Starting phenix.real_space_refine on Sun May 18 03:55:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmd_41385/05_2025/8tmd_41385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmd_41385/05_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_41385/05_2025/8tmd_41385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmd_41385/05_2025/8tmd_41385.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmd_41385/05_2025/8tmd_41385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmd_41385/05_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-5687/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: 10.48, per 1000 atoms: 0.65 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: 4.08 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: 1.75 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: 4.95 Time building geometry restraints manager: 4.74 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.770 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.280 ------------------------------------------------------------------------------- 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 : 1.743 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: 0.9582 time to fit residues: 454.9300 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 : 1.769 ------------------------------------------------------------------------------- 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 = 0.161484 restraints weight = 18187.460| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.68 r_work: 0.3269 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 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 = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 9.99 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 : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 19 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6638 (ttm170) REVERT: H 90 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.7327 (mtt180) REVERT: H 96 VAL cc_start: 0.9189 (p) cc_final: 0.8939 (t) REVERT: A 96 ARG cc_start: 0.7887 (mmt180) cc_final: 0.7346 (mpt180) REVERT: A 167 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7881 (p0) REVERT: A 289 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: C 291 MET cc_start: 0.7793 (tpp) cc_final: 0.7483 (mmt) REVERT: D 19 TYR cc_start: 0.6941 (t80) cc_final: 0.6739 (t80) REVERT: D 32 MET cc_start: 0.7583 (mtm) cc_final: 0.7037 (mtt) REVERT: D 152 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6344 (mm-30) REVERT: D 226 TRP cc_start: 0.8235 (m100) cc_final: 0.7908 (m100) REVERT: D 291 MET cc_start: 0.8403 (tpt) cc_final: 0.8083 (tpt) REVERT: E 10 LYS cc_start: 0.7501 (ptmm) cc_final: 0.6928 (ptmt) REVERT: E 35 SER cc_start: 0.7523 (t) cc_final: 0.6839 (p) REVERT: E 42 PHE cc_start: 0.6325 (t80) cc_final: 0.5993 (t80) REVERT: E 205 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7029 (mtmm) REVERT: E 210 ARG cc_start: 0.8357 (mtp180) cc_final: 0.7500 (mtm-85) REVERT: E 229 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8229 (mtm180) outliers start: 54 outliers final: 32 residues processed: 381 average time/residue: 0.9659 time to fit residues: 417.1609 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 : 1.654 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 0.0010 chunk 56 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.197262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.159779 restraints weight = 18162.298| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.91 r_work: 0.3315 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- 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 = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16377 Z= 0.175 Angle : 0.598 8.697 22214 Z= 0.316 Chirality : 0.043 0.200 2526 Planarity : 0.005 0.049 2778 Dihedral : 4.479 19.327 2149 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.61 % Allowed : 16.03 % Favored : 80.37 % 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: 2.20 (0.16), residues: 975 sheet: 0.82 (0.26), residues: 382 loop : -1.61 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 226 HIS 0.010 0.001 HIS A 257 PHE 0.023 0.002 PHE A 27 TYR 0.018 0.002 TYR H 106 ARG 0.005 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.06236 ( 998) hydrogen bonds : angle 4.70347 ( 2892) SS BOND : bond 0.00164 ( 2) SS BOND : angle 1.37522 ( 4) covalent geometry : bond 0.00409 (16375) covalent geometry : angle 0.59807 (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 421 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 356 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8446 (tt0) cc_final: 0.8202 (tt0) REVERT: H 90 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7284 (mtt180) REVERT: H 96 VAL cc_start: 0.9173 (p) cc_final: 0.8921 (t) REVERT: A 145 ASP cc_start: 0.7242 (p0) cc_final: 0.7042 (p0) REVERT: A 152 GLU cc_start: 0.7414 (mp0) cc_final: 0.7212 (mp0) REVERT: A 289 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: A 291 MET