Starting phenix.real_space_refine on Fri Feb 14 03:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r3q_4719/02_2025/6r3q_4719.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r3q_4719/02_2025/6r3q_4719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r3q_4719/02_2025/6r3q_4719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r3q_4719/02_2025/6r3q_4719.map" model { file = "/net/cci-nas-00/data/ceres_data/6r3q_4719/02_2025/6r3q_4719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r3q_4719/02_2025/6r3q_4719.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 81 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 69 5.16 5 C 6130 2.51 5 N 1599 2.21 5 O 1727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9529 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6687 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 20, 'TRANS': 820} Chain breaks: 6 Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2809 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.77, per 1000 atoms: 0.61 Number of scatterers: 9529 At special positions: 0 Unit cell: (162.8, 105.006, 105.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 3 15.00 Mg 1 11.99 O 1727 8.00 N 1599 7.00 C 6130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 60.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.725A pdb=" N MET A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 137 removed outlier: 3.750A pdb=" N THR A 112 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 removed outlier: 3.577A pdb=" N ALA A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 192 Processing helix chain 'A' and resid 219 through 237 removed outlier: 4.227A pdb=" N SER A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 261 removed outlier: 3.552A pdb=" N TYR A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 336 removed outlier: 3.615A pdb=" N PHE A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 351 through 359 removed outlier: 4.185A pdb=" N GLU A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 457 through 481 Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.899A pdb=" N ASN A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 785 through 807 Processing helix chain 'A' and resid 817 through 844 removed outlier: 4.155A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 859 removed outlier: 3.529A pdb=" N TRP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 882 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 892 through 907 Processing helix chain 'A' and resid 916 through 935 removed outlier: 3.842A pdb=" N ARG A 920 " --> pdb=" O SER A 916 " (cutoff:3.500A) Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 978 through 1037 removed outlier: 3.596A pdb=" N ALA A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1047 removed outlier: 3.723A pdb=" N VAL A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1069 No H-bonds generated for 'chain 'A' and resid 1067 through 1069' Processing helix chain 'A' and resid 1079 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1133 through 1156 removed outlier: 4.092A pdb=" N GLN A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A1156 " --> pdb=" O ASP A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 3.958A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1218 Processing helix chain 'A' and resid 1219 through 1221 No H-bonds generated for 'chain 'A' and resid 1219 through 1221' Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.681A pdb=" N ASP B 33 " --> pdb=" O GLN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 89 through 112 removed outlier: 3.881A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 174 through 185 removed outlier: 4.042A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.637A pdb=" N ARG B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 235 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 236 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 238 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.886A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 388 removed outlier: 3.558A pdb=" N ILE B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 441 removed outlier: 7.312A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 386 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY A 493 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 394 " --> pdb=" O HIS A 491 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A 491 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 396 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY A 489 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 398 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A 487 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE A 400 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 485 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 441 removed outlier: 7.312A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 386 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY A 493 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 394 " --> pdb=" O HIS A 491 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A 491 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 396 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY A 489 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 398 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A 487 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE A 400 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 485 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N HIS A 530 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 488 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 570 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1105 through 1111 removed outlier: 7.401A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY A1059 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A1052 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A1177 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN A1054 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A1175 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP A1056 " --> pdb=" O LEU A1173 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU A1173 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1111 removed outlier: 7.401A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY A1059 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A1052 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A1177 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN A1054 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A1175 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP A1056 " --> pdb=" O LEU A1173 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU A1173 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 214 removed outlier: 5.626A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL B 287 " --> pdb=" O TYR B 360 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1752 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: 3.31 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1897 1.32 - 1.44: 2347 1.44 - 1.57: 5380 1.57 - 1.69: 5 1.69 - 1.81: 106 Bond restraints: 9735 Sorted by residual: bond pdb=" C LYS A 549 " pdb=" N VAL A 550 " ideal model delta sigma weight residual 1.332 1.286 0.046 1.73e-02 3.34e+03 6.96e+00 bond pdb=" CD LYS A1107 " pdb=" CE LYS A1107 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.73e+00 bond pdb=" CG LEU A1164 " pdb=" CD2 LEU A1164 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.65e+00 bond pdb=" SD MET A 469 " pdb=" CE MET A 469 " ideal model delta sigma weight residual 1.791 1.732 0.059 2.50e-02 1.60e+03 5.48e+00 bond pdb=" CB TRP A 510 " pdb=" CG TRP A 510 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 4.94e+00 ... (remaining 9730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 12608 2.68 - 5.35: 475 5.35 - 8.03: 60 8.03 - 10.71: 20 10.71 - 13.38: 8 Bond angle restraints: 13171 Sorted by residual: angle pdb=" N LEU A 875 " pdb=" CA LEU A 875 " pdb=" C LEU A 875 " ideal model delta sigma weight residual 109.81 121.90 -12.09 2.21e+00 2.05e-01 2.99e+01 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 131.43 -9.89 1.91e+00 2.74e-01 2.68e+01 angle pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C LYS A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 122.97 118.46 4.51 9.80e-01 1.04e+00 2.12e+01 angle pdb=" C VAL B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 ... (remaining 13166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 5253 15.24 - 30.48: 382 30.48 - 45.72: 127 45.72 - 60.95: 15 60.95 - 76.19: 10 Dihedral angle restraints: 5787 sinusoidal: 2329 harmonic: 3458 Sorted by residual: dihedral pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta harmonic sigma weight residual 180.00 144.43 35.57 0 5.00e+00 4.00e-02 5.06e+01 dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual 180.00 -148.87 -31.13 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA CYS A 910 " pdb=" C CYS A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta harmonic sigma weight residual -180.00 -153.42 -26.58 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 5784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1308 0.109 - 0.218: 161 0.218 - 0.328: 13 0.328 - 0.437: 0 0.437 - 0.546: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CB VAL A 986 " pdb=" CA VAL A 986 " pdb=" CG1 VAL A 986 " pdb=" CG2 VAL A 986 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" CG LEU B 99 " pdb=" CB LEU B 99 " pdb=" CD1 LEU B 99 " pdb=" CD2 LEU B 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 1481 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 385 " -0.016 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHE A 385 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 385 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 385 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 385 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 385 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 385 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " -0.030 2.00e-02 2.50e+03 2.66e-02 1.24e+01 pdb=" CG PHE A 232 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO B 115 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.041 5.00e-02 4.00e+02 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 142 2.64 - 3.21: 8594 3.21 - 3.77: 15256 3.77 - 4.34: 19710 4.34 - 4.90: 32248 Nonbonded interactions: 75950 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 2.080 2.170 nonbonded pdb=" OG SER B 54 " pdb="MG MG B 502 " model vdw 2.113 2.170 nonbonded pdb=" OG1 THR B 204 " pdb="MG MG B 502 " model vdw 2.119 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.124 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.205 3.040 ... (remaining 75945 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: 