Starting phenix.real_space_refine on Fri Sep 11 12:44:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v9u_31827/09_2026/7v9u_31827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v9u_31827/09_2026/7v9u_31827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v9u_31827/09_2026/7v9u_31827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v9u_31827/09_2026/7v9u_31827.map" model { file = "/net/cci-nas-00/data/ceres_data/7v9u_31827/09_2026/7v9u_31827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v9u_31827/09_2026/7v9u_31827.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7v9u_31827/09_2026/7v9u_31827.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v9u_31827/09_2026/7v9u_31827.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.060 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 209 5.49 5 S 18 5.16 5 C 5183 2.51 5 N 1687 2.21 5 O 2257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9354 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2478 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain: "B" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2478 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} 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: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1205 Classifications: {'RNAv2': 57} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 8, 'rna3p_pur': 22, 'rna3p_pyr': 24} Link IDs: {'rna2p': 11, 'rna3p': 45} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNAv2': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "C" 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: "G" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNAv2': 58} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 10, 'rna3p_pur': 21, 'rna3p_pyr': 23} Link IDs: {'rna2p': 14, 'rna3p': 43} Chain breaks: 1 Chain: "H" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNAv2': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Time building chain proxies: 1.92, per 1000 atoms: 0.21 Number of scatterers: 9354 At special positions: 0 Unit cell: (123.25, 153, 93.5, 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 18 16.00 P 209 15.00 O 2257 8.00 N 1687 7.00 C 5183 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: 0.74 Conformation dependent library (CDL) restraints added in 196.8 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 58.6% alpha, 9.4% beta 65 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.725A pdb=" N ASN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 33 through 42 removed outlier: 3.674A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.645A pdb=" N PHE A 46 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.521A pdb=" N ALA A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.905A pdb=" N LEU A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) No H-bonds generated for '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 129 through 137 removed outlier: 3.728A pdb=" N PHE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.662A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.644A pdb=" N ASP A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 224 removed outlier: 3.588A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.998A pdb=" N GLY A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 272 removed outlier: 3.813A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.732A pdb=" N ILE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 310 removed outlier: 3.812A pdb=" N HIS A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 removed outlier: 3.706A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 33 through 42 Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.544A pdb=" N PHE B 46 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.576A pdb=" N ALA B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.508A pdb=" N ALA B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) 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 129 through 139 removed outlier: 3.735A pdb=" N PHE B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 4.019A 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 removed outlier: 3.653A pdb=" N LEU B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.633A pdb=" N ASP B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.644A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 257 through 272 removed outlier: 4.795A pdb=" N ILE B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 removed outlier: 4.146A pdb=" N HIS B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 277 through 281' Processing helix chain 'B' and resid 284 through 292 removed outlier: 4.025A pdb=" N ILE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.641A pdb=" N HIS B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 53 removed outlier: 3.784A 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 120 through 121 removed outlier: 4.733A pdb=" N VAL A 226 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.951A pdb=" N ARG B 61 " --> pdb=" O LYS B 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 195 removed outlier: 3.575A pdb=" N PHE B 114 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 121 removed outlier: 4.761A pdb=" N VAL B 226 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 226 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 163 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.98 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: 1851 1.33 - 1.45: 3295 1.45 - 1.57: 4394 1.57 - 1.69: 408 1.69 - 1.81: 26 Bond restraints: 9974 Sorted by residual: bond pdb=" C3' DG D 73 " pdb=" C2' DG D 73 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.40e+00 bond