cc_start: 0.8407 (mmp) cc_final: 0.8147 (mmp) REVERT: B 230 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: B 286 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7791 (mppt) REVERT: C 291 MET cc_start: 0.7766 (tpp) cc_final: 0.7326 (mmt) REVERT: D 32 MET cc_start: 0.7616 (mtm) cc_final: 0.7023 (ttt) REVERT: D 85 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7865 (tp) REVERT: D 121 GLU cc_start: 0.6851 (tm-30) cc_final: 0.6582 (tm-30) REVERT: D 152 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6399 (mm-30) REVERT: D 230 GLU cc_start: 0.7602 (tp30) cc_final: 0.7302 (tp30) REVERT: D 291 MET cc_start: 0.8277 (tpt) cc_final: 0.7748 (tpt) REVERT: E 10 LYS cc_start: 0.7465 (ptmm) cc_final: 0.6912 (ptmt) REVERT: E 35 SER cc_start: 0.7532 (t) cc_final: 0.6877 (p) REVERT: E 42 PHE cc_start: 0.6249 (t80) cc_final: 0.5995 (t80) REVERT: E 116 ASP cc_start: 0.6946 (t70) cc_final: 0.6583 (t0) REVERT: E 205 LYS cc_start: 0.7507 (ttmm) cc_final: 0.6819 (mtmm) REVERT: E 229 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8297 (mtm180) outliers start: 65 outliers final: 35 residues processed: 382 average time/residue: 0.9113 time to fit residues: 397.2899 Evaluate side-chains 379 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 74 SER Chi-restraints excluded: chain H residue 86 MET 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 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 150 VAL 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 318 MET Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 85 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 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: 2.9990 chunk 4 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.196547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.160106 restraints weight = 18098.046| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.80 r_work: 0.3276 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16377 Z= 0.209 Angle : 0.631 10.250 22214 Z= 0.331 Chirality : 0.045 0.332 2526 Planarity : 0.005 0.048 2778 Dihedral : 4.582 19.157 2149 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.27 % Allowed : 18.14 % Favored : 77.59 % 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: 1.13 (0.19), residues: 1924 helix: 2.10 (0.16), residues: 968 sheet: 0.72 (0.26), residues: 380 loop : -1.67 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 226 HIS 0.011 0.001 HIS A 257 PHE 0.023 0.002 PHE A 27 TYR 0.021 0.002 TYR D 327 ARG 0.005 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.06478 ( 998) hydrogen bonds : angle 4.68469 ( 2892) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.55035 ( 4) covalent geometry : bond 0.00502 (16375) covalent geometry : angle 0.63075 (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 434 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 357 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8721 (tt0) REVERT: H 96 VAL cc_start: 0.9208 (p) cc_final: 0.8902 (t) REVERT: A 152 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: A 269 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7230 (mtt-85) REVERT: A 289 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: B 230 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: B 286 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7809 (mppt) REVERT: C 291 MET cc_start: 0.7917 (tpp) cc_final: 0.7685 (mmt) REVERT: C 297 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7603 (tt) REVERT: D 32 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7270 (ttt) REVERT: D 85 LEU cc_start: 0.8110 (mt) cc_final: 0.7720 (tp) REVERT: D 152 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6360 (mm-30) REVERT: D 186 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7583 (tp30) REVERT: D 230 GLU cc_start: 0.7589 (tp30) cc_final: 0.7330 (tp30) REVERT: D 291 MET cc_start: 0.8376 (tpt) cc_final: 0.8052 (tpt) REVERT: E 10 LYS cc_start: 0.7568 (ptmm) cc_final: 0.6930 (ptmt) REVERT: E 12 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7612 (mm) REVERT: E 35 SER cc_start: 0.7584 (t) cc_final: 0.6938 (p) REVERT: E 42 PHE cc_start: 0.6374 (t80) cc_final: 0.6123 (t80) REVERT: E 116 ASP cc_start: 0.6935 (t70) cc_final: 0.6604 (t0) REVERT: E 205 LYS cc_start: 0.7512 (ttmm) cc_final: 0.6829 (mtmm) REVERT: E 210 ARG cc_start: 0.8335 (mtp180) cc_final: 0.7468 (mtm-85) REVERT: E 229 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8309 (mtm180) outliers start: 77 outliers final: 45 residues processed: 395 average time/residue: 0.9447 time to fit residues: 423.8770 Evaluate side-chains 404 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 348 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 38 GLN 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 86 MET 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 239 VAL 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 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 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 