Starting phenix.real_space_refine on Mon May 12 11:05:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgs_60089/05_2025/8zgs_60089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgs_60089/05_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_60089/05_2025/8zgs_60089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgs_60089/05_2025/8zgs_60089.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgs_60089/05_2025/8zgs_60089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgs_60089/05_2025/8zgs_60089.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.79, per 1000 atoms: 0.65 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: 2.21 Conformation dependent library (CDL) restraints added in 974.3 milliseconds 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: 1.16 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: 2.66 Time building geometry restraints manager: 2.57 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.830 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (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 TRP 0.019 0.001 TRP A 110 HIS 0.002 0.000 HIS A 173 PHE 0.010 0.001 PHE A 150 TYR 0.008 0.001 TYR F 166 ARG 0.004 0.000 ARG E 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 8) link_NAG-ASN : angle 3.48315 ( 24) link_BETA1-4 : bond 0.00331 ( 5) link_BETA1-4 : angle 1.86539 ( 15) hydrogen bonds : bond 0.20753 ( 419) hydrogen bonds : angle 7.06356 ( 1260) SS BOND : bond 0.00340 ( 11) SS BOND : angle 0.74892 ( 22) covalent geometry : bond 0.00714 ( 9121) covalent geometry : angle 0.74574 (12383) *********************** 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 : 1.052 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.2189 time to fit residues: 25.3800 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 : 0.945 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.170545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128224 restraints weight = 10133.350| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.69 r_work: 0.3163 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9145 Z= 0.167 Angle : 0.641 13.595 12444 Z= 0.324 Chirality : 0.046 0.191 1453 Planarity : 0.005 0.065 1519 Dihedral : 10.599 76.981 1512 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 3.63 % Allowed : 22.40 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1065 helix: 2.36 (0.31), residues: 270 sheet: 1.03 (0.29), residues: 343 loop : -0.61 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.006 0.001 HIS A 173 PHE 0.016 0.002 PHE E 339 TYR 0.016 0.002 TYR A 172 ARG 0.002 0.000 ARG E 247 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 8) link_NAG-ASN : angle 3.94798 ( 24) link_BETA1-4 : bond 0.00464 ( 5) link_BETA1-4 : angle 2.48470 ( 15) hydrogen bonds : bond 0.04969 ( 419) hydrogen bonds : angle 4.92039 ( 1260) SS BOND : bond 0.00564 ( 11) SS BOND : angle 1.24747 ( 22) covalent geometry : bond 0.00407 ( 9121) covalent geometry : angle 0.61054 (12383) *********************** 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 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.6590 (tp30) REVERT: E 238 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7889 (pt0) REVERT: E 405 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: F 384 THR cc_start: 0.8125 (t) cc_final: 0.7879 (p) outliers start: 36 outliers final: 20 residues processed: 111 average time/residue: 0.2017 time to fit residues: 31.7424 Evaluate side-chains 106 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 120 VAL 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 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 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 246 VAL 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 17 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 0.0000 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.177543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133851 restraints weight = 10271.714| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.77 r_work: 0.3206 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9145 Z= 0.127 Angle : 0.573 13.473 12444 Z= 0.289 Chirality : 0.045 0.186 1453 Planarity : 0.004 0.057 1519 Dihedral : 8.659 65.232 1506 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.83 % Allowed : 22.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1065 helix: 2.51 (0.30), residues: 271 sheet: 1.17 (0.28), residues: 343 loop : -0.57 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 PHE 0.011 0.001 PHE A 150 TYR 0.010 0.001 TYR A 172 ARG 0.002 0.000 ARG E 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 8) link_NAG-ASN : angle 3.82389 ( 24) link_BETA1-4 : bond 0.00446 ( 5) link_BETA1-4 : angle 2.44004 ( 15) hydrogen bonds : bond 0.04314 ( 419) hydrogen bonds : angle 4.41441 ( 1260) SS BOND : bond 0.00483 ( 11) SS BOND : angle 0.99728 ( 22) covalent geometry : bond 0.00298 ( 9121) covalent geometry : angle 0.54095 (12383) *********************** 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 133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.6827 (tp30) REVERT: E 165 THR cc_start: 0.8689 (p) cc_final: 0.8236 (t) REVERT: E 238 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: E 405 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: F 121 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7748 (mt) REVERT: F 282 ILE cc_start: 0.7483 (mm) cc_final: 0.7278 (mt) REVERT: F 283 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: F 384 THR cc_start: 0.8285 (t) cc_final: 0.8075 (p) outliers start: 38 outliers final: 22 residues processed: 120 average time/residue: 0.2122 time to fit residues: 35.5692 Evaluate side-chains 110 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 182 GLU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 58 LEU 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 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 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 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 13 optimal weight: 0.0030 chunk 75 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.176546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124997 restraints weight = 10221.643| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.76 r_work: 0.3161 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9145 Z= 0.140 Angle : 0.599 12.921 12444 Z= 0.298 Chirality : 0.045 0.154 1453 Planarity : 0.004 0.056 1519 Dihedral : 8.158 66.080 1506 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.44 % Allowed : 22.