Starting phenix.real_space_refine on Fri Nov 15 13:05:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgs_60089/11_2024/8zgs_60089.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgs_60089/11_2024/8zgs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgs_60089/11_2024/8zgs_60089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgs_60089/11_2024/8zgs_60089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgs_60089/11_2024/8zgs_60089.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zgs_60089/11_2024/8zgs_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-5513/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: 7.66, per 1000 atoms: 0.86 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: 2.46 Conformation dependent library (CDL) restraints added in 955.2 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: 1.33 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: 3.09 Time building geometry restraints manager: 2.79 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: 4.210 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.420 Find NCS groups from input model: 0.250 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.530 ------------------------------------------------------------------------------- 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 9121 Z= 0.342 Angle : 0.746 21.393 12383 Z= 0.380 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 *********************** 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 : 1.008 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.2479 time to fit residues: 28.6193 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 : 1.116 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 9121 Z= 0.267 Angle : 0.611 8.949 12383 Z= 0.318 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 *********************** 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 : 1.028 Fit side-chains revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.6747 (tp30) REVERT: E 238 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7754 (pt0) REVERT: E 405 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: F 384 THR cc_start: 0.8201 (t) cc_final: 0.7937 (p) outliers start: 36 outliers final: 20 residues processed: 111 average time/residue: 0.2113 time to fit residues: 33.1245 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 : 1.089 ------------------------------------------------------------------------------- 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 52 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9121 Z= 0.341 Angle : 0.635 8.657 12383 Z= 0.328 Chirality : 0.048 0.161 1453 Planarity : 0.005 0.062 1519 Dihedral : 9.789 69.766 1506 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % 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: 0.98 (0.26), residues: 1065 helix: 2.29 (0.30), residues: 271 sheet: 1.08 (0.29), residues: 343 loop : -0.73 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 103 HIS 0.007 0.001 HIS A 173 PHE 0.019 0.002 PHE E 339 TYR 0.014 0.002 TYR A 172 ARG 0.003 0.000 ARG B 97 *********************** 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 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 84 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: B 58 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.5247 (mp) REVERT: B 97 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6531 (tpp-160) REVERT: E 238 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: E 398 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8175 (t) REVERT: E 405 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: F 121 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7644 (mt) REVERT: F 282 ILE cc_start: 0.7398 (mm) cc_final: 0.7195 (mt) REVERT: F 283 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: F 384 THR cc_start: 0.8217 (t) cc_final: 0.7959 (p) outliers start: 44 outliers final: 28 residues processed: 115 average time/residue: 0.2287 time to fit residues: 36.4278 Evaluate side-chains 116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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 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 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 271 THR 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 170 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.0010 chunk 95 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 90 optimal weight: 0.0010 chunk 27 optimal weight: 3.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9121 Z= 0.144 Angle : 0.526 9.753 12383 Z= 0.272 Chirality : 0.043 0.145 1453 Planarity : 0.004 0.055 1519 Dihedral : 7.964 65.196 1506 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.63 % Allowed : 22.30 % Favored : 74.07 % 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: 1.27 (0.26), residues: 1065 helix: 2.52 (0.30), residues: 272 sheet: 1.23 (0.28), residues: 343 loop : -0.54 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.003 0.001 HIS E 130 PHE 0.010 0.001 PHE A 207 TYR 0.011 0.001 TYR A 144 ARG 0.002 0.000 ARG F 259 *********************** 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 129 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.6783 (tp30) REVERT: E 238 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: E 405 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: F 121 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7479 (mp) REVERT: F 282 ILE cc_start: 0.7360 (mm) cc_final: 0.7159 (mt) REVERT: F 283 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: F 384 THR cc_start: 0.8218 (t) cc_final: 0.8009 (p) outliers start: 36 outliers final: 17 residues