Starting phenix.real_space_refine on Sat Jun 14 20:07:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmd_41385/06_2025/8tmd_41385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmd_41385/06_2025/8tmd_41385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmd_41385/06_2025/8tmd_41385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmd_41385/06_2025/8tmd_41385.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmd_41385/06_2025/8tmd_41385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmd_41385/06_2025/8tmd_41385.cif" } resolution = 3.0 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 793 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Mg 3 5.21 5 S 57 5.16 5 C 10406 2.51 5 N 2605 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16011 Number of models: 1 Model: "" Number of chains: 10 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 983 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "A" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2797 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2900 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "C" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2797 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2838 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain: "E" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2890 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 15, 'TRANS': 331} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.75, per 1000 atoms: 0.67 Number of scatterers: 16011 At special positions: 0 Unit cell: (120.684, 144.18, 138.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 Mg 3 11.99 O 2940 8.00 N 2605 7.00 C 10406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 2.1 seconds 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3716 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 53.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.528A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.528A pdb=" N SER A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.535A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.768A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 165 through 201 removed outlier: 3.513A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 Proline residue: A 227 - end of helix removed outlier: 3.975A pdb=" N ASP A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 281 Processing helix chain 'A' and resid 282 through 300 removed outlier: 3.765A pdb=" N LYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 326 through 347 removed outlier: 3.649A pdb=" N VAL A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.531A pdb=" N PHE B 53 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 117 through 120 removed outlier: 3.552A pdb=" N HIS B 120 " --> pdb=" O LYS B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.611A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 238 Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 247 through 312 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 326 through 348 Processing helix chain 'C' and resid 69 through 80 removed outlier: 4.434A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 removed outlier: 3.605A pdb=" N LEU C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 166 through 202 removed outlier: 3.627A pdb=" N LEU C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 236 removed outlier: 4.112A pdb=" N VAL C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 312 removed outlier: 3.651A pdb=" N LEU C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.823A pdb=" N VAL D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 removed outlier: 4.186A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.615A pdb=" N LYS D 163 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.714A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 238 removed outlier: 4.211A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 247 through 311 removed outlier: 3.672A pdb=" N PHE D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 326 through 348 removed outlier: 4.253A pdb=" N VAL D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 331 " --> pdb=" O TYR D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.512A pdb=" N SER E 49 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 51 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Proline residue: E 52 - end of helix removed outlier: 3.576A pdb=" N ASP E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.792A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.545A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 238 Proline residue: E 227 - end of helix removed outlier: 3.785A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 311 removed outlier: 4.197A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 303 - end of helix removed outlier: 3.572A pdb=" N TYR E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 348 Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'L' and resid 13 through 14 Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.522A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 90 through 91 removed outlier: 3.523A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.865A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.560A pdb=" N CYS H 99 " --> pdb=" O TRP H 119 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP H 119 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG H 101 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 39 through 44 removed outlier: 6.390A pdb=" N THR A 60 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N MET A 138 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE A 62 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 44 Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 41 removed outlier: 3.544A pdb=" N GLU C 28 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR C 60 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET C 138 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE C 62 " --> pdb=" O MET C 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 44 removed outlier: 6.652A pdb=" N THR D 60 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N MET D 138 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D 62 " --> pdb=" O MET D 138 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLN D 140 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE D 64 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 39 through 44 removed outlier: 3.520A pdb=" N ASN E 33 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP E 61 " --> pdb=" O MET E 32 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU E 121 " --> pdb=" O ASP E 116 " (cutoff:3.500A) 1003 hydrogen bonds defined for protein. 2892 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: 4.81 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5040 1.34 - 1.46: 3539 1.46 - 1.58: 7691 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 16375 Sorted by residual: bond pdb=" CG1 ILE A 90 " pdb=" CD1 ILE A 90 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.92e+00 bond pdb=" SD MET E 291 " pdb=" CE MET E 291 " ideal model delta sigma weight residual 1.791 1.763 0.028 2.50e-02 1.60e+03 1.24e+00 bond pdb=" CB VAL E 254 " pdb=" CG2 VAL E 254 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CG1 ILE D 67 " pdb=" CD1 ILE D 67 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.21e+00 bond pdb=" CD1 TYR E 171 " pdb=" CE1 TYR E 171 " ideal model delta sigma weight residual 1.382 1.349 0.033 3.00e-02 1.11e+03 1.21e+00 ... (remaining 16370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 21650 1.62 - 3.24: 453 3.24 - 4.85: 84 4.85 - 6.47: 17 6.47 - 8.09: 6 Bond angle restraints: 22210 Sorted by residual: angle pdb=" C LEU E 235 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta sigma weight residual 122.09 114.28 7.81 1.79e+00 3.12e-01 1.90e+01 angle pdb=" C LEU A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta sigma weight residual 121.52 114.59 6.93 1.84e+00 2.95e-01 1.42e+01 angle pdb=" C LEU B 235 " pdb=" N TYR B 236 " pdb=" CA TYR B 236 " ideal model delta sigma weight residual 121.66 115.76 5.90 1.76e+00 3.23e-01 1.12e+01 angle pdb=" C GLU C 48 " pdb=" CA GLU C 48 " pdb=" CB GLU C 48 " ideal model delta sigma weight residual 110.42 116.84 -6.42 1.99e+00 2.53e-01 1.04e+01 angle pdb=" CA ARG B 237 " pdb=" CB ARG B 237 " pdb=" CG ARG B 237 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.30e+00 ... (remaining 22205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 8864 17.70 - 35.40: 809 35.40 - 53.09: 118 53.09 - 70.79: 25 70.79 - 88.49: 19 Dihedral angle restraints: 9835 sinusoidal: 4086 harmonic: 5749 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 149.30 -56.30 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA ARG B 237 " pdb=" C ARG B 237 " pdb=" N ASP B 238 " pdb=" CA ASP B 238 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ILE E 300 " pdb=" C ILE E 300 " pdb=" N PHE E 301 " pdb=" CA PHE E 301 " ideal model delta harmonic sigma weight residual -180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 9832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1952 0.049 - 0.097: 457 0.097 - 0.146: 114 0.146 - 0.194: 1 0.194 - 0.243: 2 Chirality restraints: 2526 Sorted by residual: chirality pdb=" CB ILE D 67 " pdb=" CA ILE D 67 " pdb=" CG1 ILE D 67 " pdb=" CG2 ILE D 67 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TRP E 226 " pdb=" N TRP E 226 " pdb=" C TRP E 226 " pdb=" CB TRP E 226 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE B 307 " pdb=" CA ILE B 307 " pdb=" CG1 ILE B 307 " pdb=" CG2 ILE B 307 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 2523 not shown) Planarity restraints: 2778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 237 " -0.202 9.50e-02 1.11e+02 9.15e-02 6.99e+00 pdb=" NE ARG B 237 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 237 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG B 237 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 