Starting phenix.real_space_refine on Wed Feb 4 09:11:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kld_62401/02_2026/9kld_62401.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kld_62401/02_2026/9kld_62401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kld_62401/02_2026/9kld_62401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kld_62401/02_2026/9kld_62401.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kld_62401/02_2026/9kld_62401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kld_62401/02_2026/9kld_62401.map" } resolution = 2.9 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6072 2.51 5 N 1656 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9594 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1045 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain breaks: 2 Chain: "A" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2094 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 15, 'TRANS': 253} Chain: "C" Number of atoms: 5007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5007 Classifications: {'peptide': 641} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 608} Chain breaks: 1 Chain: "D" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1441 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'GR2': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GR2:plan-1': 1, 'GR2:plan-2': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.80, per 1000 atoms: 0.19 Number of scatterers: 9594 At special positions: 0 Unit cell: (89.79, 99.28, 125.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1800 8.00 N 1656 7.00 C 6072 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 465.8 milliseconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 48.1% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 19 through 26 removed outlier: 3.656A pdb=" N ALA B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 48 through 64 removed outlier: 3.647A pdb=" N LEU B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 removed outlier: 3.560A pdb=" N MET B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 109 Processing helix chain 'B' and resid 110 through 126 removed outlier: 3.635A pdb=" N MET B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 65 through 68 removed outlier: 3.658A pdb=" N SER A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 69 through 84 removed outlier: 4.156A pdb=" N TYR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 135 through 155 removed outlier: 3.682A pdb=" N MET A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.650A pdb=" N PHE A 179 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 199 through 205 removed outlier: 4.137A pdb=" N GLY A 203 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.937A pdb=" N GLU A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 252 through 266 Proline residue: A 258 - end of helix Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 54 through 62 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 121 through 132 removed outlier: 4.220A pdb=" N GLY C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.507A pdb=" N ILE C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 176 through 181 removed outlier: 3.565A pdb=" N LEU C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 209 Processing helix chain 'C' and resid 211 through 218 removed outlier: 3.562A pdb=" N LEU C 218 " --> pdb=" O PHE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.356A pdb=" N PHE C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.608A pdb=" N ASN C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 547 through 553 removed outlier: 4.496A pdb=" N ALA C 551 " --> pdb=" O THR C 547 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 590 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.919A pdb=" N TRP C 620 " --> pdb=" O ASP C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 removed outlier: 3.599A pdb=" N GLU C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 680 Processing helix chain 'C' and resid 681 through 685 Processing helix chain 'C' and resid 710 through 723 Processing helix chain 'D' and resid 608 through 621 removed outlier: 4.836A pdb=" N GLY D 615 " --> pdb=" O LYS D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 640 Processing helix chain 'D' and resid 661 through 677 Processing helix chain 'D' and resid 696 through 700 removed outlier: 3.535A pdb=" N PHE D 699 " --> pdb=" O ASN D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 715 