processed: 120 average time/residue: 0.2276 time to fit residues: 37.8055 Evaluate side-chains 109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 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 82 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 290 ARG 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 121 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 170 ASN Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 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 84 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9121 Z= 0.237 Angle : 0.568 9.016 12383 Z= 0.291 Chirality : 0.045 0.152 1453 Planarity : 0.004 0.057 1519 Dihedral : 7.848 66.822 1506 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.53 % Allowed : 23.21 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.26), residues: 1065 helix: 2.57 (0.30), residues: 272 sheet: 1.25 (0.28), residues: 353 loop : -0.63 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS E 293 PHE 0.015 0.002 PHE E 339 TYR 0.013 0.001 TYR A 144 ARG 0.002 0.000 ARG A 201 *********************** 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 125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: E 238 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: E 405 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: F 121 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7602 (mt) REVERT: F 282 ILE cc_start: 0.7409 (mm) cc_final: 0.7208 (mt) REVERT: F 283 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: F 384 THR cc_start: 0.8314 (t) cc_final: 0.8105 (p) outliers start: 35 outliers final: 25 residues processed: 114 average time/residue: 0.2317 time to fit residues: 36.4662 Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 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 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 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 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 34 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9121 Z= 0.241 Angle : 0.566 8.496 12383 Z= 0.293 Chirality : 0.045 0.152 1453 Planarity : 0.004 0.055 1519 Dihedral : 7.806 63.858 1506 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 3.53 % Allowed : 23.21 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.26), residues: 1065 helix: 2.61 (0.30), residues: 272 sheet: 1.26 (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 0.004 0.001 HIS E 293 PHE 0.014 0.002 PHE E 339 TYR 0.013 0.001 TYR A 144 ARG 0.002 0.000 ARG A 201 *********************** 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 129 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: E 238 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: E 405 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: F 121 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7619 (mt) REVERT: F 282 ILE cc_start: 0.7418 (mm) cc_final: 0.7209 (mt) REVERT: F 283 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: F 384 THR cc_start: 0.8294 (t) cc_final: 0.8073 (p) outliers start: 35 outliers final: 26 residues processed: 116 average time/residue: 0.2268 time to fit residues: 36.4746 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 290 ARG Chi-restraints excluded: chain E residue 315 GLU Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain 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 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9121 Z= 0.166 Angle : 0.519 8.231 12383 Z= 0.271 Chirality : 0.043 0.143 1453 Planarity : 0.004 0.055 1519 Dihedral : 7.177 63.772 1504 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.43 % Allowed : 23.61 % Favored : 72.96 % 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: 1.37 (0.26), residues: 1065 helix: 2.68 (0.30), residues: 272 sheet: 1.33 (0.28), residues: 353 loop : -0.61 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 PHE 0.010 0.001 PHE A 150 TYR 0.012 0.001 TYR A 144 ARG 0.002 0.000 ARG A 201 *********************** 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 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 109 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8428 (mm-30) REVERT: E 238 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7731 (pt0) REVERT: E 369 ASN cc_start: 0.7069 (OUTLIER) cc_final: 0.6590 (t0) REVERT: E 405 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: F 121 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7595 (mt) REVERT: F 282 ILE cc_start: 0.7378 (mm) cc_final: 0.7159 (mt) REVERT: F 283 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: F 384 THR cc_start: 0.8198 (t) cc_final: 0.7987 (p) outliers start: 34 outliers final: 22 residues processed: 117 average time/residue: 0.2280 time to fit residues: 36.9196 Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 B residue 95 LEU Chi-restraints excluded: chain B residue 193 CYS 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 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 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 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9121 Z= 0.204 Angle : 0.539 8.495 12383 Z= 0.280 Chirality : 0.044 0.149 1453 Planarity : 0.004 0.056 1519 Dihedral : 7.225 64.139 1504 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: 1.39 (0.26), residues: 1065 helix: 2.72 (0.30), residues: 272 sheet: 1.35 (0.28), residues: 353 loop : -0.63 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS E 293 PHE 0.012 0.001 PHE E 339 TYR 0.013 0.001 TYR A 144 ARG 0.004 0.000 ARG F 374 *********************** 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 125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 