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1065 helix: 2.49 (0.30), residues: 272 sheet: 1.24 (0.28), residues: 351 loop : -0.62 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 PHE 0.013 0.002 PHE E 339 TYR 0.013 0.001 TYR A 144 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00714 ( 8) link_NAG-ASN : angle 3.76880 ( 24) link_BETA1-4 : bond 0.00385 ( 5) link_BETA1-4 : angle 2.51051 ( 15) hydrogen bonds : bond 0.04164 ( 419) hydrogen bonds : angle 4.28190 ( 1260) SS BOND : bond 0.00517 ( 11) SS BOND : angle 1.09346 ( 22) covalent geometry : bond 0.00337 ( 9121) covalent geometry : angle 0.56817 (12383) *********************** 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 136 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: E 238 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: E 398 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8195 (t) REVERT: E 405 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: F 121 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7636 (mt) REVERT: F 282 ILE cc_start: 0.7408 (mm) cc_final: 0.7190 (mt) REVERT: F 283 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: F 384 THR cc_start: 0.8274 (t) cc_final: 0.8065 (p) outliers start: 44 outliers final: 31 residues processed: 123 average time/residue: 0.2113 time to fit residues: 36.0151 Evaluate side-chains 125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 58 LEU 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 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 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 123 LEU 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 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 89 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.175142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123506 restraints weight = 10269.559| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.78 r_work: 0.3140 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9145 Z= 0.166 Angle : 0.621 10.985 12444 Z= 0.312 Chirality : 0.046 0.158 1453 Planarity : 0.004 0.056 1519 Dihedral : 8.183 64.422 1506 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 4.64 % Allowed : 21.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1065 helix: 2.47 (0.30), residues: 272 sheet: 1.22 (0.28), residues: 353 loop : -0.68 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.007 0.001 HIS A 173 PHE 0.016 0.002 PHE E 339 TYR 0.014 0.002 TYR A 144 ARG 0.002 0.000 ARG A 129 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 8) link_NAG-ASN : angle 3.50310 ( 24) link_BETA1-4 : bond 0.00432 ( 5) link_BETA1-4 : angle 2.60128 ( 15) hydrogen bonds : bond 0.04310 ( 419) hydrogen bonds : angle 4.27131 ( 1260) SS BOND : bond 0.00558 ( 11) SS BOND : angle 1.19853 ( 22) covalent geometry : bond 0.00409 ( 9121) covalent geometry : angle 0.59440 (12383) *********************** 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 : 0.921 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6801 (tpp-160) REVERT: E 238 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: E 398 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8251 (t) REVERT: E 405 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: F 121 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7652 (mt) REVERT: F 282 ILE cc_start: 0.7449 (mm) cc_final: 0.7240 (mt) REVERT: F 283 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: F 384 THR cc_start: 0.8232 (t) cc_final: 0.8002 (p) outliers start: 46 outliers final: 33 residues processed: 122 average time/residue: 0.2118 time to fit residues: 35.9044 Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 61 LEU 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 F residue 120 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 123 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 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 ** 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 = 0.3986 r_free = 0.3986 target = 0.176443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124962 restraints weight = 10218.156| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.76 r_work: 0.3239 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9145 Z= 0.133 Angle : 0.584 8.972 12444 Z= 0.295 Chirality : 0.045 0.167 1453 Planarity : 0.004 0.056 1519 Dihedral : 7.755 64.532 1506 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.43 % Allowed : 23.