237 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 240 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO A 241 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 148 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO C 149 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.028 5.00e-02 4.00e+02 ... (remaining 2775 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 148 2.64 - 3.21: 14561 3.21 - 3.77: 24780 3.77 - 4.34: 34115 4.34 - 4.90: 56004 Nonbonded interactions: 129608 Sorted by model distance: nonbonded pdb=" OH TYR E 115 " pdb=" OE1 GLU E 191 " model vdw 2.078 3.040 nonbonded pdb=" OD1 ASN B 288 " pdb=" OG1 THR C 287 " model vdw 2.146 3.040 nonbonded pdb=" OD1 ASN A 285 " pdb=" OH TYR B 279 " model vdw 2.157 3.040 nonbonded pdb=" NZ LYS B 4 " pdb=" OE1 GLU B 100 " model vdw 2.171 3.120 nonbonded pdb=" OG1 THR D 65 " pdb=" O LYS D 142 " model vdw 2.180 3.040 ... (remaining 129603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 350) selection = (chain 'B' and resid 17 through 350) selection = (chain 'C' and resid 17 through 350) selection = (chain 'D' and resid 17 through 350) selection = (chain 'E' and resid 17 through 350) } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 38.820 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16377 Z= 0.160 Angle : 0.604 8.088 22214 Z= 0.319 Chirality : 0.043 0.243 2526 Planarity : 0.005 0.091 2778 Dihedral : 13.972 88.488 6113 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.06 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1924 helix: 2.31 (0.16), residues: 965 sheet: 0.78 (0.28), residues: 376 loop : -1.35 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 323 HIS 0.016 0.001 HIS A 257 PHE 0.024 0.001 PHE A 306 TYR 0.033 0.002 TYR E 236 ARG 0.024 0.001 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.15058 ( 998) hydrogen bonds : angle 6.04994 ( 2892) SS BOND : bond 0.00027 ( 2) SS BOND : angle 2.14800 ( 4) covalent geometry : bond 0.00367 (16375) covalent geometry : angle 0.60308 (22210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: H 90 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7279 (mtt180) REVERT: H 96 VAL cc_start: 0.9099 (p) cc_final: 0.8717 (t) REVERT: A 63 ASN cc_start: 0.6863 (t0) cc_final: 0.6565 (t0) REVERT: A 96 ARG cc_start: 0.7300 (mmt180) cc_final: 0.6941 (mpt180) REVERT: B 32 MET cc_start: 0.8780 (mtt) cc_final: 0.8541 (mtt) REVERT: B 260 GLN cc_start: 0.7700 (mt0) cc_final: 0.7205 (mm-40) REVERT: D 19 TYR cc_start: 0.6805 (t80) cc_final: 0.6567 (t80) REVERT: E 10 LYS cc_start: 0.7378 (ptmm) cc_final: 0.7117 (ptmt) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 1.0070 time to fit residues: 476.9804 Evaluate side-chains 343 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 85 GLN B 92 ASN B 134 ASN D 120 HIS D 157 ASN E 63 ASN E 288 ASN E 314 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.198425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.161483 restraints weight = 18187.533| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.68 r_work: 0.3271 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16377 Z= 0.222 Angle : 0.654 9.232 22214 Z= 0.346 Chirality : 0.045 0.222 2526 Planarity : 0.005 0.051 2778 Dihedral : 4.544 20.323 2149 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.00 % Allowed : 13.09 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1924 helix: 2.16 (0.16), residues: 972 sheet: 0.79 (0.27), residues: 376 loop : -1.57 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 226 HIS 0.014 0.001 HIS A 257 PHE 0.025 0.002 PHE B 301 TYR 0.023 0.002 TYR D 327 ARG 0.005 0.001 ARG E 229 Details of bonding type rmsd hydrogen bonds : bond 0.06633 ( 998) hydrogen bonds : angle 4.92562 ( 2892) SS BOND : bond 0.00195 ( 2) SS BOND : angle 2.31427 ( 4) covalent geometry : bond 0.00532 (16375) covalent geometry : angle 0.65282 (22210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 354 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 19 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6646 (ttm170) REVERT: H 90 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7330 (mtt180) REVERT: H 96 VAL cc_start: 0.9188 (p) cc_final: 0.8937 (t) REVERT: A 96 ARG cc_start: 0.7904 (mmt180) cc_final: 0.7366 (mpt180) REVERT: A 167 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7876 (p0) REVERT: A 289 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: C 291 MET cc_start: 0.7795 (tpp) cc_final: 0.7485 (mmt) REVERT: D 19 TYR cc_start: 0.6943 (t80) cc_final: 0.6742 (t80) REVERT: D 32 MET cc_start: 0.7588 (mtm) cc_final: 0.7047 (mtt) REVERT: D 152 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6377 (mm-30) REVERT: D 226 TRP cc_start: 0.8238 (m100) cc_final: 0.7911 (m100) REVERT: D 291 MET cc_start: 0.8407 (tpt) cc_final: 0.8085 (tpt) REVERT: E 10 LYS cc_start: 0.7505 (ptmm) cc_final: 0.6934 (ptmt) REVERT: E 35 SER cc_start: 0.7529 (t) cc_final: 0.6856 (p) REVERT: E 42 PHE cc_start: 0.6329 (t80) cc_final: 