Processing helix chain 'D' and resid 729 through 743 Processing helix chain 'D' and resid 862 through 866 Processing helix chain 'D' and resid 867 through 869 No H-bonds generated for 'chain 'D' and resid 867 through 869' Processing helix chain 'D' and resid 870 through 877 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.473A pdb=" N CYS A 89 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 116 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR A 91 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 118 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A 93 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.981A pdb=" N LEU C 79 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 138 " --> pdb=" O LYS C 162 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL C 164 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 140 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU C 161 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU C 194 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 163 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER C 196 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE C 363 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N ASN C 336 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 469 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 466 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N TRP C 539 " --> pdb=" O LEU C 466 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE C 468 " --> pdb=" O TRP C 539 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N PHE C 541 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLY C 601 " --> pdb=" O VAL C 567 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLY C 569 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE C 603 " --> pdb=" O GLY C 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 682 through 685 removed outlier: 6.419A pdb=" N ILE D 682 " --> pdb=" O LEU D 721 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU D 723 " --> pdb=" O ILE D 682 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE D 684 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TRP D 654 " --> pdb=" O ASP D 879 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL D 881 " --> pdb=" O TRP D 654 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU D 656 " --> pdb=" O VAL D 881 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 744 through 746 420 hydrogen bonds defined for protein. 1161 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 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: 1.18 - 1.31: 1616 1.31 - 1.44: 2460 1.44 - 1.57: 5603 1.57 - 1.69: 1 1.69 - 1.82: 100 Bond restraints: 9780 Sorted by residual: bond pdb=" C14 GR2 A 301 " pdb=" C15 GR2 A 301 " ideal model delta sigma weight residual 1.327 1.439 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" CA SER C 184 " pdb=" CB SER C 184 " ideal model delta sigma weight residual 1.532 1.470 0.062 1.74e-02 3.30e+03 1.28e+01 bond pdb=" C16 GR2 A 301 " pdb=" O5 GR2 A 301 " ideal model delta sigma weight residual 1.350 1.418 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C13 GR2 A 301 " pdb=" O5 GR2 A 301 " ideal model delta sigma weight residual 1.413 1.475 -0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" CA THR D 763 " pdb=" C THR D 763 " ideal model delta sigma weight residual 1.525 1.493 0.031 1.25e-02 6.40e+03 6.33e+00 ... (remaining 9775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 13039 2.35 - 4.70: 180 4.70 - 7.04: 19 7.04 - 9.39: 6 9.39 - 11.74: 2 Bond angle restraints: 13246 Sorted by residual: angle pdb=" C THR C 188 " pdb=" N LEU C 189 " pdb=" CA LEU C 189 " ideal model delta sigma weight residual 121.02 113.80 7.22 1.48e+00 4.57e-01 2.38e+01 angle pdb=" N LEU C 189 " pdb=" CA LEU C 189 " pdb=" CB LEU C 189 " ideal model delta sigma weight residual 109.51 116.61 -7.10 1.58e+00 4.01e-01 2.02e+01 angle pdb=" N LEU C 189 " pdb=" CA LEU C 189 " pdb=" C LEU C 189 " ideal model delta sigma weight residual 109.96 103.48 6.48 1.49e+00 4.50e-01 1.89e+01 angle pdb=" N LEU B 83 " pdb=" CA LEU B 83 " pdb=" C LEU B 83 " ideal model delta sigma weight residual 114.56 109.43 5.13 1.27e+00 6.20e-01 1.63e+01 angle pdb=" CB MET B 32 " pdb=" CG MET B 32 " pdb=" SD MET B 32 " ideal model delta sigma weight residual 112.70 124.44 -11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 13241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5343 17.97 - 35.93: 433 35.93 - 53.90: 135 