2.170 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.570 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.011 0.082 9735 Z= 0.705 Angle : 1.245 13.383 13171 Z= 0.651 Chirality : 0.072 0.546 1484 Planarity : 0.008 0.074 1655 Dihedral : 12.612 76.192 3549 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.58 % Allowed : 8.36 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.20), residues: 1164 helix: -2.14 (0.15), residues: 684 sheet: -2.03 (0.43), residues: 136 loop : -2.85 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 918 HIS 0.016 0.003 HIS A 491 PHE 0.060 0.005 PHE A 232 TYR 0.050 0.004 TYR A 446 ARG 0.016 0.002 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.7842 (t80) cc_final: 0.7457 (t80) REVERT: A 138 MET cc_start: 0.6930 (ttt) cc_final: 0.6257 (ttt) REVERT: A 152 PHE cc_start: 0.6885 (t80) cc_final: 0.6632 (t80) REVERT: A 182 LEU cc_start: 0.8690 (mp) cc_final: 0.8428 (mp) REVERT: A 333 MET cc_start: 0.8765 (mmt) cc_final: 0.8547 (mmp) REVERT: A 987 PHE cc_start: 0.8294 (m-80) cc_final: 0.8056 (m-80) REVERT: A 1006 ARG cc_start: 0.6909 (ttm-80) cc_final: 0.6473 (mmp-170) REVERT: B 174 CYS cc_start: 0.7864 (p) cc_final: 0.7382 (p) outliers start: 6 outliers final: 2 residues processed: 179 average time/residue: 0.2202 time to fit residues: 55.7634 Evaluate side-chains 101 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 HIS A1055 HIS A1154 ASN A1169 ASN A1231 ASN B 31 GLN B 98 ASN B 239 ASN B 264 ASN B 357 HIS B 362 HIS B 371 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.105128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.083993 restraints weight = 25734.141| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.03 r_work: 0.3305 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9735 Z= 0.220 Angle : 0.699 12.664 13171 Z= 0.352 Chirality : 0.044 0.193 1484 Planarity : 0.005 0.066 1655 Dihedral : 5.668 34.843 1300 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.65 % Allowed : 11.24 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.23), residues: 1164 helix: -0.04 (0.19), residues: 686 sheet: -1.98 (0.41), residues: 137 loop : -2.31 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1159 HIS 0.004 0.001 HIS B 387 PHE 0.018 0.002 PHE A 232 TYR 0.026 0.002 TYR A 446 ARG 0.004 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8028 (t80) cc_final: 0.7354 (t80) REVERT: A 138 MET cc_start: 0.7397 (ttt) cc_final: 0.7109 (ttm) REVERT: A 181 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8180 (mm) REVERT: A 232 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8600 (m-10) REVERT: A 239 HIS cc_start: 0.8394 (t-90) cc_final: 0.8073 (t-90) REVERT: A 248 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7953 (tp) REVERT: A 795 THR cc_start: 0.8876 (t) cc_final: 0.8669 (m) REVERT: A 896 MET cc_start: 0.8233 (mtm) cc_final: 0.7998 (mtp) REVERT: A 1002 GLU cc_start: 0.8077 (pp20) cc_final: 0.7826 (tm-30) REVERT: A 1006 ARG cc_start: 0.7179 (ttm-80) cc_final: 0.6708 (mmp-170) REVERT: A 1164 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8861 (pt) REVERT: B 110 MET cc_start: 0.8158 (mmt) cc_final: 0.7812 (mmt) REVERT: B 174 CYS cc_start: 0.8113 (p) cc_final: 0.7718 (p) outliers start: 38 outliers final: 16 residues processed: 163 average time/residue: 0.1718 time to fit residues: 42.4883 Evaluate side-chains 133 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 0.0050 chunk 5 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.106283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.085481 restraints weight = 26094.777| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.07 r_work: 0.3337 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9735 Z= 0.158 Angle : 0.646 13.931 13171 Z= 0.315 Chirality : 0.042 0.169 1484 Planarity : 0.004 0.059 1655 Dihedral : 5.042 31.968 1300 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.88 % Allowed : 14.02 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1164 helix: 0.92 (0.20), residues: 684 sheet: -1.72 (0.42), residues: 133 loop : -2.04 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.019 0.001 PHE A 897 TYR 0.021 0.001 TYR A 446 ARG 0.004 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 232 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8554 (m-10) REVERT: A 248 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7921 (tp) REVERT: A 340 ARG cc_start: 0.8058 (mmp80) cc_final: 0.7852 (mmp80) REVERT: A 537 LYS cc_start: 0.8602 (ptpt) cc_final: 0.8335 (ptpp) REVERT: A 1002 GLU cc_start: 0.7960 (pp20) cc_final: 0.7744 (tp30) REVERT: A 1006 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.6662 (mmp-170) REVERT: B 99 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9305 (tp) outliers start: 30 outliers final: 16 residues processed: 150 average time/residue: 0.1828 time to fit residues: 40.8538 Evaluate side-chains 127 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 0.0870 chunk 43 optimal weight: 4.