0.5992 (t80) REVERT: E 205 LYS cc_start: 0.7725 (ttmm) cc_final: 0.7035 (mtmm) REVERT: E 210 ARG cc_start: 0.8360 (mtp180) cc_final: 0.7503 (mtm-85) REVERT: E 229 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8232 (mtm180) outliers start: 54 outliers final: 32 residues processed: 381 average time/residue: 1.2550 time to fit residues: 545.7939 Evaluate side-chains 372 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 335 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 282 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 139 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 0.0570 chunk 111 optimal weight: 0.0030 chunk 56 optimal weight: 0.4980 chunk 131 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN A 95 GLN B 288 ASN D 120 HIS D 157 ASN E 63 ASN E 314 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.198832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.161434 restraints weight = 18191.501| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.69 r_work: 0.3331 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16377 Z= 0.149 Angle : 0.574 8.260 22214 Z= 0.305 Chirality : 0.043 0.197 2526 Planarity : 0.004 0.048 2778 Dihedral : 4.403 18.832 2149 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.00 % Allowed : 16.47 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1924 helix: 2.31 (0.16), residues: 975 sheet: 0.80 (0.27), residues: 373 loop : -1.53 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 226 HIS 0.009 0.001 HIS A 257 PHE 0.023 0.002 PHE A 27 TYR 0.016 0.001 TYR C 168 ARG 0.006 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.05959 ( 998) hydrogen bonds : angle 4.65116 ( 2892) SS BOND : bond 0.00194 ( 2) SS BOND : angle 1.08124 ( 4) covalent geometry : bond 0.00332 (16375) covalent geometry : angle 0.57403 (22210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 358 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8477 (tt0) cc_final: 0.8240 (tt0) REVERT: H 90 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7225 (mtt180) REVERT: H 96 VAL cc_start: 0.9167 (p) cc_final: 0.8932 (t) REVERT: A 289 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: C 291 MET cc_start: 0.7745 (tpp) cc_final: 0.7449 (mmt) REVERT: D 32 MET cc_start: 0.7591 (mtm) cc_final: 0.6927 (ttt) REVERT: D 121 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6575 (tm-30) REVERT: D 152 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6462 (mm-30) REVERT: D 291 MET cc_start: 0.8309 (tpt) cc_final: 0.7838 (tpt) REVERT: E 10 LYS cc_start: 0.7449 (ptmm) cc_final: 0.6891 (ptmt) REVERT: E 35 SER cc_start: 0.7606 (t) cc_final: 0.6944 (p) REVERT: E 42 PHE cc_start: 0.6289 (t80) cc_final: 0.6033 (t80) REVERT: E 116 ASP cc_start: 0.6951 (t70) cc_final: 0.6613 (t0) REVERT: E 205 LYS cc_start: 0.7510 (ttmm) cc_final: 0.6830 (mtmm) REVERT: E 229 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8247 (mtm180) outliers start: 54 outliers final: 29 residues processed: 379 average time/residue: 0.9176 time to fit residues: 397.0009 Evaluate side-chains 371 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 339 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 0.0000 chunk 147 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 137 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 HIS D 157 ASN E 63 ASN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.199659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.162444 restraints weight = 18203.778| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.69 r_work: 0.3317 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16377 Z= 0.140 Angle : 0.555 9.134 22214 Z= 0.294 Chirality : 0.043 0.339 2526 Planarity : 0.004 0.046 2778 Dihedral : 4.324 17.705 2149 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.44 % Allowed : 18.30 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1924 helix: 2.43 (0.16), residues: 968 sheet: 0.81 (0.27), residues: 371 loop : -1.54 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 226 HIS 0.007 0.001 HIS A 257 PHE 0.021 0.001 PHE A 27 TYR 0.019 0.001 TYR D 327 ARG 0.005 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.05663 ( 998) hydrogen bonds : angle 4.49568 ( 2892) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.83512 ( 4) covalent geometry : bond 0.00307 (16375) covalent geometry : angle 0.55458 (22210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 349 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 96 VAL cc_start: 0.9166 (p) cc_final: 0.8920 (t) REVERT: A 269 ARG cc_start: 0.7615 (mtp180) cc_final: 0.7271 (mtt-85) REVERT: B 230 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: B 286 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7844 (mppt) REVERT: C 291 MET cc_start: 0.7813 (tpp) cc_final: 0.7563 (mmt) REVERT: D 32 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7051 (ttt) REVERT: D 121 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6598 (tm-30) REVERT: D 152 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6473 (mm-30) REVERT: D 291 MET cc_start: 0.8396 (tpt) cc_final: 0.8059 (tpt) REVERT: E 10 LYS cc_start: 0.7477 (ptmm) cc_final: 0.6844 (ptmt) REVERT: E 12 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7707 (mm) REVERT: E 35 SER cc_start: 0.7606 (t) cc_final: 0.6953 (p) REVERT: E 42 PHE cc_start: 0.6382 (t80) cc_final: 0.6142 (t80) REVERT: E 116 ASP cc_start: 0.6917 (t70) cc_final: 0.6579 (t0) REVERT: E 163 LYS cc_start: 0.7725 (ttmt) cc_final: 0.7470 (ttmm) REVERT: E 196 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7622 (mt-10) REVERT: E 205 LYS cc_start: 0.7486 (ttmm) cc_final: 0.6842 (mtmm) outliers start: 62 outliers final: 33 residues processed: 379 average time/residue: 1.0747 time to fit residues: 459.7984 Evaluate side-chains 370 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 332 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 125 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 184 optimal weight: 0.5980 chunk 22 optimal weight: 0.0010 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN B 288 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 HIS ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN E 63 ASN E 288 ASN E 314 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.198431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.161708 restraints weight = 18298.865| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.81 r_work: 0.3294 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16377 Z= 0.165 Angle : 0.582 12.184 22214 Z= 0.305 Chirality : 0.044 0.325 2526 Planarity : 0.004 0.047 2778 Dihedral : 4.366 18.597 2149 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.22 % Allowed : 19.08 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1924 helix: 2.39 (0.16), residues: 968 sheet: 0.78 (0.26), residues: 378 loop : -1.59 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 226 HIS 0.009 0.001 HIS A 257 PHE 0.024 0.002 PHE B 39 TYR 0.021 0.002 TYR D 19 ARG 0.010 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.05852 ( 998) hydrogen bonds : angle 4.48234 ( 2892) SS BOND : bond 0.00058 ( 2) SS BOND : angle 1.15817 ( 4) covalent geometry : bond 0.00386 (16375) covalent geometry : angle 0.58144 (22210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 346 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 VAL cc_start: 0.9228 (p) cc_final: 0.8885 (t) REVERT: A 116 ASP cc_start: 0.7079 (t70) cc_final: 0.6725 (t0) REVERT: A 269 ARG cc_start: 0.7627 (mtp180) cc_final: 0.7271 (mtt-85) REVERT: B 230 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: B 286 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.7828 (mppt) REVERT: C 297 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7699 (tt) REVERT: D 32 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7145 (ttt) REVERT: D 121 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6507 (tm-30) REVERT: D 152 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6426 (mm-30) REVERT: D 186 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: E 10 LYS cc_start: 0.7463 (ptmm) cc_final: 0.6796 (ptmt) REVERT: E 12 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7697 (mm) REVERT: E 35 SER cc_start: 0.7618 (t) cc_final: 0.6923 (p) REVERT: E 42 PHE cc_start: 0.6342 (t80) cc_final: 0.6116 (t80) REVERT: E 116 ASP cc_start: 0.6909 (t70) cc_final: 0.6571 (t0) REVERT: E 205 LYS cc_start: 0.7478 (ttmm) cc_final: 0.6817 (mtmm) outliers start: 76 outliers final: 45 residues processed: 388 average time/residue: 0.9482 time to fit residues: 418.3775 Evaluate side-chains 389 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 337 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 282 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 186 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN B 288 ASN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 HIS ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN E 288 ASN E 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.197226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.159864 restraints weight = 18136.203| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.16 r_work: 0.3284 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16377 Z= 0.181 Angle : 0.602 10.228 22214 Z= 0.315 Chirality : 0.044 0.380 2526 Planarity : 0.004 0.047 2778 Dihedral : 4.445 18.879 2149 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.22 % Allowed : 20.58 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 1924 helix: 2.28 (0.16), residues: 968 sheet: 0.68 (0.26), residues: 386 loop : -1.61 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 226 HIS 0.009 0.001 HIS A 257 PHE 0.028 0.002 PHE A 27 TYR 0.028 0.002 TYR D 19 ARG 0.006 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.06031 ( 998) hydrogen bonds : angle 4.53245 ( 2892) SS BOND : bond 0.00666 ( 2) SS BOND : angle 1.45443 ( 4) covalent geometry : bond 0.00428 (16375) covalent geometry : angle 0.60216 (22210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 