53.90 - 71.86: 15 71.86 - 89.83: 12 Dihedral angle restraints: 5938 sinusoidal: 2385 harmonic: 3553 Sorted by residual: dihedral pdb=" CA ASP D 726 " pdb=" CB ASP D 726 " pdb=" CG ASP D 726 " pdb=" OD1 ASP D 726 " ideal model delta sinusoidal sigma weight residual -30.00 -88.85 58.85 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CB GLU C 621 " pdb=" CG GLU C 621 " pdb=" CD GLU C 621 " pdb=" OE1 GLU C 621 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG D 644 " pdb=" CD ARG D 644 " pdb=" NE ARG D 644 " pdb=" CZ ARG D 644 " ideal model delta sinusoidal sigma weight residual -180.00 -135.43 -44.57 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 5935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1121 0.044 - 0.089: 292 0.089 - 0.133: 95 0.133 - 0.178: 5 0.178 - 0.222: 2 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA CYS C 186 " pdb=" N CYS C 186 " pdb=" C CYS C 186 " pdb=" CB CYS C 186 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA GLU C 185 " pdb=" N GLU C 185 " pdb=" C GLU C 185 " pdb=" CB GLU C 185 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA HIS D 767 " pdb=" N HIS D 767 " pdb=" C HIS D 767 " pdb=" CB HIS D 767 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 1512 not shown) Planarity restraints: 1700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 723 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.86e+01 pdb=" C ARG C 723 " 0.075 2.00e-02 2.50e+03 pdb=" O ARG C 723 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG C 724 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 746 " -0.295 9.50e-02 1.11e+02 1.32e-01 1.08e+01 pdb=" NE ARG D 746 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG D 746 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 746 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 746 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 724 " 0.234 9.50e-02 1.11e+02 1.05e-01 6.76e+00 pdb=" NE ARG C 724 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 724 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 724 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 724 " 0.009 2.00e-02 2.50e+03 ... (remaining 1697 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 387 2.72 - 3.26: 9635 3.26 - 3.81: 15890 3.81 - 4.35: 20351 4.35 - 4.90: 33805 Nonbonded interactions: 80068 Sorted by model distance: nonbonded pdb=" N GLU C 686 " pdb=" OE1 GLU C 686 " model vdw 2.173 3.120 nonbonded pdb=" O SER A 119 " pdb=" OG SER A 119 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 67 " pdb=" OD2 ASP A 76 " model vdw 2.237 3.040 nonbonded pdb=" N ASP C 202 " pdb=" OD1 ASP C 202 " model vdw 2.269 3.120 nonbonded pdb=" NZ LYS B 111 " pdb=" OD1 ASN B 112 " model vdw 2.272 3.120 ... (remaining 80063 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.810 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.030 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 9781 Z= 0.190 Angle : 0.623 11.740 13246 Z= 0.345 Chirality : 0.043 0.222 1515 Planarity : 0.005 0.132 1700 Dihedral : 14.930 89.831 3634 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.51 % Allowed : 17.62 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 0.51 (0.25), residues: 1211 helix: 0.90 (0.24), residues: 512 sheet: -0.23 (0.38), residues: 208 loop : 0.18 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 61 TYR 0.011 0.001 TYR B 58 PHE 0.019 0.001 PHE D 717 TRP 0.007 0.001 TRP D 766 HIS 0.008 0.001 HIS D 767 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9780) covalent geometry : angle 0.62327 (13246) hydrogen bonds : bond 0.16935 ( 420) hydrogen bonds : angle 6.59811 ( 1161) Misc. bond : bond 0.05774 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8725 (mmm160) cc_final: 0.8484 (tpt90) REVERT: B 112 ASN cc_start: 0.8395 (m-40) cc_final: 0.7939 (t0) REVERT: B 119 GLN cc_start: 0.8613 (tp-100) cc_final: 0.8095 (tp-100) REVERT: B 123 ASP cc_start: 0.8964 (m-30) cc_final: 0.8447 (m-30) REVERT: A 135 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8474 (mp0) REVERT: A 266 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: C 130 HIS cc_start: 0.9050 (t-90) cc_final: 0.8670 (m-70) REVERT: C 294 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7548 (mtp180) REVERT: C 373 LYS cc_start: 0.9301 (ttpt) cc_final: 0.9023 (ttpp) REVERT: C 705 MET cc_start: 0.8957 (ptm) cc_final: 0.8656 (tmm) REVERT: C 709 MET cc_start: 0.9314 (mtm) cc_final: 0.9007 (mtm) REVERT: D 616 MET cc_start: 0.7780 (mtm) cc_final: 0.7274 (ptp) REVERT: D 636 GLN cc_start: 0.9007 (pt0) cc_final: 0.8796 (pm20) REVERT: D 685 GLN cc_start: 0.8437 (pp30) cc_final: 0.8160 (pp30) REVERT: D 727 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8118 (pt0) outliers start: 16 outliers final: 8 residues processed: 130 average time/residue: 0.7085 time to fit residues: 97.6509 Evaluate side-chains 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 294 ARG Chi-restraints excluded: chain C residue 596 MET Chi-restraints excluded: chain C residue 724 ARG Chi-restraints excluded: chain D residue 762 MET Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain D residue 765 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN A 180 ASN C 47 ASN C 168 GLN C 336 ASN C 637 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.058895 restraints weight = 18585.358| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.64 r_work: 0.2589 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9781 Z= 0.140 Angle : 0.537 7.978 13246 Z= 0.274 Chirality : 0.042 0.150 1515 Planarity : 0.004 0.044 1700 Dihedral : 6.187 87.897 1353 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.17 % Allowed : 17.06 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 0.68 (0.25), residues: 1211 helix: 1.10 (0.25), residues: 504 sheet: -0.36 (0.37), residues: 213 loop : 0.33 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 61 TYR 0.011 0.001 TYR B 58 PHE 0.014 0.001 PHE D 609 TRP 0.006 0.001 TRP C 620 HIS 0.003 0.001 HIS C 671 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9780) covalent geometry : angle 0.53720 (13246) hydrogen bonds : bond 0.04242 ( 420) hydrogen bonds : angle 5.10919 ( 1161) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8745 (mmm160) cc_final: 0.8486 (tpt90) REVERT: B 112 ASN cc_start: 0.8409 (m-40) cc_final: 0.7990 (t0) REVERT: B 119 GLN cc_start: 0.8667 (tp40) cc_final: 0.8111 (tp-100) REVERT: B 123 ASP cc_start: 0.9021 (m-30) cc_final: 0.8548 (m-30) REVERT: B 142 ASP cc_start: 0.9074 (p0) cc_final: 0.8867 (p0) REVERT: C 130 HIS cc_start: 0.9030 (t-90) cc_final: 0.8652 (m-70) REVERT: C 373 LYS cc_start: 0.9358 (ttpt) cc_final: 0.9049 (ttpp) REVERT: C 705 MET cc_start: 0.8945 (ptm) cc_final: 0.8650 (tmm) REVERT: C 709 MET cc_start: 0.9319 (mtm) cc_final: 0.8987 (mtm) REVERT: C 718 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8364 (mt-10) REVERT: D 656 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8625 (tt) REVERT: D 727 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8549 (mt-10) outliers start: 23 outliers final: 9 residues processed: 128 average time/residue: 0.6369 time to fit residues: 87.2286 Evaluate side-chains 122 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 656 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 736 ILE Chi-restraints excluded: chain D residue 738 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 113 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.059399 restraints weight = 18524.287| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.62 r_work: 0.2593 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9781 Z= 0.134 Angle : 0.511 7.581 13246 Z= 0.260 Chirality : 0.042 0.145 1515 Planarity : 0.003 0.041 1700 Dihedral : 4.584 59.232 1331 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.83 % Allowed : 16.97 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 0.68 (0.25), residues: 1211 helix: 1.15 (0.25), residues: 505 sheet: -0.45 (0.36), residues: 214 loop : 0.32 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.023 0.001 TYR A 131 PHE 0.012 0.001 PHE D 717 TRP 0.007 0.001 TRP C 639 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9780) covalent geometry : angle 0.51065 (13246) hydrogen bonds : bond 0.03657 ( 420) hydrogen bonds : angle 4.82463 ( 1161) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8516 (mmm160) REVERT: B 112 ASN cc_start: 0.8361 (m-40) cc_final: 0.8007 (t0) REVERT: B 119 GLN cc_start: 0.8653 (tp40) cc_final: 0.8089 (tp-100) REVERT: B 123 ASP cc_start: 0.9043 (m-30) cc_final: 0.8543 (m-30) REVERT: A 117 MET cc_start: 0.9091 (mtt) cc_final: 0.8836 (mtm) REVERT: A 135 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: A 266 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: A 269 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8693 (t) REVERT: C 45 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8893 (mt) REVERT: C 130 HIS cc_start: 0.9045 (t-90) cc_final: 0.8665 (m-70) REVERT: C 373 LYS cc_start: 0.9365 (ttpt) cc_final: 0.9050 (ttpp) REVERT: C 705 MET cc_start: 0.8936 (ptm) cc_final: 0.8636 (tmm) REVERT: C 709 MET cc_start: 0.9311 (mtm) cc_final: 0.8979 (mtm) REVERT: C 718 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8370 (mt-10) REVERT: D 656 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8670 (tt) REVERT: D 685 GLN cc_start: 0.8438 (pp30) cc_final: 0.8236 (pp30) REVERT: D 727 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8586 (mt-10) REVERT: D 730 MET cc_start: 0.8660 (mmm) cc_final: 0.8377 (mmm) outliers start: 30 outliers final: 10 residues processed: 142 average time/residue: 0.6228 time to fit residues: 94.7628 Evaluate side-chains 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 656 LEU Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 736 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 0.0970 chunk 90 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN C 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.058492 restraints weight = 18663.837| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.62 r_work: 0.2559 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9781 Z= 0.180 Angle : 0.529 7.525 13246 Z= 0.270 Chirality : 0.043 0.148 1515 Planarity : 0.004 0.039 1700 Dihedral : 4.518 54.476 1331 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.54 % Allowed : 17.91 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 0.64 (0.25), residues: 1211 helix: 1.07 (0.24), residues: 511 sheet: -0.40 (0.37), residues: 205 loop : 0.30 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 576 TYR 0.011 0.001 TYR B 58 PHE 0.015 0.001 PHE D 609 TRP 0.008 0.001 TRP C 620 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9780) covalent geometry : angle 0.52878 (13246) hydrogen bonds : bond 0.03688 ( 420) hydrogen bonds : angle 4.77321 ( 1161) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8785 (mmm160) cc_final: 0.8486 (mmm160) REVERT: B 112 ASN cc_start: 0.8377 (m-40) cc_final: 0.7961 (t0) REVERT: B 119 GLN cc_start: 0.8644 (tp40) cc_final: 0.8061 (tp-100) REVERT: B 123 ASP cc_start: 0.9031 (m-30) cc_final: 0.8505 (m-30) REVERT: A 135 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: A 266 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7782 (mp10) REVERT: A 269 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8712 (t) REVERT: C 45 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8873 (mt) REVERT: C 130 HIS cc_start: 0.9054 (t-90) cc_final: 0.8672 (m-70) REVERT: C 373 LYS cc_start: 0.9370 (ttpt) cc_final: 0.9041 (ttpp) REVERT: C 705 MET cc_start: 0.8976 (ptm) cc_final: 0.8660 (tmm) REVERT: C 709 MET cc_start: 0.9349 (mtm) cc_final: 0.9030 (mtm) REVERT: D 616 MET cc_start: 0.7861 (mtm) cc_final: 0.7240 (ptp) REVERT: D 727 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8583 (mt-10) outliers start: 27 outliers final: 12 residues processed: 137 average time/residue: 0.6228 time to fit residues: 91.4178 Evaluate side-chains 130 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 124 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 736 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.059947 restraints weight = 18555.140| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.55 r_work: 0.2600 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9781 Z= 0.107 Angle : 0.505 7.753 13246 Z= 0.255 Chirality : 0.041 0.146 1515 Planarity : 0.003 0.039 1700 Dihedral : 4.251 49.566 1331 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.98 % Allowed : 18.57 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 0.77 (0.25), residues: 1211 helix: 1.31 (0.25), residues: 497 sheet: -0.44 (0.37), residues: 205 loop : 0.30 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 710 TYR 0.009 0.001 TYR B 58 PHE 0.010 0.001 PHE D 717 TRP 0.007 0.001 TRP C 639 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9780) covalent geometry : angle 0.50480 (13246) hydrogen bonds : bond 0.03226 ( 420) hydrogen bonds : angle 4.59616 ( 1161) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8796 (mmm160) cc_final: 0.8491 (mmm160) REVERT: B 95 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8244 (tm130) REVERT: B 112 ASN cc_start: 0.8370 (m-40) cc_final: 0.7825 (t0) REVERT: B 119 GLN cc_start: 0.8629 (tp40) cc_final: 0.7997 (tp-100) REVERT: B 123 ASP cc_start: 0.9016 (m-30) cc_final: 0.8482 (m-30) REVERT: A 135 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: A 269 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8670 (t) REVERT: C 45 