Starting phenix.real_space_refine on Fri Feb 14 19:51:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v9x_31829/02_2025/7v9x_31829.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9x_31829/02_2025/7v9x_31829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v9x_31829/02_2025/7v9x_31829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9x_31829/02_2025/7v9x_31829.map" model { file = "/net/cci-nas-00/data/ceres_data/7v9x_31829/02_2025/7v9x_31829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9x_31829/02_2025/7v9x_31829.cif" } resolution = 2.82 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= 0.005 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 210 5.49 5 S 23 5.16 5 C 5946 2.51 5 N 1901 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10550 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "C" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1096 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 2 Chain: "D" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "H" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "I" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Time building chain proxies: 6.33, per 1000 atoms: 0.60 Number of scatterers: 10550 At special positions: 0 Unit cell: (94.35, 129.2, 155.55, 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 23 16.00 P 210 15.00 O 2470 8.00 N 1901 7.00 C 5946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.50 Conformation dependent library (CDL) restraints added in 840.4 milliseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 60.5% alpha, 10.9% beta 64 base pairs and 116 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 removed outlier: 3.633A pdb=" N LEU A 7 " --> pdb=" O SER A 3 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 33 through 44 removed outlier: 3.581A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.733A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.691A pdb=" N LEU A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.756A pdb=" N VAL A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 174 through 188 removed outlier: 4.625A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.606A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.655A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.766A pdb=" N GLN C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 217 through 230 Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.575A pdb=" N ARG C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.937A pdb=" N ASN B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 33 through 43 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.615A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 128 through 139 removed outlier: 4.060A pdb=" N VAL B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 188 removed outlier: 4.232A pdb=" N SER B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.664A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 256 through 273 removed outlier: 3.619A pdb=" N TYR B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.679A pdb=" N LYS B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 removed outlier: 3.643A pdb=" N ARG A 63 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 256 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.979A pdb=" N ARG B 63 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 194 removed outlier: 3.543A pdb=" N PHE B 114 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 226 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 194 removed outlier: 3.543A pdb=" N PHE B 114 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 332 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 161 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 116 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1841 1.33 - 1.45: 3746 1.45 - 1.57: 5159 1.57 - 1.69: 410 1.69 - 1.81: 34 Bond restraints: 11190 Sorted by residual: bond pdb=" C3' DG D 73 " pdb=" O3' DG D 73 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" C3' DC D 3 " pdb=" O3' DC D 3 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" C3' DG G 73 " pdb=" O3' DG G 73 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C3' A E 66 " pdb=" O3' A E 66 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.26e+00 bond pdb=" CB TRP B 284 " pdb=" CG TRP B 284 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.24e+00 ... (remaining 11185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 15780 2.10 - 4.20: 241 4.20 - 6.30: 26 6.30 - 8.40: 3 8.40 - 10.50: 1 Bond angle restraints: 16051 Sorted by residual: angle pdb=" CB MET C 287 " pdb=" CG MET C 287 " pdb=" SD MET C 287 " ideal model delta sigma weight residual 112.70 102.20 10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C3' A E 66 " pdb=" O3' A E 66 " pdb=" P U E 67 " ideal model delta sigma weight residual 120.20 125.43 -5.23 1.50e+00 4.44e-01 1.22e+01 angle pdb=" CA MET C 287 " pdb=" CB MET C 287 " pdb=" CG MET C 287 " ideal model delta sigma weight residual 114.10 120.41 -6.31 2.00e+00 2.50e-01 9.95e+00 angle pdb=" C3' C E 8 " pdb=" O3' C E 8 " pdb=" P C E 9 " ideal model delta sigma weight residual 120.20 124.82 -4.62 1.50e+00 4.44e-01 9.50e+00 angle pdb=" C3' A H 66 " pdb=" O3' A H 66 " pdb=" P U H 67 " ideal model delta sigma weight residual 120.20 124.34 -4.14 1.50e+00 4.44e-01 7.61e+00 ... (remaining 16046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 6105 35.67 - 71.33: 642 71.33 - 107.00: 37 107.00 - 142.67: 5 142.67 - 178.33: 17 Dihedral angle restraints: 6806 sinusoidal: 4581 harmonic: 2225 Sorted by residual: dihedral pdb=" O4' U H 68 " pdb=" C1' U H 68 " pdb=" N1 U H 68 " pdb=" C2 U H 68 " ideal model delta sinusoidal sigma weight residual 200.00 23.34 176.66 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U E 68 " pdb=" C1' U E 68 " pdb=" N1 U E 68 " pdb=" C2 U E 68 " ideal