347 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 VAL cc_start: 0.9220 (p) cc_final: 0.8882 (t) REVERT: A 269 ARG cc_start: 0.7496 (mtp180) cc_final: 0.7103 (mtt-85) REVERT: A 289 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: B 286 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7806 (mppt) REVERT: C 297 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7612 (tt) REVERT: D 32 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7177 (ttt) REVERT: D 121 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6469 (tm-30) REVERT: D 152 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6364 (mm-30) REVERT: D 186 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7531 (tp30) REVERT: D 190 ASP cc_start: 0.7676 (t0) cc_final: 0.7277 (m-30) REVERT: E 10 LYS cc_start: 0.7476 (ptmm) cc_final: 0.6880 (ptmt) REVERT: E 12 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7559 (mm) REVERT: E 35 SER cc_start: 0.7595 (t) cc_final: 0.6897 (p) REVERT: E 42 PHE cc_start: 0.6515 (t80) cc_final: 0.6306 (t80) REVERT: E 116 ASP cc_start: 0.6826 (t70) cc_final: 0.6476 (t0) REVERT: E 205 LYS cc_start: 0.7380 (ttmm) cc_final: 0.6706 (mtmm) outliers start: 76 outliers final: 49 residues processed: 384 average time/residue: 0.9289 time to fit residues: 407.7818 Evaluate side-chains 395 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 339 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 282 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 188 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 119 optimal weight: 8.9990 chunk 175 optimal weight: 0.0000 chunk 101 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN B 288 ASN D 120 HIS D 157 ASN E 63 ASN E 288 ASN E 314 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.198989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.161444 restraints weight = 18238.589| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.17 r_work: 0.3295 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.004 0.047 16377 Z= 0.168 Angle : 0.594 9.375 22214 Z= 0.310 Chirality : 0.044 0.348 2526 Planarity : 0.004 0.046 2778 Dihedral : 4.440 18.789 2149 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.05 % Allowed : 21.08 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1924 helix: 2.31 (0.16), residues: 968 sheet: 0.58 (0.25), residues: 388 loop : -1.61 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 226 HIS 0.008 0.001 HIS A 257 PHE 0.028 0.002 PHE A 27 TYR 0.027 0.002 TYR D 19 ARG 0.006 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.05947 ( 998) hydrogen bonds : angle 4.51001 ( 2892) SS BOND : bond 0.00076 ( 2) SS BOND : angle 1.18699 ( 4) covalent geometry : bond 0.00395 (16375) covalent geometry : angle 0.59377 (22210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 349 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 96 VAL cc_start: 0.9223 (p) cc_final: 0.8887 (t) REVERT: A 116 ASP cc_start: 0.6892 (t70) cc_final: 0.6576 (t0) REVERT: A 269 ARG cc_start: 0.7484 (mtp180) cc_final: 0.7260 (mtt-85) REVERT: A 289 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: B 238 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: B 286 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.7821 (mppt) REVERT: C 171 TYR cc_start: 0.6144 (t80) cc_final: 0.5865 (t80) REVERT: C 297 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7660 (tt) REVERT: D 27 PHE cc_start: 0.5884 (t80) cc_final: 0.5645 (t80) REVERT: D 32 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7173 (ttt) REVERT: D 121 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6545 (tm-30) REVERT: D 152 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6346 (mm-30) REVERT: D 186 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: D 190 ASP cc_start: 0.7700 (t0) cc_final: 0.7311 (m-30) REVERT: E 10 LYS cc_start: 0.7509 (ptmm) cc_final: 0.6834 (ptmt) REVERT: E 12 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7604 (mm) REVERT: E 35 SER cc_start: 0.7587 (t) cc_final: 0.6903 (p) REVERT: E 116 ASP cc_start: 0.6850 (t0) cc_final: 0.6518 (t0) REVERT: E 205 LYS cc_start: 0.7379 (ttmm) cc_final: 0.6715 (mtmm) outliers start: 73 outliers final: 51 residues processed: 386 average time/residue: 0.9253 time to fit residues: 410.6053 Evaluate side-chains 399 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 340 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 282 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 166 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 94 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 44 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN B 288 ASN D 120 HIS D 157 ASN E 63 ASN E 288 ASN E 314 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.199133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.162871 restraints weight = 18068.627| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.26 r_work: 0.3277 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16377 Z= 0.161 Angle : 