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8856 (mt) REVERT: C 130 HIS cc_start: 0.9034 (t-90) cc_final: 0.8664 (m-70) REVERT: C 373 LYS cc_start: 0.9357 (ttpt) cc_final: 0.9035 (ttpp) REVERT: C 705 MET cc_start: 0.8906 (ptm) cc_final: 0.8601 (tmm) REVERT: C 709 MET cc_start: 0.9297 (mtm) cc_final: 0.8977 (mtm) REVERT: D 616 MET cc_start: 0.7928 (mtm) cc_final: 0.7306 (ptp) REVERT: D 727 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8560 (mt-10) REVERT: D 730 MET cc_start: 0.8620 (mmm) cc_final: 0.8328 (mmm) outliers start: 21 outliers final: 8 residues processed: 134 average time/residue: 0.5929 time to fit residues: 85.3776 Evaluate side-chains 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 736 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 99 optimal weight: 0.0060 chunk 111 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** D 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.091079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.059697 restraints weight = 18402.179| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.56 r_work: 0.2595 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9781 Z= 0.118 Angle : 0.504 8.934 13246 Z= 0.256 Chirality : 0.041 0.148 1515 Planarity : 0.003 0.040 1700 Dihedral : 4.083 44.295 1330 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.79 % Allowed : 19.32 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 0.79 (0.25), residues: 1211 helix: 1.36 (0.25), residues: 497 sheet: -0.50 (0.36), residues: 205 loop : 0.30 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.010 0.001 TYR B 58 PHE 0.018 0.001 PHE D 609 TRP 0.008 0.001 TRP C 639 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9780) covalent geometry : angle 0.50376 (13246) hydrogen bonds : bond 0.03261 ( 420) hydrogen bonds : angle 4.58094 ( 1161) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8821 (mmm160) cc_final: 0.8579 (mmm160) REVERT: B 112 ASN cc_start: 0.8338 (m110) cc_final: 0.7889 (t0) REVERT: B 119 GLN cc_start: 0.8618 (tp40) cc_final: 0.7998 (tp-100) REVERT: B 123 ASP cc_start: 0.9009 (m-30) cc_final: 0.8475 (m-30) REVERT: B 156 GLN cc_start: 0.9069 (mm110) cc_final: 0.8800 (mm110) REVERT: A 66 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8592 (ttt-90) REVERT: A 117 MET cc_start: 0.9055 (mtt) cc_final: 0.8771 (mtm) REVERT: A 135 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: A 269 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8695 (t) REVERT: C 40 LEU cc_start: 0.8109 (mp) cc_final: 0.7879 (tt) REVERT: C 45 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8804 (mt) REVERT: C 130 HIS cc_start: 0.9034 (t-90) cc_final: 0.8653 (m-70) REVERT: C 705 MET cc_start: 0.8907 (ptm) cc_final: 0.8597 (tmm) REVERT: C 709 MET cc_start: 0.9312 (mtm) cc_final: 0.8989 (mtm) REVERT: D 616 MET cc_start: 0.7945 (mtm) cc_final: 0.7327 (ptp) REVERT: D 683 MET cc_start: 0.8478 (mmm) cc_final: 0.8231 (tpp) REVERT: D 727 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8555 (mt-10) REVERT: D 730 MET cc_start: 0.8629 (mmm) cc_final: 0.8343 (mmm) outliers start: 19 outliers final: 9 residues processed: 129 average time/residue: 0.6611 time to fit residues: 91.0223 Evaluate side-chains 118 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 736 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN C 168 GLN ** D 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.089935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.058489 restraints weight = 18367.712| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.52 r_work: 0.2563 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9781 Z= 0.178 Angle : 0.540 10.069 13246 Z= 0.272 Chirality : 0.043 0.148 1515 Planarity : 0.003 0.038 1700 Dihedral : 4.072 37.493 1329 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.07 % Allowed : 19.32 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 0.65 (0.25), residues: 1211 helix: 1.21 (0.25), residues: 507 sheet: -0.51 (0.36), residues: 205 loop : 0.21 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 294 TYR 0.026 0.001 TYR A 131 PHE 0.015 0.001 PHE B 99 TRP 0.008 0.001 TRP C 620 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9780) covalent geometry : angle 0.54023 (13246) hydrogen bonds : bond 0.03476 ( 420) hydrogen bonds : angle 4.64594 ( 1161) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8799 (mmm160) cc_final: 0.8563 (mmm160) REVERT: B 112 ASN cc_start: 0.8405 (m110) cc_final: 0.7946 (t0) REVERT: B 119 GLN