150 VAL 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 228 LEU 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 229 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 125 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 101 GLN H 31 ASN D 120 HIS D 157 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 = 0.4031 r_free = 0.4031 target = 0.196028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.158586 restraints weight = 18310.245| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.47 r_work: 0.3294 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1759 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= 0.184 Angle : 0.610 11.478 22214 Z= 0.319 Chirality : 0.044 0.361 2526 Planarity : 0.005 0.048 2778 Dihedral : 4.540 18.688 2149 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.44 % Allowed : 19.47 % Favored : 76.10 % 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: 1.15 (0.19), residues: 1924 helix: 2.15 (0.16), residues: 969 sheet: 0.63 (0.25), residues: 386 loop : -1.67 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 226 HIS 0.009 0.001 HIS A 257 PHE 0.025 0.002 PHE A 27 TYR 0.022 0.002 TYR D 19 ARG 0.009 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.06272 ( 998) hydrogen bonds : angle 4.62321 ( 2892) SS BOND : bond 0.00083 ( 2) SS BOND : angle 1.19777 ( 4) covalent geometry : bond 0.00433 (16375) covalent geometry : angle 0.60938 (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 433 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 353 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8503 (tt0) cc_final: 0.8300 (tt0) REVERT: H 96 VAL cc_start: 0.9210 (p) cc_final: 0.8894 (t) REVERT: A 152 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: A 189 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8186 (t70) REVERT: A 269 ARG cc_start: 0.7580 (mtp180) cc_final: 0.7235 (mtt-85) REVERT: A 289 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: B 286 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7777 (mppt) REVERT: C 297 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7565 (tt) REVERT: D 32 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7197 (ttt) REVERT: D 85 LEU cc_start: 0.8096 (mt) cc_final: 0.7794 (tp) REVERT: D 152 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6308 (mm-30) REVERT: D 162 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7334 (ttm-80) REVERT: D 186 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: E 10 LYS cc_start: 0.7593 (ptmm) cc_final: 0.6899 (ptmt) REVERT: E 12 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7587 (mm) REVERT: E 35 SER cc_start: 0.7555 (t) cc_final: 0.6889 (p) REVERT: E 42 PHE cc_start: 0.6275 (t80) cc_final: 0.6029 (t80) REVERT: E 116 ASP cc_start: 0.6895 (t70) cc_final: 0.6591 (t0) REVERT: E 205 LYS cc_start: 0.7429 (ttmm) cc_final: 0.6757 (mtmm) REVERT: E 210 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7393 (mtm-85) outliers start: 80 outliers final: 47 residues processed: 396 average time/residue: 0.9303 time to fit residues: 419.7984 Evaluate side-chains 403 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 347 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 86 MET 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 177 LEU 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 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 186 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN B 288 ASN D 120 HIS D 157 ASN E 140 GLN E 314 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.197777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.161420 restraints weight = 18028.319| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.75 r_work: 0.3276 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16377 Z= 0.202 Angle : 0.625 10.174 22214 Z= 0.327 Chirality : 0.045 0.375 2526 Planarity : 0.005 0.049 2778 Dihedral : 4.602 19.188 2149 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.94 % Allowed : 19.91 % Favored : 75.15 % 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: 1.08 (0.19), residues: 1924 helix: 2.10 (0.16), residues: 968 sheet: 0.58 (0.26), residues: 386 loop : -1.69 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 226 HIS 0.010 0.001 HIS A 257 PHE 0.027 0.002 PHE A 27 TYR 0.027 0.002 TYR D 19 ARG 0.010 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.06395 ( 998) hydrogen bonds : angle 4.64024 ( 2892) SS BOND : bond 0.00210 ( 2) SS BOND : angle 1.39893 ( 4) covalent geometry : bond 0.00484 (16375) covalent geometry : angle 0.62462 (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 448 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 359 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8753 (tt0) REVERT: L 90 GLN cc_start: 0.8635 (tt0) cc_final: 0.8357 (tt0) REVERT: H 96 VAL cc_start: 0.9246 (p) cc_final: 0.8893 (t) REVERT: A 41 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6542 (mp0) REVERT: A 152 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: A 189 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8183 (t70) REVERT: A 269 ARG cc_start: 0.7608 (mtp180) cc_final: 0.7279 (mtt-85) REVERT: A 289 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: B 177 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7966 (tt) REVERT: B 291 MET cc_start: 0.8410 (ttm) cc_final: 0.8202 (ttt) REVERT: C 297 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7569 (tt) REVERT: D 32 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7378 (ttt) REVERT: D 152 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6385 (mm-30) REVERT: D 186 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7615 (tp30) REVERT: E 10 LYS cc_start: 0.7572 (ptmm) cc_final: 0.6892 (ptmt) REVERT: E 12 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7652 (mm) REVERT: E 35 SER cc_start: 0.7579 (t) cc_final: 0.6929 (p) REVERT: E 42 PHE cc_start: 0.6340 (t80) cc_final: 0.6104 (t80) REVERT: E 116 ASP cc_start: 0.6930 (t0) cc_final: 0.6622 (t0) REVERT: E 205 LYS cc_start: 0.7491 (ttmm) cc_final: 0.6825 (mtmm) REVERT: E 210 ARG cc_start: 0.8337 (mtp180) cc_final: 0.7481 (mtm-85) outliers start: 89 outliers final: 54 residues processed: 407 average time/residue: 0.9178 time to fit residues: 425.5175 Evaluate side-chains 415 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 351 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 38 GLN 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 86 MET 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 177 LEU Chi-restraints excluded: chain A residue 189 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 293 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 177 LEU 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 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 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 Chi-restraints excluded: chain E residue 310 ILE 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: 0.8980 chunk 125 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 175 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN D 120 HIS D 157 ASN E 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.196264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.158543 restraints weight = 18252.171| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.40 r_work: 0.3286 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 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 = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16377 Z= 0.186 Angle : 0.617 9.810 22214 Z= 0.323 Chirality : 0.044 0.350 2526 Planarity : 0.005 0.049 2778 Dihedral : 4.588 19.080 2149 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.99 % Allowed : 20.91 % Favored : 74.10 % 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: 1.11 (0.19), residues: 1924 helix: 2.14 (0.16), residues: 968 sheet: 0.61 (0.26), residues: 378 loop : -1.69 (0.26), residues: 578 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 0.028 0.002 PHE A 27 TYR 0.028 0.002 TYR D 19 ARG 0.009 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.06278 ( 998) hydrogen bonds : angle 4.60876 ( 2892) SS BOND : bond 0.00047 ( 2) SS BOND : angle 1.30624 ( 4) covalent geometry : bond 0.00442 (16375) covalent geometry : angle 0.61646 (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 448 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 358 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8615 (tt0) cc_final: 0.8367 (tt0) REVERT: H 96 VAL cc_start: 0.9238 (p) cc_final: 0.8906 (t) REVERT: A 152 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: A 189 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8164 (t70) REVERT: A 269 ARG cc_start: 0.7569 (mtp180) cc_final: 0.7359 (mtt-85) REVERT: A 289 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: B 177 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7953 (tt) REVERT: B 220 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6177 (mm-30) REVERT: B 286 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7794 (mppt) REVERT: C 202 ARG cc_start: 0.6538 (ttp-110) cc_final: 0.6273 (ptt-90) REVERT: C 297 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7592 (tt) REVERT: D 32 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7332 (ttt) REVERT: D 152 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6404 (mm-30) REVERT: D 186 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7502 (tp30) REVERT: E 10 LYS cc_start: 0.7584 (ptmm) cc_final: 0.6911 (ptmt) REVERT: E 12 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7621 (mm) REVERT: E 35 SER cc_start: 0.7573 (t) cc_final: 0.6913 (p) REVERT: E 42 PHE cc_start: 0.6497 (t80) cc_final: 0.6280 (t80) REVERT: E 116 ASP cc_start: 0.6895 (t0) cc_final: 0.6611 (t0) REVERT: E 163 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7363 (ttpt) REVERT: E 187 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8135 (mtpp) REVERT: E 205 LYS cc_start: 0.7400 (ttmm) cc_final: 0.6742 (mtmm) REVERT: E 210 ARG cc_start: 0.8276 (mtp180) cc_final: 0.7410 (mtm-85) outliers start: 90 outliers final: 57 residues processed: 406 average time/residue: 0.9153 time to fit residues: 426.3526 Evaluate side-chains 421 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 353 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 86 MET 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 177 LEU 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 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 331 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 177 LEU 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 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 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 183 VAL Chi-restraints excluded: chain D residue 186 GLU 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 163 LYS 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: 0.9990 chunk 154 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 63 optimal weight: 0.0970 chunk 94 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 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 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 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.196075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.158282 restraints weight = 18077.589| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.32 r_work: 0.3274 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16377 Z= 0.180 Angle : 0.618 11.051 22214 Z= 0.322 Chirality : 0.044 0.318 2526 Planarity : 0.005 0.049 2778 Dihedral : 4.555 18.943 2149 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.88 % Allowed : 21.46 % 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: 1.14 (0.20), residues: 1924 helix: 2.17 (0.16), residues: 968 sheet: 0.59 (0.26), residues: 378 loop : -1.67 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 226 HIS 0.007 0.001 HIS A 257 PHE 0.030 0.002 PHE A 27 TYR 0.030 0.002 TYR D 19 ARG 0.008 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.06190 ( 998) hydrogen bonds : angle 4.58991 ( 2892) SS BOND : bond 0.00018 ( 2) SS BOND : angle 1.20275 ( 4) covalent geometry : bond 0.00423 (16375) covalent geometry : angle 0.61796 (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 448 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 360 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8630 (tt0) cc_final: 0.8402 (tt0) REVERT: H 96 VAL cc_start: 0.9249 (p) cc_final: 0.8905 (t) REVERT: A 41 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6759 (mp0) REVERT: A 116 ASP cc_start: 0.6876 (t70) cc_final: 0.6616 (t0) REVERT: A 152 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: A 189 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8176 (t70) REVERT: A 269 ARG cc_start: 0.7592 (mtp180) cc_final: 0.7375 (mtt-85) REVERT: A 289 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: A 292 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8271 (mtmt) REVERT: B 220 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6217 (mm-30) REVERT: B 230 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: B 286 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.7814 (mppt) REVERT: C 297 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7601 (tt) REVERT: D 32 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7254 (ttt) REVERT: D 93 VAL cc_start: 0.7024 (t) cc_final: 0.6671 (m) REVERT: D 145 ASP cc_start: 0.7621 (p0) cc_final: 0.7404 (p0) REVERT: D 152 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6396 (mm-30) REVERT: D 186 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7509 (tp30) REVERT: E 10 LYS cc_start: 0.7550 (ptmm) cc_final: 0.6868 (ptmt) REVERT: E 12 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7631 (mm) REVERT: E 35 SER cc_start: 0.7595 (t) cc_final: 0.6945 (p) REVERT: E 42 PHE cc_start: 0.6518 (t80) cc_final: 0.6308 (t80) REVERT: E 116 ASP cc_start: 0.6917 (t0) cc_final: 0.6594 (t0) REVERT: E 163 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7640 (ttmt) REVERT: E 187 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8161 (mtpp) REVERT: E 205 LYS cc_start: 0.7406 (ttmm) cc_final: 0.6745 (mtmm) REVERT: E 222 ARG cc_start: 0.8718 (ttt-90) cc_final: 0.8207 (ttp-110) outliers start: 88 outliers final: 56 residues processed: 408 average time/residue: 0.9184 time to fit residues: 426.8721 Evaluate side-chains 418 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 351 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 86 MET 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 177 LEU 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 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 65 THR Chi-restraints excluded: chain B residue 106 VAL 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 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 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 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 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 163 LYS 