0.592 11.056 22214 Z= 0.308 Chirality : 0.043 0.359 2526 Planarity : 0.004 0.046 2778 Dihedral : 4.407 18.547 2149 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.77 % Allowed : 22.35 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1924 helix: 2.34 (0.16), residues: 968 sheet: 0.61 (0.26), residues: 380 loop : -1.61 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 226 HIS 0.007 0.001 HIS A 257 PHE 0.028 0.002 PHE A 27 TYR 0.028 0.002 TYR D 19 ARG 0.006 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.05858 ( 998) hydrogen bonds : angle 4.47757 ( 2892) SS BOND : bond 0.00225 ( 2) SS BOND : angle 1.05875 ( 4) covalent geometry : bond 0.00374 (16375) covalent geometry : angle 0.59190 (22210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 342 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 VAL cc_start: 0.9228 (p) cc_final: 0.8896 (t) REVERT: A 41 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6629 (mp0) REVERT: A 116 ASP cc_start: 0.6889 (t70) cc_final: 0.6562 (t0) REVERT: A 269 ARG cc_start: 0.7478 (mtp180) cc_final: 0.7225 (mtt-85) REVERT: A 289 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: B 193 ASP cc_start: 0.7535 (t70) cc_final: 0.7328 (t0) REVERT: B 238 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: B 286 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.7804 (mppt) REVERT: C 138 MET cc_start: 0.3717 (pmm) cc_final: 0.2943 (pp-130) REVERT: C 171 TYR cc_start: 0.6145 (t80) cc_final: 0.5871 (t80) REVERT: C 297 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7651 (tt) REVERT: D 27 PHE cc_start: 0.5809 (t80) cc_final: 0.5597 (t80) REVERT: D 32 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7184 (ttt) REVERT: D 121 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6526 (tm-30) REVERT: D 152 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6355 (mm-30) REVERT: D 186 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7439 (tp30) REVERT: D 190 ASP cc_start: 0.7742 (t0) cc_final: 0.7327 (m-30) REVERT: D 341 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6574 (mmp) REVERT: E 10 LYS cc_start: 0.7485 (ptmm) cc_final: 0.6800 (ptmt) REVERT: E 12 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7588 (mm) REVERT: E 35 SER cc_start: 0.7604 (t) cc_final: 0.6895 (p) REVERT: E 205 LYS cc_start: 0.7345 (ttmm) cc_final: 0.6675 (mtmm) REVERT: E 229 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8431 (mtp180) outliers start: 68 outliers final: 50 residues processed: 378 average time/residue: 1.0278 time to fit residues: 443.3400 Evaluate side-chains 398 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 338 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 114 ASN B 92 ASN B 288 ASN D 120 HIS D 157 ASN E 63 ASN E 288 ASN E 314 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.197899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.159765 restraints weight = 18130.612| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.13 r_work: 0.3275 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16377 Z= 0.181 Angle : 0.611 10.480 22214 Z= 0.318 Chirality : 0.044 0.383 2526 Planarity : 0.004 0.046 2778 Dihedral : 4.461 18.755 2149 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.99 % Allowed : 22.35 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.20), residues: 1924 helix: 2.26 (0.16), residues: 968 sheet: 0.71 (0.26), residues: 373 loop : -1.65 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 226 HIS 0.008 0.001 HIS A 257 PHE 0.029 0.002 PHE A 27 TYR 0.030 0.002 TYR D 19 ARG 0.006 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.06055 ( 998) hydrogen bonds : angle 4.51836 ( 2892) SS BOND : bond 0.00018 ( 2) SS BOND : angle 1.40518 ( 4) covalent geometry : bond 0.00430 (16375) covalent geometry : angle 0.61062 (22210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 344 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 96 VAL cc_start: 0.9244 (p) cc_final: 0.8899 (t) REVERT: A 116 ASP cc_start: 0.6897 (t70) cc_final: 0.6564 (t0) REVERT: A 269 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7367 (mtt-85) REVERT: A 289 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: B 286 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7810 (mppt) REVERT: C 138 MET cc_start: 0.3802 (pmm) cc_final: 0.3200 (pp-130) REVERT: C 202 ARG cc_start: 0.6567 (ttp-110) cc_final: 0.6295 (ptt-90) REVERT: C 297 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7646 (tt) REVERT: D 32 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7202 (ttt) REVERT: D 121 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6636 (tm-30) REVERT: D 152 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6360 (mm-30) REVERT: D 186 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: D 190 ASP cc_start: 0.7752 (t0) cc_final: 0.7352 (m-30) REVERT: D 341 MET cc_start: 0.6752 (mmm) cc_final: 0.6516 (mmp) REVERT: E 10 LYS cc_start: 0.7482 (ptmm) cc_final: 0.6821 (ptmt) REVERT: E 12 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7594 (mm) REVERT: E 35 SER cc_start: 0.7566 (t) cc_final: 0.6907 (p) REVERT: E 116 ASP cc_start: 0.6892 (t0) cc_final: 0.6545 (t0) REVERT: E 205 LYS cc_start: 0.7360 (ttmm) cc_final: 0.6689 (mtmm) outliers start: 72 outliers final: 51 residues processed: 383 average time/residue: 0.9755 time to fit residues: 428.4487 Evaluate side-chains 396 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 338 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 282 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 179 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 114 ASN A 140 GLN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 HIS D 157 ASN E 63 ASN E 288 ASN E 314 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.197065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.158962 restraints weight = 18235.572| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.55 r_work: 0.3286 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16377 Z= 0.177 Angle : 0.616 10.162 22214 Z= 0.321 Chirality : 0.044 0.382 2526 Planarity : 0.004 0.046 2778 Dihedral : 4.476 18.706 2149 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.88 % Allowed : 22.68 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1924 helix: 2.26 (0.16), residues: 968 sheet: 0.71 (0.26), residues: 373 loop : -1.66 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 226 HIS 0.008 0.001 HIS A 257 PHE 0.030 0.002 PHE A 27 TYR 0.031 0.002 TYR D 19 ARG 0.009 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.06038 ( 998) hydrogen bonds : angle 4.51877 ( 2892) SS BOND : bond 0.00065 ( 2) SS BOND : angle 1.32307 ( 4) covalent geometry : bond 0.00419 (16375) covalent geometry : angle 0.61587 (22210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 345 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 VAL cc_start: 0.9239 (p) cc_final: 0.8901 (t) REVERT: A 116 ASP cc_start: 0.6881 (t70) cc_final: 0.6569 (t0) REVERT: A 269 ARG cc_start: 0.7544 (mtp180) cc_final: 0.7309 (mtt-85) REVERT: A 289 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: A 292 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8122 (mtpt) REVERT: B 238 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: B 286 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7783 (mppt) REVERT: C 138 MET cc_start: 0.3883 (pmm) cc_final: 0.3310 (pp-130) REVERT: C 202 ARG cc_start: 0.6564 (ttp-110) cc_final: 0.6296 (ptt-90) REVERT: C 297 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7636 (tt) REVERT: D 32 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7192 (ttt) REVERT: D 121 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6596 (tm-30) REVERT: D 152 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6348 (mm-30) REVERT: D 186 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: D 190 ASP cc_start: 0.7721 (t0) cc_final: 0.7317 (m-30) REVERT: D 341 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.6490 (mmp) REVERT: E 10 LYS cc_start: 0.7490 (ptmm) cc_final: 0.6832 (ptmt) REVERT: E 12 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7575 (mm) REVERT: E 35 SER cc_start: 0.7633 (t) cc_final: 0.7023 (p) REVERT: E 163 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7647 (ttmt) REVERT: E 205 LYS cc_start: 0.7336 (ttmm) cc_final: 0.6670 (mtmm) REVERT: E 220 GLU cc_start: 0.7730 (tp30) cc_final: 0.7110 (tp30) outliers start: 70 outliers final: 51 residues processed: 380 average time/residue: 1.0197 time to fit residues: 446.9913 Evaluate side-chains 399 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 282 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 141 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 143 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 114 ASN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN D 120 HIS D 157 ASN E 63 ASN E 288 ASN E 314 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.197221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.160040 restraints weight = 18080.288| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.61 r_work: 0.3285 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16377 Z= 0.181 Angle : 0.625 9.994 22214 Z= 0.325 Chirality : 0.045 0.377 2526 Planarity : 0.004 0.046 2778 Dihedral : 4.490 18.932 2149 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.77 % Allowed : 22.85 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1924 helix: 2.22 (0.16), residues: 968 sheet: 0.69 (0.26), residues: 373 loop : -1.66 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 226 HIS 0.008 0.001 HIS A 257 PHE 0.031 0.002 PHE A 27 TYR 0.031 0.002 TYR D 19 ARG 0.010 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.06087 ( 998) hydrogen bonds : angle 4.54193 ( 2892) SS BOND : bond 0.00045 ( 2) SS BOND : angle 1.34390 ( 4) covalent geometry : bond 0.00428 (16375) covalent geometry : angle 0.62484 (22210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12927.74 seconds wall clock time: 224 minutes 0.06 seconds (13440.06 seconds total)