model delta sinusoidal sigma weight residual 200.00 43.99 156.01 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' C H 65 " pdb=" C1' C H 65 " pdb=" N1 C H 65 " pdb=" C2 C H 65 " ideal model delta sinusoidal sigma weight residual 200.00 71.06 128.94 1 1.50e+01 4.44e-03 6.95e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1466 0.040 - 0.079: 342 0.079 - 0.119: 87 0.119 - 0.159: 17 0.159 - 0.198: 4 Chirality restraints: 1916 Sorted by residual: chirality pdb=" C3' A E 66 " pdb=" C4' A E 66 " pdb=" O3' A E 66 " pdb=" C2' A E 66 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" C1' C H 65 " pdb=" O4' C H 65 " pdb=" C2' C H 65 " pdb=" N1 C H 65 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" C1' C E 65 " pdb=" O4' C E 65 " pdb=" C2' C E 65 " pdb=" N1 C E 65 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 1913 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A E 17 " -0.023 2.00e-02 2.50e+03 1.08e-02 3.19e+00 pdb=" N9 A E 17 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A E 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A E 17 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A E 17 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A E 17 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A E 17 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A E 17 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A E 17 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A E 17 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A E 17 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 80 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C LEU B 80 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU B 80 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 81 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 6 " -0.018 2.00e-02 2.50e+03 8.09e-03 1.80e+00 pdb=" N9 DA D 6 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DA D 6 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA D 6 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA D 6 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA D 6 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA D 6 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA D 6 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA D 6 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA D 6 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA D 6 " 0.002 2.00e-02 2.50e+03 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1933 2.77 - 3.30: 8918 3.30 - 3.84: 18963 3.84 - 4.37: 23081 4.37 - 4.90: 35214 Nonbonded interactions: 88109 Sorted by model distance: nonbonded pdb=" OD1 ASN B 8 " pdb=" NH2 ARG B 11 " model vdw 2.241 3.120 nonbonded pdb=" O TYR C 211 " pdb=" NH2 ARG B 31 " model vdw 2.254 3.120 nonbonded pdb=" O LEU A 39 " pdb=" OG1 THR A 43 " model vdw 2.260 3.040 nonbonded pdb=" NZ LYS B 60 " pdb=" OE2 GLU B 121 " model vdw 2.274 3.120 nonbonded pdb=" O PHE B 287 " pdb=" OG SER B 290 " model vdw 2.276 3.040 ... (remaining 88104 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' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.350 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.005 0.041 11190 Z= 0.280 Angle : 0.626 10.501 16051 Z= 0.335 Chirality : 0.039 0.198 1916 Planarity : 0.004 0.045 1259 Dihedral : 24.075 178.334 5372 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.30), residues: 750 helix: 0.89 (0.27), residues: 394 sheet: 1.50 (0.64), residues: 62 loop : -1.26 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 284 HIS 0.005 0.001 HIS B 280 PHE 0.013 0.002 PHE B 92 TYR 0.013 0.001 TYR B 179 ARG 0.005 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.879 Fit side-chains REVERT: A 45 ASP cc_start: 0.7618 (m-30) cc_final: 0.7343 (m-30) REVERT: A 231 LYS cc_start: 0.6377 (mptt) cc_final: 0.6075 (mptt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 1.3027 time to fit residues: 124.6852 Evaluate side-chains 63 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.0040 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.146309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.098713 restraints weight = 14499.300| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.69 r_work: 0.3132 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11190 Z= 0.279 Angle : 0.626 8.919 16051 Z= 0.333 Chirality : 0.039 0.196 1916 Planarity : 0.005 0.037 1259 Dihedral : 26.279 179.704 3825 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.47 % Allowed : 8.65 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.30), residues: 750 helix: 0.97 (0.26), residues: 402 sheet: 2.00 (0.62), residues: 58 loop : -1.46 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.014 0.001 TYR B 179 ARG 0.007 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8062 (m-30) cc_final: 0.7666 (m-30) REVERT: A 62 MET cc_start: 0.7391 (pmm) cc_final: 0.6626 (ppp) REVERT: A 119 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: A 231 LYS cc_start: 0.6095 (mptt) cc_final: 0.5825 (mptt) REVERT: B 251 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7673 (mm-30) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 1.2540 time to fit residues: 94.9530 Evaluate side-chains 72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.098902 restraints weight = 14819.061| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.78 r_work: 0.3142 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11190 Z= 0.235 Angle : 0.601 8.711 16051 Z= 0.321 Chirality : 0.038 0.195 1916 Planarity : 0.004 0.035 1259 Dihedral : 26.243 179.720 3825 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.76 % Allowed : 10.26 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.30), residues: 750 helix: 0.99 (0.26), residues: 400 sheet: 2.00 (0.61), residues: 58 loop : -1.50 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 284 