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1065 helix: 2.53 (0.30), residues: 272 sheet: 1.26 (0.28), residues: 353 loop : -0.66 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 PHE 0.011 0.001 PHE E 378 TYR 0.022 0.001 TYR B 201 ARG 0.002 0.000 ARG F 374 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 8) link_NAG-ASN : angle 3.07545 ( 24) link_BETA1-4 : bond 0.00401 ( 5) link_BETA1-4 : angle 2.43865 ( 15) hydrogen bonds : bond 0.04035 ( 419) hydrogen bonds : angle 4.14011 ( 1260) SS BOND : bond 0.00542 ( 11) SS BOND : angle 1.05888 ( 22) covalent geometry : bond 0.00317 ( 9121) covalent geometry : angle 0.56164 (12383) *********************** 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 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6678 (tpp-160) REVERT: E 238 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: E 405 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: F 121 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7651 (mt) REVERT: F 282 ILE cc_start: 0.7428 (mm) cc_final: 0.7212 (mt) REVERT: F 283 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: F 384 THR cc_start: 0.8270 (t) cc_final: 0.8056 (p) outliers start: 34 outliers final: 22 residues processed: 114 average time/residue: 0.2231 time to fit residues: 34.8104 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 : 1.062 ------------------------------------------------------------------------------- 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 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 61 LEU 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 238 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL 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 F residue 120 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 246 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.173580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.128704 restraints weight = 10357.411| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.98 r_work: 0.3179 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9145 Z= 0.208 Angle : 0.669 9.728 12444 Z= 0.336 Chirality : 0.048 0.164 1453 Planarity : 0.005 0.061 1519 Dihedral : 8.639 67.807 1504 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 4.74 % Allowed : 21.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1065 helix: 2.34 (0.30), residues: 269 sheet: 1.16 (0.28), residues: 353 loop : -0.85 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 103 HIS 0.008 0.001 HIS A 173 PHE 0.020 0.002 PHE E 339 TYR 0.016 0.002 TYR A 144 ARG 0.003 0.000 ARG F 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 8) link_NAG-ASN : angle 3.36687 ( 24) link_BETA1-4 : bond 0.00465 ( 5) link_BETA1-4 : angle 2.80250 ( 15) hydrogen bonds : bond 0.04553 ( 419) hydrogen bonds : angle 4.31982 ( 1260) SS BOND : bond 0.00637 ( 11) SS BOND : angle 1.40251 ( 22) covalent geometry : bond 0.00523 ( 9121) covalent geometry : angle 0.64359 (12383) *********************** 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 138 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 91 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6996 (tpp-160) REVERT: E 238 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: E 398 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8303 (t) REVERT: E 405 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: F 121 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7796 (mt) REVERT: F 282 ILE cc_start: 0.7571 (mm) cc_final: 0.7348 (mt) REVERT: F 283 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: F 384 THR cc_start: 0.8295 (t) cc_final: 0.8039 (p) outliers start: 47 outliers final: 32 residues processed: 125 average time/residue: 0.2229 time to fit residues: 38.7440 Evaluate side-chains 125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 87 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 77 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 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 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 123 LEU 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 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.174471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125056 restraints weight = 10450.074| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.97 r_work: 0.3158 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9145 Z= 0.171 Angle : 0.621 9.736 12444 Z= 0.314 Chirality : 0.046 0.154 1453 Planarity : 0.004 0.059 1519 Dihedral : 8.457 66.739 1504 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 4.54 % Allowed : 22.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1065 helix: 2.45 (0.30), residues: 272 sheet: 1.14 (0.28), residues: 353 loop : -0.80 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.007 0.001 HIS A 173 PHE 0.015 0.002 PHE E 339 TYR 0.015 0.002 TYR A 144 ARG 0.003 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 8) link_NAG-ASN : angle 3.20572 ( 24) link_BETA1-4 : bond 0.00446 ( 5) link_BETA1-4 : angle 2.58605 ( 15) hydrogen bonds : bond 0.04270 ( 419) hydrogen bonds : angle 4.22828 ( 1260) SS BOND : bond 0.00553 ( 11) SS BOND : angle 1.23652 ( 22) covalent geometry : bond 0.00425 ( 9121) covalent geometry : angle 0.59769 (12383) *********************** 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 137 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: B 97 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6765 (tpp-160) REVERT: E 238 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: E 398 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8243 (t) REVERT: E 405 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: F 121 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7622 (mp) REVERT: F 282 ILE cc_start: 0.7500 (mm) cc_final: 0.7284 (mt) REVERT: F 283 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: F 384 THR cc_start: 0.8258 (t) cc_final: 0.8002 (p) outliers start: 45 outliers final: 33 residues processed: 124 average time/residue: 0.2126 time to fit residues: 36.6133 Evaluate side-chains 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 104 THR Chi-restraints excluded: chain E residue 197 THR 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 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 123 LEU 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 413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.0470 chunk 31 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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** E 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.177047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132784 restraints weight = 10326.444| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.92 