Starting phenix.real_space_refine on Wed Mar 4 22:40:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bwm_30233/03_2026/7bwm_30233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bwm_30233/03_2026/7bwm_30233.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bwm_30233/03_2026/7bwm_30233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bwm_30233/03_2026/7bwm_30233.map" model { file = "/net/cci-nas-00/data/ceres_data/7bwm_30233/03_2026/7bwm_30233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bwm_30233/03_2026/7bwm_30233.cif" } 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9352 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 5997 2.51 5 N 1674 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9532 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9532 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1219, 9473 Classifications: {'peptide': 1219} Link IDs: {'PCIS': 2, 'PTRANS': 75, 'TRANS': 1141} Chain breaks: 12 Conformer: "B" Number of residues, atoms: 1219, 9473 Classifications: {'peptide': 1219} Link IDs: {'PCIS': 2, 'PTRANS': 75, 'TRANS': 1141} Chain breaks: 12 bond proxies already assigned to first conformer: 9640 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG A 385 " occ=0.70 ... (20 atoms not shown) pdb=" NH2BARG A 385 " occ=0.30 residue: pdb=" N AASN A 911 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 911 " occ=0.50 residue: pdb=" N ATRP A1025 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A1025 " occ=0.50 residue: pdb=" N AGLN A1188 " occ=0.70 ... (16 atoms not shown) pdb=" NE2BGLN A1188 " occ=0.30 residue: pdb=" N AASP A1257 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A1257 " occ=0.50 residue: pdb=" N AGLU A1371 " occ=0.70 ... (16 atoms not shown) pdb=" OE2BGLU A1371 " occ=0.30 Time building chain proxies: 3.77, per 1000 atoms: 0.40 Number of scatterers: 9532 At special positions: 0 Unit cell: (80.04, 100.05, 120.06, 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 8 16.00 O 1853 8.00 N 1674 7.00 C 5997 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: 0.73 Conformation dependent library (CDL) restraints added in 773.3 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: 2258 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 15 sheets defined 25.6% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.619A pdb=" N VAL A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.835A pdb=" N VAL A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 209' Processing helix chain 'A' and resid 210 through 213 Processing helix chain 'A' and resid 248 through 254 removed outlier: 3.607A pdb=" N SER A 251 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASN A 252 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 254 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.744A pdb=" N PHE A 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 removed outlier: 3.556A pdb=" N ILE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.899A pdb=" N MET A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.777A pdb=" N THR A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 426 removed outlier: 4.105A pdb=" N ASP A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.821A pdb=" N TRP A 441 " --> pdb=" O HIS A 438 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 442' Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 607 through 610 removed outlier: 3.572A pdb=" N SER A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 611 through 619 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.894A pdb=" N GLY A 633 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 634 " --> pdb=" O PRO A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 662 through 666 removed outlier: 3.772A pdb=" N GLN A 666 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 753 through 757 removed outlier: 3.511A pdb=" N ASN A 756 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 757 " --> pdb=" O LYS A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 753 through 757' Processing helix chain 'A' and resid 761 through 767 removed outlier: 3.676A pdb=" N ARG A 765 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 767 " --> pdb=" O TYR A 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 767' Processing helix chain 'A' and resid 779 through 785 removed outlier: 3.932A pdb=" N PHE A 783 " --> pdb=" O TRP A 780 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 784 " --> pdb=" O SER A 781 " (cutoff:3.500A) Proline residue: A 785 - end of helix Processing helix chain 'A' and resid 797 through 808 removed outlier: 3.624A pdb=" N ASP A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 804 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.557A pdb=" N ASP A 826 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 981 through 985 removed outlier: 3.524A pdb=" N PHE A 984 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1002 removed outlier: 3.929A pdb=" N GLN