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE B 92 TYR 0.012 0.001 TYR B 179 ARG 0.006 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.8048 (m-30) cc_final: 0.7679 (m-30) REVERT: A 62 MET cc_start: 0.7386 (pmm) cc_final: 0.6662 (ppp) REVERT: A 119 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: A 231 LYS cc_start: 0.6094 (mptt) cc_final: 0.5789 (mptt) REVERT: C 249 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7700 (m-40) REVERT: B 251 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: B 282 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7856 (ttp-170) outliers start: 12 outliers final: 4 residues processed: 72 average time/residue: 1.3943 time to fit residues: 107.7798 Evaluate side-chains 71 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.148741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100774 restraints weight = 14738.871| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.74 r_work: 0.3175 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11190 Z= 0.163 Angle : 0.576 8.493 16051 Z= 0.307 Chirality : 0.037 0.190 1916 Planarity : 0.004 0.047 1259 Dihedral : 26.206 179.458 3825 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.32 % Allowed : 11.44 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.30), residues: 750 helix: 1.17 (0.26), residues: 400 sheet: 2.09 (0.62), residues: 58 loop : -1.38 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 PHE 0.012 0.001 PHE B 92 TYR 0.010 0.001 TYR B 179 ARG 0.008 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7909 (m-30) cc_final: 0.7602 (m-30) REVERT: A 62 MET cc_start: 0.7382 (pmm) cc_final: 0.6643 (ppp) REVERT: A 119 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8381 (m-30) REVERT: A 231 LYS cc_start: 0.6038 (mptt) cc_final: 0.5634 (mptt) REVERT: B 251 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: B 282 ARG cc_start: 0.8136 (ttm110) cc_final: 0.7840 (ttp-170) outliers start: 9 outliers final: 3 residues processed: 72 average time/residue: 1.2910 time to fit residues: 100.3066 Evaluate side-chains 74 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 0.0670 chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.145507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097045 restraints weight = 14750.748| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.79 r_work: 0.3117 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11190 Z= 0.330 Angle : 0.640 10.158 16051 Z= 0.340 Chirality : 0.040 0.201 1916 Planarity : 0.004 0.039 1259 Dihedral : 26.231 179.074 3825 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.35 % Allowed : 11.88 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.30), residues: 750 helix: 1.13 (0.26), residues: 396 sheet: 1.93 (0.61), residues: 58 loop : -1.51 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 284 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.015 0.002 TYR B 179 ARG 0.008 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7990 (m-30) cc_final: 0.7680 (m-30) REVERT: A 119 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: A 231 LYS cc_start: 0.6101 (mptt) cc_final: 0.5793 (mptt) REVERT: C 249 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7662 (m-40) REVERT: B 251 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: B 282 ARG cc_start: 0.8190 (ttm110) cc_final: 0.7874 (ttp-170) outliers start: 16 outliers final: 8 residues processed: 77 average time/residue: 1.3712 time to fit residues: 114.0026 Evaluate side-chains 79 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 78 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 57 optimal weight: 0.0270 chunk 33 optimal weight: 7.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.147841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099893 restraints weight = 14812.213| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.75 r_work: 0.3169 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11190 Z= 0.191 Angle : 0.587 9.255 16051 Z= 0.312 Chirality : 0.037 0.189 1916 Planarity : 0.004 0.038 1259 Dihedral : 26.187 179.850 3825 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.61 % Allowed : 12.76 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.30), residues: 750 helix: 1.23 (0.27), residues: 398 sheet: 2.02 (0.63), residues: 58 loop : -1.47 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE B 92 TYR 0.010 0.001 TYR B 179 ARG 0.009 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7876 (m-30) cc_final: 0.7587 (m-30) REVERT: A 62 MET cc_start: 0.7374 (pmm) cc_final: 0.5904 (ttp) REVERT: A 119 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: A 231 LYS cc_start: 0.6123 (mptt) cc_final: 0.5804 (mptt) REVERT: B 251 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: B 282 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7850 (ttp-170) outliers start: 11 outliers final: 6 residues processed: 71 average time/residue: 1.2943 time to fit residues: 99.3489 Evaluate side-chains 75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 83 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.146359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098560 restraints weight = 14769.720| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.74 r_work: 0.3141 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11190 Z= 0.252 Angle : 0.603 9.130 16051 Z= 0.320 Chirality : 0.038 0.196 1916 Planarity : 0.004 0.036 1259 Dihedral : 26.161 179.599 3825 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.91 % Allowed : 13.05 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.30), residues: 750 helix: 1.24 (0.27), residues: 400 sheet: 1.25 (0.58), residues: 68 loop : -1.44 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.013 0.001 TYR B 179 ARG 0.008 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7906 (m-30) cc_final: 0.7636 (m-30) REVERT: A 119 