r_work: 0.3180 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1791 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= 0.115 Angle : 0.552 9.114 12444 Z= 0.283 Chirality : 0.044 0.146 1453 Planarity : 0.004 0.055 1519 Dihedral : 7.497 65.050 1504 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.53 % Allowed : 23.31 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1065 helix: 2.60 (0.30), residues: 272 sheet: 1.18 (0.28), residues: 353 loop : -0.67 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 PHE 0.013 0.001 PHE B 53 TYR 0.014 0.001 TYR A 144 ARG 0.002 0.000 ARG F 374 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 8) link_NAG-ASN : angle 2.84210 ( 24) link_BETA1-4 : bond 0.00425 ( 5) link_BETA1-4 : angle 2.30164 ( 15) hydrogen bonds : bond 0.03818 ( 419) hydrogen bonds : angle 4.02794 ( 1260) SS BOND : bond 0.00444 ( 11) SS BOND : angle 0.92972 ( 22) covalent geometry : bond 0.00264 ( 9121) covalent geometry : angle 0.53163 (12383) *********************** 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 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: E 238 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: E 369 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.6528 (t0) REVERT: E 398 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8263 (t) REVERT: E 405 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: F 121 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7670 (mp) REVERT: F 282 ILE cc_start: 0.7513 (mm) cc_final: 0.7304 (mt) REVERT: F 283 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: F 384 THR cc_start: 0.8321 (t) cc_final: 0.8110 (p) outliers start: 35 outliers final: 25 residues processed: 120 average time/residue: 0.2272 time to fit residues: 37.5630 Evaluate side-chains 120 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 107 MET Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 238 GLU 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 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 121 ILE Chi-restraints excluded: chain F residue 123 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.172777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127851 restraints weight = 10328.172| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.94 r_work: 0.3136 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9145 Z= 0.243 Angle : 0.690 9.984 12444 Z= 0.347 Chirality : 0.049 0.164 1453 Planarity : 0.005 0.063 1519 Dihedral : 8.515 68.470 1504 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 3.33 % Allowed : 23.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1065 helix: 2.34 (0.30), residues: 272 sheet: 1.10 (0.28), residues: 353 loop : -0.90 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 103 HIS 0.009 0.001 HIS A 173 PHE 0.023 0.002 PHE E 339 TYR 0.025 0.002 TYR E 368 ARG 0.007 0.001 ARG F 374 Details of bonding type rmsd link_NAG-ASN : bond 0.00599 ( 8) link_NAG-ASN : angle 3.24677 ( 24) link_BETA1-4 : bond 0.00432 ( 5) link_BETA1-4 : angle 2.89596 ( 15) hydrogen bonds : bond 0.04576 ( 419) hydrogen bonds : angle 4.24716 ( 1260) SS BOND : bond 0.00669 ( 11) SS BOND : angle 1.50398 ( 22) covalent geometry : bond 0.00620 ( 9121) covalent geometry : angle 0.66622 (12383) ********************** 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 122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 166 PHE cc_start: 0.8414 (t80) cc_final: 0.8209 (t80) REVERT: B 97 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6816 (tpp-160) REVERT: E 238 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: E 398 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8259 (t) REVERT: E 405 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: F 121 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7744 (mp) REVERT: F 282 ILE cc_start: 0.7555 (mm) cc_final: 0.7337 (mt) REVERT: F 283 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: F 338 ASN cc_start: 0.8603 (t0) cc_final: 0.8375 (t0) REVERT: F 384 THR cc_start: 0.8309 (t) cc_final: 0.8061 (p) outliers start: 33 outliers final: 26 residues processed: 114 average time/residue: 0.2139 time to fit residues: 33.6174 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 : 0.912 ------------------------------------------------------------------------------- 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 238 GLU 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 121 ILE Chi-restraints excluded: chain F residue 123 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 0.5980 chunk 81 optimal weight: 0.0010 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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** E 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.176801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133568 restraints weight = 10319.491| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.80 r_work: 0.3192 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9145 Z= 0.113 Angle : 0.554 9.336 12444 Z= 0.285 Chirality : 0.043 0.149 1453 Planarity : 0.004 0.056 1519 Dihedral : 7.446 65.286 1504 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1065 helix: 2.66 (0.30), residues: 272 sheet: 1.18 (0.28), residues: 353 loop : -0.72 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 PHE 0.012 0.001 PHE A 207 TYR 0.014 0.001 TYR A 144 ARG 0.006 0.000 ARG F 374 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 8) link_NAG-ASN : angle 2.82199 ( 24) link_BETA1-4 : bond 0.00401 ( 5) link_BETA1-4 : angle 2.31414 ( 15) hydrogen bonds : bond 0.03834 ( 419) hydrogen bonds : angle 4.02404 ( 1260) SS BOND : bond 0.00454 ( 11) SS BOND : angle 0.92993 ( 22) covalent geometry : bond 0.00255 ( 9121) covalent geometry : angle 0.53409 (12383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4661.96 seconds wall clock time: 81 minutes 29.95 seconds (4889.95 seconds total)