A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1023 removed outlier: 3.605A pdb=" N GLN A1023 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'A' and resid 1049 through 1059 Processing helix chain 'A' and resid 1067 through 1071 removed outlier: 4.354A pdb=" N THR A1071 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1179 through 1187 Processing helix chain 'A' and resid 1195 through 1201 Processing helix chain 'A' and resid 1218 through 1223 removed outlier: 3.580A pdb=" N LYS A1223 " --> pdb=" O SER A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1263 through 1275 removed outlier: 3.780A pdb=" N VAL A1267 " --> pdb=" O ASP A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1307 removed outlier: 3.534A pdb=" N SER A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1338 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 removed outlier: 3.574A pdb=" N VAL A 92 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 128 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP A 140 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A 130 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.577A pdb=" N LEU A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 188 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 199 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN A 190 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ARG A 197 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR A 196 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 390 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 377 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE A 388 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA6, first strand: chain 'A' and resid 257 through 259 removed outlier: 5.857A pdb=" N ALA A 286 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 257 through 259 removed outlier: 5.857A pdb=" N ALA A 286 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 319 through 320 removed outlier: 3.681A pdb=" N GLN A 323 " --> pdb=" O GLU A 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 497 Processing sheet with id=AB1, first strand: chain 'A' and resid 574 through 582 removed outlier: 5.110A pdb=" N VAL A 576 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 591 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 578 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 586 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 789 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AB3, first strand: chain 'A' and resid 913 through 914 Processing sheet with id=AB4, first strand: chain 'A' and resid 1006 through 1008 Processing sheet with id=AB5, first strand: chain 'A' and resid 1107 through 1109 removed outlier: 8.658A pdb=" N GLY A1367 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU A1139 " --> pdb=" O GLY A1367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1162 through 1167 removed outlier: 5.466A pdb=" N VAL A1176 " --> pdb=" O ARG A1163 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A1165 " --> pdb=" O GLU A1174 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU A1174 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A1287 " --> pdb=" O MET A1377 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 567 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: 1.80 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3173 1.34 - 1.46: 1638 1.46 - 1.57: 4947 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 9774 Sorted by residual: bond pdb=" C PHE A 850 " pdb=" N LEU A 851 " ideal model delta sigma weight residual 1.329 1.270 0.059 1.86e-02 2.89e+03 1.01e+01 bond pdb=" C PHE A 722 " pdb=" N VAL A 723 " ideal model delta sigma weight residual 1.329 1.301 0.028 1.31e-02 5.83e+03 4.42e+00 bond pdb=" C SER A 784 " pdb=" N PRO A 785 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.27e+00 bond pdb=" CA SER A 799 " pdb=" C SER A 799 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.35e-02 5.49e+03 2.99e+00 bond pdb=" N HIS A 653 " pdb=" CA HIS A 653 " ideal model delta sigma weight residual 1.456 1.476 -0.020 1.25e-02 6.40e+03 2.65e+00 ... (remaining 9769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 13020 2.16 - 4.32: 269 4.32 - 6.49: 31 6.49 - 8.65: 8 8.65 - 10.81: 3 Bond angle restraints: 13331 Sorted by residual: angle pdb=" N VAL A1363 " pdb=" CA VAL A1363 " pdb=" C VAL A1363 " ideal model delta sigma weight residual 113.71 107.50 6.21 9.50e-01 1.11e+00 4.27e+01 angle pdb=" C THR A 950 " pdb=" CA THR A 950 " pdb=" CB THR A 950 " ideal model delta sigma weight residual 109.83 105.02 4.81 9.90e-01 1.02e+00 2.36e+01 angle pdb=" C SER A 948 " pdb=" N LEU A 949 " pdb=" CA LEU A 949 " ideal model delta sigma weight residual 121.54 130.73 -9.19 1.91e+00 2.74e-01 2.32e+01 angle pdb=" N THR A 950 " pdb=" CA THR A 950 " pdb=" C THR A 950 " ideal model delta sigma weight residual 113.51 120.67 -7.16 1.52e+00 4.33e-01 2.22e+01 angle pdb=" C ASP A 667 " pdb=" N ARG A 668 " pdb=" CA ARG A 668 " ideal model delta sigma weight residual 122.21 111.72 10.49 2.87e+00 1.21e-01 1.34e+01 ... (remaining 13326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.57: 5373 19.57 - 39.14: 287 39.14 - 58.71: 92 58.71 - 78.29: 15 78.29 - 97.86: 6 Dihedral angle restraints: 5773 sinusoidal: 2261 harmonic: 3512 Sorted by residual: dihedral pdb=" CA GLN A1282 " pdb=" C GLN A1282 " pdb=" N PRO A1283 " pdb=" CA PRO A1283 " ideal model delta harmonic sigma weight residual 0.00 34.48 -34.48 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA THR A 951 " pdb=" C THR A 951 " pdb=" N GLN A 952 " pdb=" CA GLN A 952 " ideal model delta harmonic sigma weight residual 180.00 146.58 33.42 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA THR A 950 " pdb=" C THR A 950 " pdb=" N THR A 951 " pdb=" CA THR A 951 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 5770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1005 0.043 - 0.086: 324 0.086 - 0.128: 108 0.128 - 0.171: 6 0.171 - 0.214: 3 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA GLN A 960 " pdb=" N GLN A 960 " pdb=" C GLN A 960 " pdb=" CB GLN A 960 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA THR A 950 " pdb=" N THR A 950 " pdb=" C THR A 950 " pdb=" CB THR A 950 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO A1283 " pdb=" N PRO A1283 " pdb=" C PRO A1283 " pdb=" CB PRO A1283 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 1443 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 973 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 974 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 974 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 974 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1099 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO A1100 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1100 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1100 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 478 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 479 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.020 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 139 2.62 - 3.19: 8094 3.19 - 3.76: 14707 3.76 - 4.33: 22272 4.33 - 4.90: 35629 Nonbonded interactions: 80841 Sorted by model distance: nonbonded pdb=" O THR A 950 " pdb=" OG1 THR A 951 " model vdw 2.048 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" OD1 ASP A 378 " model vdw 2.102 3.040 nonbonded pdb=" O LEU A1271 " pdb=" OG SER A1274 " model vdw 2.150 3.040 nonbonded pdb=" O LEU A 120 " pdb=" OG1 THR A 124 " model vdw 2.174 3.040 nonbonded pdb=" OD1 ASP A 142 " pdb=" OG SER A 144 " model vdw 2.193 3.040 ... (remaining 80836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 0.059 9774 Z= 0.233 Angle : 0.784 10.810 13331 Z= 0.467 Chirality : 0.046 0.214 1446 Planarity : 0.005 0.042 1761 Dihedral : 14.238 97.857 3515 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.78 % Favored : 93.96 % Rotamer: Outliers : 7.21 % Allowed : 7.12 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.18 % 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: -3.28 (0.20), residues: 1211 helix: -2.75 (0.26), residues: 213 sheet: -1.23 (0.36), residues: 169 loop : -2.38 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1157 TYR 0.013 0.002 TYR A 696 PHE 0.009 0.001 PHE A 488 TRP 0.012 0.002 TRP A 496 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 9774) covalent geometry : angle 0.78437 (13331) hydrogen bonds : bond 0.21892 ( 220) hydrogen bonds : angle 8.68831 ( 567) *********************** 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 192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 118 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7638 (mp) REVERT: A 287 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8749 (mp) REVERT: A 293 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8067 (pttp) REVERT: A 309 ASP cc_start: 0.7783 (m-30) cc_final: 0.7557 (m-30) REVERT: A 323 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.5932 (pm20) REVERT: A 513 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8288 (m) REVERT: A 914 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7813 (mptt) outliers start: 74 outliers final: 24 residues processed: 183 average time/residue: 0.5834 time to fit residues: 114.1143 Evaluate side-chains 106 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 803 GLN Chi-restraints excluded: chain A residue 820 ASN Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1256 ASP Chi-restraints excluded: chain A residue 1288 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 175 GLN A 323 GLN A 469 GLN A 490 ASN A 661 ASN A 685 ASN A 716 GLN A 866 GLN A1192 GLN A1279 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.127146 restraints weight = 46058.258| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 7.46 r_work: 0.2967 rms_B_bonded: 7.25 restraints_weight: 2.0000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9774 Z= 