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8390 (m-30) REVERT: A 231 LYS cc_start: 0.6171 (mptt) cc_final: 0.5860 (mptt) REVERT: B 251 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: B 282 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7927 (ttp-170) outliers start: 13 outliers final: 7 residues processed: 75 average time/residue: 1.3599 time to fit residues: 109.7797 Evaluate side-chains 75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 77 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.147395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099365 restraints weight = 14765.212| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.75 r_work: 0.3159 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11190 Z= 0.196 Angle : 0.594 10.132 16051 Z= 0.316 Chirality : 0.037 0.192 1916 Planarity : 0.004 0.040 1259 Dihedral : 26.151 179.878 3825 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.61 % Allowed : 13.20 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.31), residues: 750 helix: 1.30 (0.27), residues: 400 sheet: 1.29 (0.58), residues: 68 loop : -1.41 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE B 92 TYR 0.015 0.001 TYR C 218 ARG 0.009 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7871 (m-30) cc_final: 0.7600 (m-30) REVERT: A 119 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8353 (m-30) REVERT: A 207 LYS cc_start: 0.8247 (ptmm) cc_final: 0.7924 (pttp) REVERT: A 231 LYS cc_start: 0.6123 (mptt) cc_final: 0.5804 (mptt) REVERT: C 242 SER cc_start: 0.8344 (t) cc_final: 0.7966 (m) REVERT: B 251 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: B 282 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7898 (ttp-170) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 1.2961 time to fit residues: 98.1665 Evaluate side-chains 75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 76 optimal weight: 0.0870 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.147628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099598 restraints weight = 14846.428| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.75 r_work: 0.3149 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11190 Z= 0.192 Angle : 0.590 10.529 16051 Z= 0.313 Chirality : 0.037 0.192 1916 Planarity : 0.004 0.036 1259 Dihedral : 26.143 179.855 3825 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.32 % Allowed : 13.34 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.31), residues: 750 helix: 1.32 (0.27), residues: 400 sheet: 1.31 (0.59), residues: 68 loop : -1.40 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE B 92 TYR 0.014 0.001 TYR C 218 ARG 0.008 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7885 (m-30) cc_final: 0.7613 (m-30) REVERT: A 119 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: A 207 LYS cc_start: 0.8250 (ptmm) cc_final: 0.7924 (pttp) REVERT: A 231 LYS cc_start: 0.6067 (mptt) cc_final: 0.5749 (mptt) REVERT: C 242 SER cc_start: 0.8305 (t) cc_final: 0.7934 (m) REVERT: B 251 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: B 282 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7886 (ttp-170) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 1.4632 time to fit residues: 111.4069 Evaluate side-chains 74 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 11 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.0470 chunk 77 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 88 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 60 optimal weight: 0.4980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.148774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100888 restraints weight = 14798.287| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.75 r_work: 0.3176 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11190 Z= 0.156 Angle : 0.583 9.881 16051 Z= 0.309 Chirality : 0.036 0.188 1916 Planarity : 0.004 0.043 1259 Dihedral : 26.129 179.790 3825 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.17 % Allowed : 13.78 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.31), residues: 750 helix: 1.39 (0.27), residues: 398 sheet: 1.37 (0.59), residues: 68 loop : -1.38 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 PHE 0.012 0.001 PHE B 92 TYR 0.025 0.001 TYR C 218 ARG 0.010 0.000 ARG C 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7850 (m-30) cc_final: 0.7585 (m-30) REVERT: A 62 MET cc_start: 0.7307 (pmm) cc_final: 0.5872 (ttp) REVERT: A 119 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: A 207 LYS cc_start: 0.8241 (ptmm) cc_final: 0.7919 (pttp) REVERT: A 231 LYS cc_start: 0.6038 (mptt) cc_final: 0.5608 (mptt) REVERT: C 242 SER cc_start: 0.8291 (t) cc_final: 0.7932 (m) REVERT: B 251 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: B 282 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7899 (ttp-170) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 1.3649 time to fit residues: 99.9776 Evaluate side-chains 71 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 55 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.146750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098538 restraints weight = 14761.106| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.75 r_work: 0.3149 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11190 Z= 0.256 Angle : 0.609 10.643 16051 Z= 0.322 Chirality : 0.038 0.196 1916 Planarity : 0.004 0.036 1259 Dihedral : 26.119 179.836 3825 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.32 % Allowed : 13.93 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.31), residues: 750 helix: 1.33 (0.27), residues: 400 sheet: 1.28 (0.58), residues: 68 loop : -1.40 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.013 0.001 TYR C 218 ARG 0.009 0.000 ARG C 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7770.25 seconds wall clock time: 137 minutes 29.11 seconds (8249.11 seconds total)