pdb=" C3' DA C 7 " pdb=" C2' DA C 7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.71e+00 bond pdb=" C3' DG C 73 " pdb=" C2' DG C 73 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.46e+00 bond pdb=" C4' DC C 83 " pdb=" C3' DC C 83 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.00e-02 1.00e+04 8.29e+00 bond pdb=" C3' DA D 7 " pdb=" C2' DA D 7 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.27e+00 ... (remaining 9969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 13310 1.51 - 3.01: 856 3.01 - 4.52: 187 4.52 - 6.02: 57 6.02 - 7.53: 6 Bond angle restraints: 14416 Sorted by residual: angle pdb=" N3 DT C 16 " pdb=" C4 DT C 16 " pdb=" O4 DT C 16 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT D 16 " pdb=" C4 DT D 16 " pdb=" O4 DT D 16 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT C 82 " pdb=" C4 DT C 82 " pdb=" O4 DT C 82 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT D 82 " pdb=" C4 DT D 82 " pdb=" O4 DT D 82 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT D 78 " pdb=" C4 DT D 78 " pdb=" O4 DT D 78 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 14411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 4948 35.76 - 71.51: 566 71.51 - 107.26: 28 107.26 - 143.02: 3 143.02 - 178.77: 3 Dihedral angle restraints: 5548 sinusoidal: 3744 harmonic: 1804 Sorted by residual: dihedral pdb=" C4' C G 55 " pdb=" C3' C G 55 " pdb=" C2' C G 55 " pdb=" C1' C G 55 " ideal model delta sinusoidal sigma weight residual 36.34 -39.14 75.49 1 3.10e+00 1.04e-01 7.49e+02 dihedral pdb=" C4' C G 39 " pdb=" C3' C G 39 " pdb=" C2' C G 39 " pdb=" C1' C G 39 " ideal model delta sinusoidal sigma weight residual 36.35 -38.46 74.80 1 3.10e+00 1.04e-01 7.37e+02 dihedral pdb=" C4' C E 39 " pdb=" C3' C E 39 " pdb=" C2' C E 39 " pdb=" C1' C E 39 " ideal model delta sinusoidal sigma weight residual 36.34 -38.45 74.80 1 3.10e+00 1.04e-01 7.37e+02 ... (remaining 5545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1357 0.067 - 0.134: 176 0.134 - 0.200: 12 0.200 - 0.267: 151 0.267 - 0.334: 35 Chirality restraints: 1731 Sorted by residual: chirality pdb=" C3' C G 55 " pdb=" C4' C G 55 " pdb=" O3' C G 55 " pdb=" C2' C G 55 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" P C G 9 " pdb=" OP1 C G 9 " pdb=" OP2 C G 9 " pdb=" O5' C G 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" C3' C E 55 " pdb=" C4' C E 55 " pdb=" O3' C E 55 " pdb=" C2' C E 55 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1728 not shown) Planarity restraints: 1057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 236 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO A 237 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 220 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO B 221 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A E 13 " 0.021 2.00e-02 2.50e+03 9.76e-03 2.62e+00 pdb=" N9 A E 13 " -0.022 2.00e-02 2.50e+03 pdb=" C8 A E 13 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A E 13 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A E 13 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A E 13 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A E 13 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A E 13 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A E 13 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A E 13 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A E 13 " -0.002 2.00e-02 2.50e+03 ... (remaining 1054 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 737 2.72 - 3.27: 8464 3.27 - 3.81: 16545 3.81 - 4.36: 20877 4.36 - 4.90: 31372 Nonbonded interactions: 77995 Sorted by model distance: nonbonded pdb=" O THR A 301 " pdb=" OG SER A 304 " model vdw 2.180 3.040 nonbonded pdb=" O ASN B 142 " pdb=" OG SER B 146 " model vdw 2.187 3.040 nonbonded pdb=" O THR B 301 " pdb=" OG SER B 304 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP A 292 " pdb=" OG SER A 295 " model vdw 2.191 3.040 nonbonded pdb=" O SER A 218 " pdb=" O2' G F 1 " model vdw 2.197 3.040 ... (remaining 77990 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 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 9 through 81) } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 2.170 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.540 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 0.043 9974 Z= 0.363 Angle : 0.880 7.531 14416 Z= 0.490 Chirality : 0.090 0.334 1731 Planarity : 0.005 0.053 1057 Dihedral : 23.344 178.775 4388 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.32), residues: 614 helix: -0.90 (0.29), residues: 308 sheet: 0.62 (0.69), residues: 62 loop : -1.46 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 297 TYR 0.011 0.001 TYR A 179 PHE 0.025 0.002 PHE B 92 TRP 0.015 0.003 TRP B 284 HIS 0.009 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.36 ( 9974) covalent geometry : angle 0.88019 / 0.49 (14416) hydrogen bonds : bond 0.12549 / 8.09 ( 389) hydrogen bonds : angle 4.88678 / 3.44 ( 939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.6634 (pttp) cc_final: 0.6325 (mtmm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1654 time to fit residues: 13.3713 Evaluate side-chains 50 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0010 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.188453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.146975 restraints weight = 15102.408| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.60 r_work: 0.3715 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9974 Z= 0.231 Angle : 1.328 23.035 14416 Z= 0.536 Chirality : 0.132 1.269 1731 Planarity : 0.005 0.047 1057 Dihedral : 23.771 177.784 3146 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.18 % Allowed : 7.61 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.32), residues: 614 helix: -0.36 (0.29), residues: 312 sheet: 0.78 (0.69), residues: 62 loop : -1.39 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 282 TYR 0.014 0.001 TYR A 302 PHE 0.015 0.001 PHE B 92 TRP 0.008 0.002 TRP B 284 HIS 0.005 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.23 ( 9974) covalent geometry : angle 1.32829 / 0.54 (14416) hydrogen bonds : bond 0.05704 / 3.67 ( 389) hydrogen bonds : angle 3.76436 / 2.70 ( 939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7205 (pttp) cc_final: 0.6617 (tmtt) REVERT: B 282 ARG cc_start: 0.7443 (mtm-85) cc_final: 0.7152 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 0.1498 time to fit residues: 10.3340 Evaluate side-chains 49 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 202 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.189006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.146658 restraints weight = 14931.880| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.67 r_work: 0.3721 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9974 Z= 0.172 Angle : 1.015 14.088 14416 Z= 0.427 Chirality : 0.097 1.031 1731 Planarity : 0.005 0.050 1057 Dihedral : 23.895 179.050 3146 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.54 % Allowed : 11.23 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.33), residues: 614 helix: -0.10 (0.29), residues: 310 sheet: 0.86 (0.69), residues: 62 loop : -1.34 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.012 0.001 TYR A 302 PHE 0.014 0.001 PHE B 92 TRP 0.008 0.002 TRP A 284 HIS 0.008 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 ( 9974) covalent geometry : angle 1.01500 / 0.43 (14416) hydrogen bonds : bond 0.05196 / 3.28 ( 389) hydrogen bonds : angle 3.54619 / 2.56 ( 939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 LYS cc_start: 0.7348 (pttp) cc_final: 0.6743 (tmtt) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.1171 time to fit residues: 8.4921 Evaluate side-chains 51 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 202 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.187583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.144589 restraints weight = 14988.594| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.41 r_work: 0.3711 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9974 Z= 0.185 Angle : 0.979 11.946 14416 Z= 0.416 Chirality : 0.086 0.964 1731 Planarity : 0.005 0.049 1057 Dihedral : 23.727 177.757 3146 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.45 % Allowed : 12.50 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.33), residues: 614 helix: -0.17 (0.29), residues: 310 sheet: 0.69 (0.68), residues: 62 loop : -1.45 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.020 0.002 TYR A 302 PHE 0.014 0.002 PHE B 92 TRP 0.006 0.002 TRP B 284 HIS 0.008 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 9974) covalent geometry : angle 0.97861 / 0.42 (14416) hydrogen bonds : bond 0.05220 / 3.28 ( 389) hydrogen bonds : angle 3.56489 / 2.56 ( 939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.1332 time to fit residues: 9.5918 Evaluate side-chains 53 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.185841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.142729 restraints weight = 14810.871| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.72 r_work: 0.3655 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9974 Z= 0.214 Angle : 0.988 12.023 14416 Z= 0.425 Chirality : 0.084 0.928 1731 Planarity : 0.005 0.051 1057 Dihedral : 23.695 177.511 3146 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.45 % Allowed : 14.31 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.32), residues: 614 helix: -0.39 (0.28), residues: 310 sheet: 0.50 (0.68), residues: 62 loop : -1.62 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.011 0.002 TYR A 179 PHE 0.015 0.002 PHE B 92 TRP 0.008 0.002 TRP B 284 HIS 0.008 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 ( 9974) covalent geometry : angle 0.98800 / 0.42 (14416) hydrogen bonds : bond 0.05624 / 3.55 ( 389) hydrogen bonds : angle 3.66494 / 2.62 ( 939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.236 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.1335 time to fit residues: 9.5567 Evaluate side-chains 56 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 HIS B 280 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.189307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.146410 restraints weight = 14917.490| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.41 r_work: 0.3736 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9974 Z= 0.147 Angle : 0.911 11.497 14416 Z= 0.388 Chirality : 0.077 0.847 1731 Planarity : 0.004 0.046 1057 Dihedral : 23.737 179.713 3146 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.27 % Allowed : 15.04 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.33), residues: 614 helix: -0.06 (0.29), residues: 312 sheet: 0.67 (0.69), residues: 62 loop : -1.36 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 282 TYR 0.011 0.001 TYR A 302 PHE 0.009 0.001 PHE B 92 TRP 0.009 0.002 TRP A 78 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 ( 9974) covalent geometry : angle 0.91115 / 0.39 (14416) hydrogen bonds : bond 0.04887 / 3.01 ( 389) hydrogen bonds : angle 3.42450 / 2.49 ( 939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.1307 time to fit residues: 9.9907 Evaluate side-chains 56 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.187661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.144641 restraints weight = 