063 (p) outliers start: 46 outliers final: 33 residues processed: 121 average time/residue: 0.1093 time to fit residues: 18.2573 Evaluate side-chains 129 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 93 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125049 restraints weight = 10323.039| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.78 r_work: 0.3214 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9145 Z= 0.126 Angle : 0.569 9.216 12444 Z= 0.289 Chirality : 0.044 0.150 1453 Planarity : 0.004 0.058 1519 Dihedral : 7.771 64.979 1506 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.24 % Allowed : 22.40 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.27 (0.26), residues: 1065 helix: 2.57 (0.30), residues: 272 sheet: 1.26 (0.28), residues: 353 loop : -0.65 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.014 0.001 TYR B 201 PHE 0.011 0.001 PHE E 378 TRP 0.017 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9121) covalent geometry : angle 0.54619 (12383) SS BOND : bond 0.00482 ( 11) SS BOND : angle 0.99539 ( 22) hydrogen bonds : bond 0.03992 ( 419) hydrogen bonds : angle 4.12301 ( 1260) link_BETA1-4 : bond 0.00461 ( 5) link_BETA1-4 : angle 2.40246 ( 15) link_NAG-ASN : bond 0.00584 ( 8) link_NAG-ASN : angle 3.09082 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6654 (tpp-160) REVERT: E 238 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: E 398 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8231 (t) REVERT: E 405 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: F 121 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7668 (mt) REVERT: F 282 ILE cc_start: 0.7425 (mm) cc_final: 0.7208 (mt) REVERT: F 283 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: F 374 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.6572 (mtm180) REVERT: F 384 THR cc_start: 0.8263 (t) cc_final: 0.8051 (p) outliers start: 42 outliers final: 28 residues processed: 120 average time/residue: 0.1078 time to fit residues: 17.8599 Evaluate side-chains 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 HIS ** 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 = 0.3976 r_free = 0.3976 target = 0.175313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123894 restraints weight = 10294.306| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.77 r_work: 0.3226 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9145 Z= 0.149 Angle : 0.594 9.430 12444 Z= 0.301 Chirality : 0.045 0.148 1453 Planarity : 0.004 0.059 1519 Dihedral : 7.808 66.594 1504 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 4.64 % Allowed : 22.10 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.22 (0.26), residues: 1065 helix: 2.54 (0.30), residues: 272 sheet: 1.26 (0.28), residues: 353 loop : -0.72 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.014 0.001 TYR A 144 PHE 0.014 0.002 PHE E 339 TRP 0.017 0.001 TRP B 103 HIS 0.006 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9121) covalent geometry : angle 0.57123 (12383) SS BOND : bond 0.00537 ( 11) SS BOND : angle 1.09398 ( 22) hydrogen bonds : bond 0.04106 ( 419) hydrogen bonds : angle 4.12430 ( 1260) link_BETA1-4 : bond 0.00438 ( 5) link_BETA1-4 : angle 2.54312 ( 15) link_NAG-ASN : bond 0.00542 ( 8) link_NAG-ASN : angle 3.09242 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 93 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6743 (tpp-160) REVERT: E 238 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: E 398 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8245 (t) REVERT: E 405 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: F 121 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7668 (mt) REVERT: F 282 ILE cc_start: 0.7441 (mm) cc_final: 0.7219 (mt) REVERT: F 283 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: F 374 ARG cc_start: 0.7959 (mtt-85) cc_final: 0.6600 (mtm180) REVERT: F 384 THR cc_start: 0.8279 (t) cc_final: 0.8059 (p) outliers start: 46 outliers final: 32 residues processed: 124 average time/residue: 0.1090 time to fit residues: 18.6280 Evaluate side-chains 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 193 CYS Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain E residue 413 ILE Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 0.0000 chunk 11 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.178123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129552 restraints weight = 10300.847| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.02 r_work: 0.3212 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9145 Z= 0.105 Angle : 0.536 8.898 12444 Z= 0.275 Chirality : 0.043 0.146 1453 Planarity : 0.004 0.054 1519 Dihedral : 7.142 64.620 1504 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.33 % Allowed : 23.01 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.39 (0.26), residues: 1065 helix: 2.70 (0.30), residues: 272 sheet: 1.31 (0.28), residues: 353 loop : -0.59 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 374 TYR 0.013 0.001 TYR A 144 PHE 0.010 0.001 PHE A 150 TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9121) covalent geometry : angle 0.51670 (12383) SS BOND : bond 0.00460 ( 11) SS BOND : angle 0.89765 ( 22) hydrogen bonds : bond 0.03699 ( 419) hydrogen bonds : angle 3.98995 ( 1260) link_BETA1-4 : bond 0.00450 ( 5) link_BETA1-4 : angle 2.20091 ( 15) link_NAG-ASN : bond 0.00481 ( 8) link_NAG-ASN : angle 2.77517 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.369 Fit side-chains REVERT: A 182 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.6802 (tp30) REVERT: E 238 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: E 369 ASN cc_start: 0.7034 (OUTLIER) cc_final: 