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 Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 184 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.196422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.158901 restraints weight = 18158.902| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.33 r_work: 0.3287 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2045 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= 0.174 Angle : 0.619 10.119 22214 Z= 0.322 Chirality : 0.045 0.329 2526 Planarity : 0.005 0.050 2778 Dihedral : 4.536 18.748 2149 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.49 % Allowed : 22.35 % Favored : 73.16 % 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: 1.14 (0.20), residues: 1924 helix: 2.18 (0.16), residues: 968 sheet: 0.60 (0.26), residues: 378 loop : -1.67 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 226 HIS 0.007 0.001 HIS A 257 PHE 0.030 0.002 PHE A 27 TYR 0.030 0.002 TYR D 19 ARG 0.009 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.06122 ( 998) hydrogen bonds : angle 4.57895 ( 2892) SS BOND : bond 0.00108 ( 2) SS BOND : angle 1.18316 ( 4) covalent geometry : bond 0.00409 (16375) covalent geometry : angle 0.61923 (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 441 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 360 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8612 (tt0) cc_final: 0.8406 (tt0) REVERT: H 96 VAL cc_start: 0.9243 (p) cc_final: 0.8900 (t) REVERT: A 41 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6742 (mp0) REVERT: A 116 ASP cc_start: 0.6851 (t70) cc_final: 0.6577 (t0) REVERT: A 152 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: A 189 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8158 (t70) REVERT: A 269 ARG cc_start: 0.7572 (mtp180) cc_final: 0.7353 (mtt-85) REVERT: A 289 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: B 220 GLU cc_start: 0.6585 (mm-30) cc_final: 0.6184 (mm-30) REVERT: B 230 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: B 286 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7799 (mppt) REVERT: C 138 MET cc_start: 0.3945 (pmm) cc_final: 0.3321 (pp-130) REVERT: C 171 TYR cc_start: 0.6152 (t80) cc_final: 0.5920 (t80) REVERT: C 297 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7629 (tt) REVERT: D 32 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7162 (ttt) REVERT: D 93 VAL cc_start: 0.7131 (t) cc_final: 0.6803 (m) REVERT: D 152 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6414 (mm-30) REVERT: D 186 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: D 341 MET cc_start: 0.6802 (mmm) cc_final: 0.6562 (mmt) REVERT: E 10 LYS cc_start: 0.7487 (ptmm) cc_final: 0.6830 (ptmt) REVERT: E 12 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7618 (mm) REVERT: E 35 SER cc_start: 0.7565 (t) cc_final: 0.6966 (p) REVERT: E 42 PHE cc_start: 0.6511 (t80) cc_final: 0.6306 (t80) REVERT: E 116 ASP cc_start: 0.6915 (t0) cc_final: 0.6587 (t0) REVERT: E 163 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7652 (ttmt) REVERT: E 187 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8159 (mtpp) REVERT: E 205 LYS cc_start: 0.7375 (ttmm) cc_final: 0.6710 (mtmm) REVERT: E 222 ARG cc_start: 0.8722 (ttt-90) cc_final: 0.8213 (ttp-110) outliers start: 81 outliers final: 58 residues processed: 405 average time/residue: 0.9585 time to fit residues: 442.0616 Evaluate side-chains 414 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 345 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 86 MET 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 177 LEU 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 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 65 THR Chi-restraints excluded: chain B residue 106 VAL 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 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 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 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 163 LYS 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 Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 150 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.195616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.158065 restraints weight = 18222.454| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.67 r_work: 0.3262 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16377 Z= 0.193 Angle : 0.643 10.119 22214 Z= 0.334 Chirality : 0.045 0.327 2526 Planarity : 0.005 0.050 2778 Dihedral : 4.581 19.359 2149 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.22 % Allowed : 22.74 % Favored : 73.04 % 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: 1.07 (0.19), residues: 1924 helix: 2.11 (0.16), residues: 968 sheet: 0.58 (0.26), residues: 378 loop : -1.70 (0.26), residues: 578 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 0.030 0.002 TYR D 19 ARG 0.010 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.06299 ( 998) hydrogen bonds : angle 4.60824 ( 2892) SS