0.179 Angle : 0.662 10.933 13331 Z= 0.339 Chirality : 0.046 0.229 1446 Planarity : 0.005 0.047 1761 Dihedral : 9.173 81.518 1370 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 4.78 % Allowed : 12.96 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.18 % 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: -2.29 (0.21), residues: 1211 helix: -1.66 (0.30), residues: 217 sheet: -0.59 (0.38), residues: 154 loop : -1.76 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 136 TYR 0.011 0.002 TYR A 696 PHE 0.017 0.001 PHE A 126 TRP 0.012 0.002 TRP A1098 HIS 0.003 0.001 HIS A 912 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9774) covalent geometry : angle 0.66166 (13331) hydrogen bonds : bond 0.04338 ( 220) hydrogen bonds : angle 6.28991 ( 567) *********************** 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 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 82 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7743 (mp) REVERT: A 247 ASP cc_start: 0.7638 (t0) cc_final: 0.7226 (p0) REVERT: A 287 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8905 (mp) REVERT: A 292 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7416 (ptpt) REVERT: A 293 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8284 (pttm) REVERT: A 309 ASP cc_start: 0.8016 (m-30) cc_final: 0.7754 (m-30) REVERT: A 323 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.5850 (pm20) REVERT: A 465 LYS cc_start: 0.7972 (mttt) cc_final: 0.7652 (mmtm) REVERT: A 513 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8330 (m) REVERT: A 687 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7495 (tppt) REVERT: A 914 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8010 (mptt) REVERT: A 960 GLN cc_start: 0.6149 (OUTLIER) cc_final: 0.5874 (pm20) REVERT: A 1017 LYS cc_start: 0.7420 (mttp) cc_final: 0.7218 (mmtp) REVERT: A 1255 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6652 (p0) REVERT: A 1256 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7400 (t0) REVERT: A 1258 LEU cc_start: 0.8835 (tp) cc_final: 0.8579 (tp) outliers start: 49 outliers final: 20 residues processed: 121 average time/residue: 0.6431 time to fit residues: 83.0854 Evaluate side-chains 109 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1256 ASP Chi-restraints excluded: chain A residue 1288 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 490 ASN A 866 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128004 restraints weight = 42775.947| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 7.08 r_work: 0.3010 rms_B_bonded: 6.82 restraints_weight: 2.0000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9774 Z= 0.128 Angle : 0.611 10.125 13331 Z= 0.311 Chirality : 0.044 0.221 1446 Planarity : 0.004 0.035 1761 Dihedral : 8.297 84.692 1361 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 4.09 % Allowed : 14.23 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % 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: -1.72 (0.22), residues: 1211 helix: -1.04 (0.33), residues: 218 sheet: -0.29 (0.40), residues: 155 loop : -1.41 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.009 0.001 TYR A 696 PHE 0.019 0.001 PHE A1115 TRP 0.011 0.001 TRP A 418 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9774) covalent geometry : angle 0.61102 (13331) hydrogen bonds : bond 0.03437 ( 220) hydrogen bonds : angle 5.89236 ( 567) *********************** 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 123 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 81 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7803 (mp) REVERT: A 247 ASP cc_start: 0.7539 (t0) cc_final: 0.7068 (p0) REVERT: A 287 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8976 (mp) REVERT: A 292 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7403 (ptpt) REVERT: A 309 ASP cc_start: 0.7967 (m-30) cc_final: 0.7477 (m-30) REVERT: A 323 GLN cc_start: 0.6038 (OUTLIER) cc_final: 0.5773 (pm20) REVERT: A 687 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7393 (mppt) REVERT: A 914 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8025 (mptt) REVERT: A 960 GLN cc_start: 0.6098 (OUTLIER) cc_final: 0.5579 (mp10) REVERT: A 1253 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7387 (ptmm) REVERT: A 1256 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7363 (t0) REVERT: A 1377 MET cc_start: 0.5259 (OUTLIER) cc_final: 0.5046 (mtp) outliers start: 42 outliers final: 16 residues processed: 113 average time/residue: 0.5882 time to fit residues: 71.3837 Evaluate side-chains 103 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1253 LYS Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1256 ASP Chi-restraints excluded: chain A residue 1377 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 0.0000 chunk 95 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.164306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130413 restraints weight = 44974.730| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 