14895.093| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.51 r_work: 0.3688 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9974 Z= 0.177 Angle : 0.922 11.628 14416 Z= 0.395 Chirality : 0.077 0.846 1731 Planarity : 0.005 0.049 1057 Dihedral : 23.614 178.113 3146 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.81 % Allowed : 14.86 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.33), residues: 614 helix: -0.16 (0.29), residues: 312 sheet: 0.64 (0.69), residues: 62 loop : -1.41 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 31 TYR 0.016 0.002 TYR A 302 PHE 0.012 0.002 PHE B 92 TRP 0.007 0.002 TRP B 284 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 9974) covalent geometry : angle 0.92190 / 0.40 (14416) hydrogen bonds : bond 0.05307 / 3.31 ( 389) hydrogen bonds : angle 3.49578 / 2.52 ( 939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 60 average time/residue: 0.1340 time to fit residues: 10.6831 Evaluate side-chains 58 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.188994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.145844 restraints weight = 14885.756| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.40 r_work: 0.3727 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9974 Z= 0.148 Angle : 0.900 11.439 14416 Z= 0.384 Chirality : 0.076 0.827 1731 Planarity : 0.005 0.047 1057 Dihedral : 23.635 179.093 3146 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.99 % Allowed : 15.40 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.33), residues: 614 helix: -0.01 (0.29), residues: 312 sheet: 0.69 (0.69), residues: 62 loop : -1.34 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 31 TYR 0.017 0.001 TYR A 302 PHE 0.010 0.001 PHE B 92 TRP 0.008 0.002 TRP A 78 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 9974) covalent geometry : angle 0.90041 / 0.38 (14416) hydrogen bonds : bond 0.05011 / 3.09 ( 389) hydrogen bonds : angle 3.42899 / 2.49 ( 939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.1270 time to fit residues: 9.5430 Evaluate side-chains 61 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.0070 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.188686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.145786 restraints weight = 14864.262| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.46 r_work: 0.3716 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9974 Z= 0.160 Angle : 0.903 11.433 14416 Z= 0.387 Chirality : 0.075 0.800 1731 Planarity : 0.005 0.053 1057 Dihedral : 23.557 178.755 3146 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.99 % Allowed : 15.58 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.33), residues: 614 helix: -0.07 (0.29), residues: 312 sheet: 0.69 (0.69), residues: 62 loop : -1.36 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.020 0.001 TYR A 302 PHE 0.011 0.002 PHE B 215 TRP 0.008 0.002 TRP A 78 HIS 0.007 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 9974) covalent geometry : angle 0.90344 / 0.39 (14416) hydrogen bonds : bond 0.05138 / 3.17 ( 389) hydrogen bonds : angle 3.43308 / 2.49 ( 939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 57 average time/residue: 0.1340 time to fit residues: 10.1191 Evaluate side-chains 57 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 21 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.189803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147048 restraints weight = 14899.034| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.38 r_work: 0.3746 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9974 Z= 0.143 Angle : 0.890 11.288 14416 Z= 0.380 Chirality : 0.074 0.790 1731 Planarity : 0.005 0.068 1057 Dihedral : 23.564 179.326 3146 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.63 % Allowed : 16.12 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.33), residues: 614 helix: 0.09 (0.29), residues: 312 sheet: 0.75 (0.69), residues: 62 loop : -1.28 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 31 TYR 0.017 0.001 TYR B 260 PHE 0.009 0.001 PHE B 92 TRP 0.009 0.002 TRP A 78 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 9974) covalent geometry : angle 0.88995 / 0.38 (14416) hydrogen bonds : bond 0.04914 / 3.01 ( 389) hydrogen bonds : angle 3.37442 / 2.46 ( 939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 55 average time/residue: 0.1352 time to fit residues: 9.8138 Evaluate side-chains 58 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 298 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 0.0270 chunk 53 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 0.0670 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.191259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.149210 restraints weight = 14873.781| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.53 r_work: 0.3755 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9974 Z= 0.137 Angle : 0.878 11.156 14416 Z= 0.375 Chirality : 0.072 0.752 1731 Planarity : 0.004 0.047 1057 Dihedral : 23.529 179.886 3146 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.45 % Allowed : 16.30 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.33), residues: 614 helix: 0.23 (0.30), residues: 312 sheet: 0.87 (0.69), residues: 62 loop : -1.19 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 31 TYR 0.015 0.001 TYR B 260 PHE 0.008 0.001 PHE B 92 TRP 0.009 0.001 TRP B 78 HIS 0.006 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 ( 9974) covalent geometry : angle 0.87831 / 0.37 (14416) hydrogen bonds : bond 0.04821 / 2.93 ( 389) hydrogen bonds : angle 3.29423 / 2.42 ( 939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.04 seconds wall clock time: 38 minutes 39.33 seconds (2319.33 seconds total)