109 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8402 (mm-30) REVERT: E 238 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: E 398 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8231 (t) REVERT: E 405 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: F 121 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7602 (mt) REVERT: F 282 ILE cc_start: 0.7391 (mm) cc_final: 0.7180 (mt) REVERT: F 283 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6928 (mp0) outliers start: 35 outliers final: 27 residues processed: 114 average time/residue: 0.2238 time to fit residues: 35.4464 Evaluate side-chains 120 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 LEU 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 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 197 THR Chi-restraints excluded: chain E residue 209 ILE 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 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 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9121 Z= 0.221 Angle : 0.553 8.771 12383 Z= 0.287 Chirality : 0.044 0.148 1453 Planarity : 0.004 0.057 1519 Dihedral : 7.343 64.639 1504 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.53 % Allowed : 23.51 % Favored : 72.96 % 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: 1.37 (0.26), residues: 1065 helix: 2.69 (0.30), residues: 272 sheet: 1.35 (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 F 400 PHE 0.013 0.001 PHE E 339 TYR 0.014 0.001 TYR A 144 ARG 0.005 0.000 ARG F 374 *********************** 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 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 109 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8384 (mm-30) REVERT: E 238 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7766 (pt0) REVERT: E 398 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8221 (t) REVERT: E 405 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: F 121 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7582 (mt) REVERT: F 282 ILE cc_start: 0.7391 (mm) cc_final: 0.7175 (mt) REVERT: F 283 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: F 374 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7437 (mmt90) outliers start: 35 outliers final: 26 residues processed: 114 average time/residue: 0.2214 time to fit residues: 34.8782 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 : 1.040 ------------------------------------------------------------------------------- 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 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 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 197 THR Chi-restraints excluded: chain E residue 209 ILE 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 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 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 96 optimal weight: 0.0030 chunk 83 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9121 Z= 0.159 Angle : 0.526 10.683 12383 Z= 0.273 Chirality : 0.043 0.173 1453 Planarity : 0.004 0.054 1519 Dihedral : 6.942 63.450 1504 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.13 % Allowed : 24.52 % Favored : 72.35 % 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: 1.43 (0.26), residues: 1065 helix: 2.70 (0.30), residues: 272 sheet: 1.36 (0.28), residues: 354 loop : -0.56 (0.28), residues: 439 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 0.010 0.001 PHE A 207 TYR 0.023 0.001 TYR B 201 ARG 0.003 0.000 ARG F 374 ********************** 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 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 1.015 Fit side-chains REVERT: A 109 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8349 (mm-30) REVERT: E 165 THR cc_start: 0.8723 (p) cc_final: 0.8372 (t) REVERT: E 238 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: E 369 ASN cc_start: 0.7000 (OUTLIER) cc_final: 0.6520 (t0) REVERT: E 398 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8201 (t) REVERT: E 405 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: F 121 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7511 (mp) REVERT: F 282 ILE cc_start: 0.7380 (mm) cc_final: 0.7152 (mt) REVERT: F 283 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: F 374 ARG cc_start: 0.7534 (mtt-85) cc_final: 0.7247 (mmt90) outliers start: 31 outliers final: 22 residues processed: 108 average time/residue: 0.2319 time to fit residues: 34.7487 Evaluate side-chains 115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 193 CYS 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 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 283 GLU Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 358 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 155 ASN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131905 restraints weight = 10224.267| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.90 r_work: 0.3215 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9121 Z= 0.228 Angle : 0.551 8.738 12383 Z= 0.285 Chirality : 0.045 0.216 1453 Planarity : 0.004 0.056 1519 Dihedral : 7.114 64.502 1504 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.94 % Allowed : 23.71 % Favored : 72.35 % 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: 1.36 (0.26), residues: 1065 helix: 2.63 (0.30), residues: 272 sheet: 1.37 (0.28), residues: 353 loop : -0.64 (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 E 293 PHE 0.014 0.001 PHE E 339 TYR 0.020 0.001 TYR B 201 ARG 0.003 0.000 ARG F 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2152.83 seconds wall clock time: 40 minutes 15.32 seconds (2415.32 seconds total)