7.43 r_work: 0.3020 rms_B_bonded: 7.18 restraints_weight: 2.0000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9774 Z= 0.106 Angle : 0.587 9.400 13331 Z= 0.300 Chirality : 0.043 0.216 1446 Planarity : 0.004 0.034 1761 Dihedral : 7.704 84.625 1345 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 2.92 % Allowed : 15.69 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % 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: -1.36 (0.23), residues: 1211 helix: -0.58 (0.35), residues: 217 sheet: -0.11 (0.41), residues: 155 loop : -1.20 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 136 TYR 0.011 0.001 TYR A 763 PHE 0.015 0.001 PHE A1115 TRP 0.011 0.001 TRP A1159 HIS 0.002 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9774) covalent geometry : angle 0.58662 (13331) hydrogen bonds : bond 0.03115 ( 220) hydrogen bonds : angle 5.68765 ( 567) *********************** 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 115 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7820 (mp) REVERT: A 247 ASP cc_start: 0.7510 (t0) cc_final: 0.6958 (p0) REVERT: A 287 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8935 (mp) REVERT: A 309 ASP cc_start: 0.7943 (m-30) cc_final: 0.7522 (m-30) REVERT: A 490 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8937 (t0) REVERT: A 687 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7396 (mppt) REVERT: A 914 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8042 (mptt) REVERT: A 960 GLN cc_start: 0.6139 (OUTLIER) cc_final: 0.5640 (mp10) REVERT: A 1255 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6448 (p0) REVERT: A 1256 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7254 (t0) outliers start: 30 outliers final: 13 residues processed: 107 average time/residue: 0.5862 time to fit residues: 67.5468 Evaluate side-chains 97 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1256 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 0.4980 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128348 restraints weight = 47463.950| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 7.90 r_work: 0.2998 rms_B_bonded: 7.24 restraints_weight: 2.0000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9774 Z= 0.135 Angle : 0.608 9.606 13331 Z= 0.310 Chirality : 0.045 0.212 1446 Planarity : 0.004 0.043 1761 Dihedral : 7.037 58.255 1338 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.64 % Rotamer: Outliers : 3.02 % Allowed : 16.08 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.31 (0.22), residues: 1211 helix: -0.54 (0.34), residues: 222 sheet: -0.12 (0.41), residues: 155 loop : -1.16 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 136 TYR 0.009 0.001 TYR A 763 PHE 0.015 0.001 PHE A1115 TRP 0.010 0.001 TRP A1159 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9774) covalent geometry : angle 0.60815 (13331) hydrogen bonds : bond 0.03363 ( 220) hydrogen bonds : angle 5.66484 ( 567) *********************** 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 105 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8045 (mppt) cc_final: 0.7472 (tmtt) REVERT: A 146 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7861 (mp) REVERT: A 247 ASP cc_start: 0.7548 (t0) cc_final: 0.6957 (p0) REVERT: A 687 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7415 (mppt) REVERT: A 776 GLN cc_start: 0.7278 (tp-100) cc_final: 0.6965 (tp40) REVERT: A 914 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8019 (mptt) REVERT: A 960 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5749 (mp10) REVERT: A 1377 MET cc_start: 0.5226 (OUTLIER) cc_final: 0.5016 (mtp) outliers start: 31 outliers final: 18 residues processed: 99 average time/residue: 0.5982 time to fit residues: 63.6085 Evaluate side-chains 96 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1377 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 120 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128065 restraints weight = 46996.232| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 7.55 r_work: 0.2982 rms_B_bonded: 7.22 restraints_weight: 2.0000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9774 Z= 0.154 Angle : 0.619 9.849 13331 Z= 0.316 Chirality : 0.045 0.215 1446 Planarity : 0.004 0.039 1761 Dihedral : 6.826 54.619 1334 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 2.92 % Allowed : 16.76 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.32 (0.22), residues: 1211 helix: -0.53 (0.34), residues: 222 sheet: -0.16 (0.40), residues: 155 loop : -1.16 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.010 0.001 TYR A 696 PHE 0.015 0.001 PHE A1115 TRP 0.011 0.001 TRP A1098 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9774) covalent geometry : angle 0.61876 (13331) hydrogen bonds : bond 0.03463 ( 220) hydrogen bonds : angle 5.68155 ( 567) *********************** 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 105 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7881 (mp) REVERT: A 247 ASP cc_start: 0.7578 (t0) cc_final: 0.6990 (p0) REVERT: A 292 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7212 (mtpp) REVERT: A 675 ASP cc_start: 0.7976 (m-30) cc_final: 0.7708 (m-30) REVERT: A 687 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7448 (mppt) REVERT: A 776 GLN cc_start: 0.7334 (tp-100) cc_final: 0.6950 (tp40) REVERT: A 914 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7992 (mptt) REVERT: A 1253 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7380 (ptmm) REVERT: A 1259 LYS cc_start: 0.8721 (ttpp) cc_final: 0.8449 (mtpt) outliers start: 30 outliers final: 18 residues processed: 97 average time/residue: 0.5801 time to fit residues: 60.6391 Evaluate side-chains 96 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 951 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1253 LYS Chi-restraints excluded: chain A residue 1255 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 94 optimal weight: 0.0010 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.0170 chunk 83 optimal weight: 0.9990 overall best weight: 0.5226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130085 restraints weight = 37638.288| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 7.06 r_work: 0.3087 rms_B_bonded: 6.15 restraints_weight: 2.0000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9774 Z= 0.097 Angle : 0.567 8.650 13331 Z= 0.289 Chirality : 0.043 0.194 1446 Planarity : 0.004 0.042 1761 Dihedral : 6.331 56.110 1331 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 2.14 % Allowed : 17.54 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.07 (0.23), residues: 1211 helix: -0.30 (0.35), residues: 222 sheet: -0.03 (0.41), residues: 155 loop : -1.00 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 136 TYR 0.010 0.001 TYR A 763 PHE 0.017 0.001 PHE A 126 TRP 0.013 0.001 TRP A 418 HIS 0.002 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9774) covalent geometry : angle 0.56738 (13331) hydrogen bonds : bond 0.02729 ( 220) hydrogen bonds : angle 5.46730 ( 567) *********************** 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 108 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.7980 (mppt) cc_final: 0.7297 (tptt) REVERT: A 136 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7912 (ttp-110) REVERT: A 247 ASP cc_start: 0.7401 (t0) cc_final: 0.6827 (p0) REVERT: A 292 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7108 (mtpp) REVERT: A 687 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7340 (mppt) REVERT: A 776 GLN cc_start: 0.7310 (tp-100) cc_final: 0.6831 (tp40) REVERT: A 914 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8009 (mptt) REVERT: A 1259 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8377 (mtmt) outliers start: 22 outliers final: 15 residues processed: 101 average time/residue: 0.6182 time to fit residues: 66.9471 Evaluate side-chains 94 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1255 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.164882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130685 restraints weight = 48502.463| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 8.13 r_work: 0.3021 rms_B_bonded: 7.39 restraints_weight: 2.0000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9774 Z= 0.109 Angle : 0.575 10.376 13331 Z= 0.293 Chirality : 0.044 0.190 1446 Planarity : 0.004 0.047 1761 Dihedral : 6.070 55.874 1327 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 1.95 % Allowed : 17.93 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.99 (0.23), residues: 1211 helix: -0.26 (0.35), residues: 223 sheet: 0.01 (0.41), residues: 155 loop : -0.93 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 136 TYR 0.009 0.001 TYR A 763 PHE 0.020 0.001 PHE A1115 TRP 0.010 0.001 TRP A1159 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9774) covalent geometry : angle 0.57538 (13331) hydrogen bonds : bond 0.02863 ( 220) hydrogen bonds : angle 5.43692 ( 567) *********************** 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 103 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.7998 (mppt) cc_final: 0.7304 (tptt) REVERT: A 136 ARG cc_start: 0.8240 (mtm110) cc_final: 0.7962 (ttp-110) REVERT: A 292 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.6938 (mmmt) REVERT: A 687 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7341 (mppt) REVERT: A 776 GLN cc_start: 0.7396 (tp-100) cc_final: 0.6896 (tp40) REVERT: A 914 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8059 (mmtm) outliers start: 20 outliers final: 13 residues processed: 95 average time/residue: 0.5412 time to fit residues: 55.5535 Evaluate side-chains 94 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 687 LYS Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain A residue 1148 THR Chi-restraints excluded: chain A residue 1255 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 22 optimal weight: 0.0010 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 