cc_start: 0.8646 (tp40) cc_final: 0.8008 (tp-100) REVERT: B 123 ASP cc_start: 0.9022 (m-30) cc_final: 0.8457 (m-30) REVERT: A 66 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8628 (ttt-90) REVERT: A 135 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: A 266 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: A 269 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8734 (t) REVERT: C 45 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8844 (mt) REVERT: C 130 HIS cc_start: 0.9031 (t-90) cc_final: 0.8661 (m-70) REVERT: C 705 MET cc_start: 0.8968 (ptm) cc_final: 0.8649 (tmm) REVERT: C 709 MET cc_start: 0.9314 (mtm) cc_final: 0.9015 (mtm) REVERT: D 616 MET cc_start: 0.7910 (mtm) cc_final: 0.7327 (ptp) REVERT: D 683 MET cc_start: 0.8563 (mmm) cc_final: 0.8346 (tpp) REVERT: D 727 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8548 (mt-10) REVERT: D 730 MET cc_start: 0.8697 (mmm) cc_final: 0.8415 (mmm) outliers start: 22 outliers final: 9 residues processed: 128 average time/residue: 0.6344 time to fit residues: 86.7100 Evaluate side-chains 123 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 736 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** D 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.059527 restraints weight = 18486.307| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.56 r_work: 0.2623 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9781 Z= 0.120 Angle : 0.523 8.438 13246 Z= 0.264 Chirality : 0.042 0.149 1515 Planarity : 0.003 0.039 1700 Dihedral : 3.953 32.882 1329 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.60 % Allowed : 19.79 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 (0.25), residues: 1211 helix: 1.32 (0.25), residues: 499 sheet: -0.52 (0.36), residues: 205 loop : 0.23 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 666 TYR 0.011 0.001 TYR B 58 PHE 0.017 0.001 PHE D 609 TRP 0.007 0.001 TRP C 639 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9780) covalent geometry : angle 0.52277 (13246) hydrogen bonds : bond 0.03184 ( 420) hydrogen bonds : angle 4.55985 ( 1161) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8551 (mmm160) REVERT: B 112 ASN cc_start: 0.8382 (m110) cc_final: 0.7893 (t0) REVERT: B 119 GLN cc_start: 0.8670 (tp40) cc_final: 0.8045 (tp-100) REVERT: B 123 ASP cc_start: 0.9024 (m-30) cc_final: 0.8467 (m-30) REVERT: B 156 GLN cc_start: 0.9086 (mm110) cc_final: 0.8828 (mm-40) REVERT: A 66 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8644 (ttt-90) REVERT: A 135 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: A 269 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8661 (t) REVERT: C 45 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8860 (mt) REVERT: C 130 HIS cc_start: 0.9026 (t-90) cc_final: 0.8670 (m-70) REVERT: C 705 MET cc_start: 0.8909 (ptm) cc_final: 0.8606 (tmm) REVERT: C 709 MET cc_start: 0.9271 (mtm) cc_final: 0.8976 (mtm) REVERT: D 616 MET cc_start: 0.7962 (mtm) cc_final: 0.7417 (ptp) REVERT: D 727 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8612 (mt-10) REVERT: D 730 MET cc_start: 0.8627 (mmm) cc_final: 0.8345 (mmm) outliers start: 17 outliers final: 9 residues processed: 125 average time/residue: 0.6235 time to fit residues: 83.3573 Evaluate side-chains 119 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 736 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.0370 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN C 168 GLN ** D 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.090700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.058407 restraints weight = 18427.379| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.61 r_work: 0.2570 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9781 Z= 0.154 Angle : 0.559 11.416 13246 Z= 0.281 Chirality : 0.043 0.170 1515 Planarity : 0.003 0.038 1700 Dihedral : 3.956 29.876 1329 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.70 % Allowed : 20.36 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 0.64 (0.25), residues: 1211 helix: 1.20 (0.25), residues: 507 sheet: -0.53 (0.36), residues: 205 loop : 0.22 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 666 TYR 0.026 0.001 TYR A 131 PHE 0.010 0.001 PHE A 84 TRP 0.007 0.001 TRP C 639 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9780) covalent geometry : angle 0.55902 (13246) hydrogen bonds : bond 0.03400 ( 420) hydrogen bonds : angle 4.65001 ( 1161) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8538 (mmm160) REVERT: B 112 ASN cc_start: 0.8351 (m110) cc_final: 0.7945 (t0) REVERT: B 119 GLN cc_start: 0.8662 (tp40) cc_final: 0.8035 (tp-100) REVERT: B 123 ASP cc_start: 0.9026 (m-30) cc_final: 0.8449 (m-30) REVERT: A 66 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8593 (ttt-90) REVERT: A 135 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: A 266 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: A 269 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8747 (t) REVERT: C 45 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8844 (mt) REVERT: C 130 HIS cc_start: 0.9036 (t-90) cc_final: 0.8659 (m-70) REVERT: C 705 MET cc_start: 0.8953 (ptm) cc_final: 0.8629 (tmm) REVERT: C 709 MET cc_start: 0.9316 (mtm) cc_final: 0.9005 (mtm) REVERT: D 727 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8600 (mt-10) REVERT: D 730 MET cc_start: 0.8671 (mmm) cc_final: 0.8381 (mmm) outliers start: 18 outliers final: 10 residues processed: 123 average time/residue: 0.6164 time to fit residues: 81.2844 Evaluate side-chains 124 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 736 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN C 168 GLN ** D 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.059525 restraints weight = 18457.304| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.61 r_work: 0.2595 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9781 Z= 0.113 Angle : 0.576 13.878 13246 Z= 0.286 Chirality : 0.042 0.250 1515 Planarity : 0.003 0.039 1700 Dihedral : 3.882 27.679 1329 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.32 % Allowed : 20.64 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: 0.75 (0.25), residues: 1211 helix: 1.36 (0.25), residues: 497 sheet: -0.47 (0.36), residues: 203 loop : 0.21 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 666 TYR 0.011 0.001 TYR B 58 PHE 0.022 0.001 PHE B 99 TRP 0.007 0.001 TRP C 639 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9780) covalent geometry : angle 0.57615 (13246) hydrogen bonds : bond 0.03253 ( 420) hydrogen bonds : angle 4.59756 ( 1161) Misc. bond : bond 0.00015 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.8754 (mmm160) cc_final: 0.8076 (mmm160) REVERT: B 112 ASN cc_start: 0.8370 (m110) cc_final: 0.7940 (t0) REVERT: B 119 GLN cc_start: 0.8648 (tp40) cc_final: 0.8044 (tp-100) REVERT: B 123 ASP cc_start: 0.9006 (m-30) cc_final: 0.8439 (m-30) REVERT: B 156 GLN cc_start: 0.9080 (mm110) cc_final: 0.8809 (mm-40) REVERT: A 66 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8597 (ttt-90) REVERT: A 135 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: C 45 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8850 (mt) REVERT: C 130 HIS cc_start: 0.9035 (t-90) cc_final: 0.8659 (m-70) REVERT: C 705 MET cc_start: 0.8920 (ptm) cc_final: 0.8598 (tmm) REVERT: C 709 MET cc_start: 0.9303 (mtm) cc_final: 0.8986 (mtm) REVERT: D 727 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8598 (mt-10) REVERT: D 730 MET cc_start: 0.8629 (mmm) cc_final: 0.8338 (mmm) outliers start: 14 outliers final: 7 residues processed: 124 average time/residue: 0.6533 time to fit residues: 86.5492 Evaluate side-chains 120 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 736 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 3 optimal weight: 0.0170 chunk 66 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN C 168 GLN ** D 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.060424 restraints weight = 18245.254| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.52 r_work: 0.2646 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9781 Z= 0.112 Angle : 0.573 11.940 13246 Z= 0.285 Chirality : 0.042 0.200 1515 Planarity : 0.003 0.039 1700 Dihedral : 3.742 16.472 1327 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.04 % Allowed : 21.39 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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 (0.25), residues: 1211 helix: 1.39 (0.25), residues: 497 sheet: -0.50 (0.36), residues: 203 loop : 0.24 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 666 TYR 0.026 0.001 TYR A 131 PHE 0.013 0.001 PHE D 609 TRP 0.009 0.001 TRP C 639 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9780) covalent geometry : angle 0.57295 (13246) hydrogen bonds : bond 0.03182 ( 420) hydrogen bonds : angle 4.56292 ( 1161) Misc. bond : bond 0.00017 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3835.88 seconds wall clock time: 66 minutes 15.35 seconds (3975.35 seconds total)