0.6534 (t0) REVERT: E 405 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: F 121 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7703 (mt) REVERT: F 282 ILE cc_start: 0.7415 (mm) cc_final: 0.7181 (mt) REVERT: F 283 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: F 374 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.6566 (mtm180) REVERT: F 384 THR cc_start: 0.8172 (t) cc_final: 0.7968 (p) outliers start: 33 outliers final: 21 residues processed: 118 average time/residue: 0.1050 time to fit residues: 17.0801 Evaluate side-chains 116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 57 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126352 restraints weight = 10293.011| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.75 r_work: 0.3205 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9145 Z= 0.114 Angle : 0.549 8.950 12444 Z= 0.279 Chirality : 0.044 0.146 1453 Planarity : 0.004 0.055 1519 Dihedral : 7.053 64.939 1504 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.93 % Allowed : 23.31 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.41 (0.26), residues: 1065 helix: 2.68 (0.30), residues: 272 sheet: 1.37 (0.28), residues: 353 loop : -0.59 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 374 TYR 0.013 0.001 TYR A 144 PHE 0.011 0.001 PHE A 207 TRP 0.016 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9121) covalent geometry : angle 0.52804 (12383) SS BOND : bond 0.00452 ( 11) SS BOND : angle 0.90267 ( 22) hydrogen bonds : bond 0.03718 ( 419) hydrogen bonds : angle 3.97483 ( 1260) link_BETA1-4 : bond 0.00430 ( 5) link_BETA1-4 : angle 2.25237 ( 15) link_NAG-ASN : bond 0.00503 ( 8) link_NAG-ASN : angle 2.91636 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6638 (tpp-160) REVERT: E 238 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: E 405 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: F 121 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7544 (mp) REVERT: F 282 ILE cc_start: 0.7415 (mm) cc_final: 0.7189 (mt) REVERT: F 283 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: F 374 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.6572 (mtm180) REVERT: F 384 THR cc_start: 0.8169 (t) cc_final: 0.7965 (p) outliers start: 29 outliers final: 22 residues processed: 112 average time/residue: 0.1096 time to fit residues: 16.8494 Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.178004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126674 restraints weight = 10303.698| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.78 r_work: 0.3256 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9145 Z= 0.109 Angle : 0.539 8.836 12444 Z= 0.276 Chirality : 0.043 0.144 1453 Planarity : 0.004 0.054 1519 Dihedral : 6.869 64.482 1504 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.23 % Allowed : 23.31 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.44 (0.26), residues: 1065 helix: 2.71 (0.30), residues: 272 sheet: 1.38 (0.28), residues: 353 loop : -0.57 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 374 TYR 0.013 0.001 TYR A 144 PHE 0.011 0.001 PHE A 207 TRP 0.017 0.001 TRP B 103 HIS 0.008 0.001 HIS F 400 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9121) covalent geometry : angle 0.51934 (12383) SS BOND : bond 0.00438 ( 11) SS BOND : angle 0.86652 ( 22) hydrogen bonds : bond 0.03641 ( 419) hydrogen bonds : angle 3.92640 ( 1260) link_BETA1-4 : bond 0.00447 ( 5) link_BETA1-4 : angle 2.16236 ( 15) link_NAG-ASN : bond 0.00525 ( 8) link_NAG-ASN : angle 2.80694 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.6764 (tp30) REVERT: B 97 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6614 (tpp-160) REVERT: E 165 THR cc_start: 0.8607 (p) cc_final: 0.8247 (t) REVERT: E 238 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: E 369 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6542 (t0) REVERT: E 405 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: F 121 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7540 (mp) REVERT: F 282 ILE cc_start: 0.7327 (mm) cc_final: 0.7123 (mt) REVERT: F 283 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: F 374 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.6566 (mtm180) outliers start: 32 outliers final: 23 residues processed: 113 average time/residue: 0.1089 time to fit residues: 16.7691 Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.177134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125833 restraints weight = 10229.056| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.76 r_work: 0.3198 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9145 Z= 0.129 Angle : 0.561 9.087 12444 Z= 0.286 Chirality : 0.044 0.148 1453 Planarity : 0.004 0.055 1519 Dihedral : 6.972 65.191 1504 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.53 % Allowed : 23.21 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 1.40 (0.26), residues: 1065 helix: 2.69 (0.30), residues: 272 sheet: 1.37 (0.28), residues: 353 loop : -0.62 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 311 TYR 0.014 0.001 TYR A 144 PHE 0.012 0.001 PHE E 378 TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS E 293 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9121) covalent geometry : angle 0.54122 (12383) SS BOND : bond 0.00478 ( 11) SS BOND : angle 0.98109 ( 22) hydrogen bonds : bond 0.03757 ( 419) hydrogen bonds : angle 3.94218 ( 1260) link_BETA1-4 : bond 0.00420 ( 5) link_BETA1-4 : angle 2.29441 ( 15) link_NAG-ASN : bond 0.00514 ( 8) link_NAG-ASN : angle 2.82444 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2564.57 seconds wall clock time: 44 minutes 45.05 seconds (2685.05 seconds total)