106 optimal weight: 7.9990 chunk 109 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131783 restraints weight = 42247.374| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 6.64 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9774 Z= 0.095 Angle : 0.562 10.125 13331 Z= 0.285 Chirality : 0.043 0.188 1446 Planarity : 0.004 0.045 1761 Dihedral : 5.900 57.082 1327 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.66 % Allowed : 18.91 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.89 (0.23), residues: 1211 helix: -0.31 (0.35), residues: 229 sheet: 0.08 (0.41), residues: 155 loop : -0.81 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 136 TYR 0.010 0.001 TYR A 763 PHE 0.019 0.001 PHE A1115 TRP 0.011 0.001 TRP A 418 HIS 0.002 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9774) covalent geometry : angle 0.56221 (13331) hydrogen bonds : bond 0.02684 ( 220) hydrogen bonds : angle 5.34186 ( 567) *********************** 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 98 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.7927 (mppt) cc_final: 0.7538 (tmtt) REVERT: A 136 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7580 (ttp-110) REVERT: A 233 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7948 (t) REVERT: A 292 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6759 (mmmt) REVERT: A 776 GLN cc_start: 0.6999 (tp-100) cc_final: 0.6520 (tp40) REVERT: A 1253 LYS cc_start: 0.7433 (ptmm) cc_final: 0.7163 (ptpp) outliers start: 17 outliers final: 10 residues processed: 92 average time/residue: 0.5792 time to fit residues: 57.1718 Evaluate side-chains 90 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 1255 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 90 optimal weight: 0.0170 chunk 10 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.0010 chunk 5 optimal weight: 4.9990 overall best weight: 0.6030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131804 restraints weight = 40637.311| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 6.21 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9774 Z= 0.098 Angle : 0.559 10.125 13331 Z= 0.284 Chirality : 0.043 0.188 1446 Planarity : 0.004 0.044 1761 Dihedral : 5.192 47.054 1315 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.36 % Allowed : 19.40 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.83 (0.23), residues: 1211 helix: -0.25 (0.35), residues: 229 sheet: 0.07 (0.40), residues: 155 loop : -0.77 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 136 TYR 0.009 0.001 TYR A 763 PHE 0.019 0.001 PHE A1115 TRP 0.010 0.001 TRP A 418 HIS 0.002 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9774) covalent geometry : angle 0.55943 (13331) hydrogen bonds : bond 0.02780 ( 220) hydrogen bonds : angle 5.30550 ( 567) ********************** 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 93 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.7255 (mmm160) REVERT: A 98 LYS cc_start: 0.7922 (mppt) cc_final: 0.7390 (tptt) REVERT: A 136 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7613 (ttp-110) REVERT: A 164 PHE cc_start: 0.7770 (m-80) cc_final: 0.7449 (m-80) REVERT: A 233 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7868 (t) REVERT: A 247 ASP cc_start: 0.6953 (t0) cc_final: 0.6685 (p0) REVERT: A 292 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6844 (mmmt) REVERT: A 1253 LYS cc_start: 0.7397 (ptmm) cc_final: 0.7133 (ptpp) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.5514 time to fit residues: 52.2556 Evaluate side-chains 90 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 1255 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 59 optimal weight: 0.0570 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 2 optimal weight: 0.0370 chunk 44 optimal weight: 0.6980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.166805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134160 restraints weight = 54975.996| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 8.35 r_work: 0.3043 rms_B_bonded: 7.53 restraints_weight: 2.0000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9774 Z= 0.094 Angle : 0.829 42.895 13331 Z= 0.386 Chirality : 0.042 0.187 1446 Planarity : 0.004 0.042 1761 Dihedral : 5.147 46.768 1315 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.36 % Allowed : 19.49 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.80 (0.23), residues: 1211 helix: -0.24 (0.35), residues: 229 sheet: 0.08 (0.40), residues: 155 loop : -0.73 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 136 TYR 0.009 0.001 TYR A 763 PHE 0.019 0.001 PHE A1115 TRP 0.011 0.001 TRP A 418 HIS 0.002 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9774) covalent geometry : angle 0.82881 (13331) hydrogen bonds : bond 0.02628 ( 220) hydrogen bonds : angle 5.27984 ( 567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.35 seconds wall clock time: 52 minutes 12.77 seconds (3132.77 seconds total)