BOND : bond 0.00049 ( 2) SS BOND : angle 1.30916 ( 4) covalent geometry : bond 0.00462 (16375) covalent geometry : angle 0.64233 (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 424 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 348 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8609 (tt0) cc_final: 0.8402 (tt0) REVERT: H 96 VAL cc_start: 0.9259 (p) cc_final: 0.8899 (t) REVERT: A 41 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: A 116 ASP cc_start: 0.6941 (t70) cc_final: 0.6670 (t0) REVERT: A 152 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: A 189 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8216 (t70) REVERT: A 269 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7439 (mtt-85) REVERT: A 289 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7530 (mt-10) REVERT: A 292 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8333 (mtmt) REVERT: B 220 GLU cc_start: 0.6622 (mm-30) cc_final: 0.6229 (mm-30) REVERT: B 230 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: B 286 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7855 (mppt) REVERT: C 138 MET cc_start: 0.4078 (pmm) cc_final: 0.3258 (pp-130) REVERT: C 202 ARG cc_start: 0.6171 (ttp-110) cc_final: 0.5807 (ptt-90) REVERT: C 297 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7632 (tt) REVERT: D 32 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7345 (ttt) REVERT: D 93 VAL cc_start: 0.7176 (t) cc_final: 0.6870 (m) REVERT: D 152 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6416 (mm-30) REVERT: D 186 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: D 341 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6543 (mmt) REVERT: E 10 LYS cc_start: 0.7518 (ptmm) cc_final: 0.6874 (ptmt) REVERT: E 35 SER cc_start: 0.7650 (t) cc_final: 0.7041 (p) REVERT: E 116 ASP cc_start: 0.6981 (t0) cc_final: 0.6648 (t0) REVERT: E 163 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7712 (ttmt) REVERT: E 187 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8302 (mtpp) REVERT: E 202 ARG cc_start: 0.8207 (pmt170) cc_final: 0.7836 (ptp90) REVERT: E 205 LYS cc_start: 0.7453 (ttmm) cc_final: 0.6803 (mtmm) REVERT: E 222 ARG cc_start: 0.8721 (ttt-90) cc_final: 0.8204 (ttp-110) outliers start: 76 outliers final: 55 residues processed: 388 average time/residue: 0.9905 time to fit residues: 442.3353 Evaluate side-chains 415 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 348 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 24 CYS 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 86 MET Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 41 GLU 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 177 LEU Chi-restraints excluded: chain A residue 189 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 331 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 106 VAL 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 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 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 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 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 47 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 163 LYS 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 Chi-restraints excluded: chain E residue 310 ILE 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: 1.9990 chunk 88 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 179 optimal weight: 0.0000 chunk 82 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 6 optimal weight: 0.0000 chunk 143 optimal weight: 0.0370 chunk 106 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.2866 ------------------------------------------------------------------------------- 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 ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 HIS D 157 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 = 0.199719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.162466 restraints weight = 18108.958| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.62 r_work: 0.3320 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16377 Z= 0.138 Angle : 0.592 10.178 22214 Z= 0.309 Chirality : 0.043 0.308 2526 Planarity : 0.004 0.050 2778 Dihedral : 4.373 18.361 2149 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.16 % Allowed : 23.96 % Favored : 72.88 % 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: 2.35 (0.16), residues: 968 sheet: 0.67 (0.27), residues: 361 loop : -1.60 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 226 HIS 0.004 0.000 HIS A 257 PHE 0.028 0.002 PHE A 27 TYR 0.027 0.002 TYR D 19 ARG 0.009 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.05552 ( 998) hydrogen bonds : angle 4.45018 ( 2892) SS BOND : bond 0.00049 ( 2) SS BOND : angle 1.15161 ( 4) covalent geometry : bond 0.00299 (16375) covalent geometry : angle 0.59199 (22210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11978.17 seconds wall clock time: 206 minutes 50.98 seconds (12410.98 seconds total)