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.105242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084268 restraints weight = 25805.578| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.03 r_work: 0.3311 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9735 Z= 0.182 Angle : 0.644 14.334 13171 Z= 0.312 Chirality : 0.042 0.168 1484 Planarity : 0.004 0.058 1655 Dihedral : 4.766 30.915 1298 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.65 % Allowed : 14.99 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1164 helix: 1.32 (0.20), residues: 687 sheet: -1.42 (0.44), residues: 131 loop : -1.84 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.015 0.001 PHE A 160 TYR 0.019 0.001 TYR A 446 ARG 0.006 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 1.058 Fit side-chains REVERT: A 138 MET cc_start: 0.7477 (ttt) cc_final: 0.7107 (ttm) REVERT: A 181 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8071 (mm) REVERT: A 232 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8596 (m-10) REVERT: A 248 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7971 (tp) REVERT: A 841 MET cc_start: 0.5986 (ttp) cc_final: 0.5743 (ptm) REVERT: A 1002 GLU cc_start: 0.8086 (pp20) cc_final: 0.7869 (tp30) REVERT: A 1006 ARG cc_start: 0.7106 (ttm-80) cc_final: 0.6644 (mmp-170) REVERT: B 99 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9317 (tp) outliers start: 38 outliers final: 20 residues processed: 147 average time/residue: 0.1766 time to fit residues: 39.3971 Evaluate side-chains 135 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 HIS ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.103369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082260 restraints weight = 26218.378| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.02 r_work: 0.3267 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9735 Z= 0.253 Angle : 0.682 14.566 13171 Z= 0.333 Chirality : 0.044 0.226 1484 Planarity : 0.004 0.054 1655 Dihedral : 4.819 31.638 1298 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.51 % Allowed : 14.89 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1164 helix: 1.45 (0.20), residues: 684 sheet: -1.52 (0.43), residues: 135 loop : -1.92 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 PHE 0.016 0.002 PHE A 232 TYR 0.022 0.002 TYR A 446 ARG 0.006 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 1.124 Fit side-chains REVERT: A 138 MET cc_start: 0.7495 (ttt) cc_final: 0.7139 (ttm) REVERT: A 181 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8172 (mm) REVERT: A 232 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8660 (m-10) REVERT: A 248 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7974 (tp) REVERT: A 385 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8218 (p90) REVERT: A 464 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8345 (mm-30) REVERT: A 792 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8279 (tt) REVERT: A 841 MET cc_start: 0.5906 (ttp) cc_final: 0.5680 (ptm) REVERT: A 896 MET cc_start: 0.8279 (mtm) cc_final: 0.7988 (mmm) REVERT: A 1002 GLU cc_start: 0.8104 (pp20) cc_final: 0.7603 (tm-30) REVERT: A 1006 ARG cc_start: 0.7203 (ttm-80) cc_final: 0.6687 (mmp-170) REVERT: B 99 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9325 (tp) outliers start: 47 outliers final: 27 residues processed: 147 average time/residue: 0.1675 time to fit residues: 38.1627 Evaluate side-chains 139 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.103555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082463 restraints weight = 26160.051| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.01 r_work: 0.3274 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9735 Z= 0.223 Angle : 0.678 15.020 13171 Z= 0.325 Chirality : 0.044 0.188 1484 Planarity : 0.004 0.046 1655 Dihedral : 4.771 30.358 1298 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.32 % Allowed : 15.66 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1164 helix: 1.60 (0.20), residues: 679 sheet: -1.55 (0.42), residues: 135 loop : -1.62 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1159 HIS 0.006 0.001 HIS A 530 PHE 0.015 0.001 PHE A 232 TYR 0.020 0.001 TYR A 446 ARG 0.006 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.7494 (ttt) cc_final: 0.7201 (ttm) REVERT: A 232 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8633 (m-10) REVERT: A 248 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7965 (tp) REVERT: A 385 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8061 (p90) REVERT: A 464 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 537 LYS cc_start: 0.8536 (ptpp) cc_final: 0.8198 (ptpp) REVERT: A 1002 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: A 1006 ARG cc_start: 0.7183 (ttm-80) cc_final: 0.6675 (mmp-170) REVERT: B 99 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9344 (tp) outliers start: 45 outliers final: 31 residues processed: 145 average time/residue: 0.1742 time to fit residues: 39.2432 Evaluate side-chains 143 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.105061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.084124 restraints weight = 26409.991| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.04 r_work: 0.3306 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9735 Z= 0.173 Angle : 0.656 15.761 13171 Z= 0.312 Chirality : 0.043 0.208 1484 Planarity : 0.004 0.041 1655 Dihedral : 4.579 28.753 1298 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.55 % Allowed : 16.71 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1164 helix: 1.74 (0.20), residues: 684 sheet: -1.53 (0.42), residues: 135 loop : -1.49 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.004 0.001 HIS A 530 PHE 0.013 0.001 PHE A 232 TYR 0.019 0.001 TYR A 446 ARG 0.005 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.7515 (ttt) cc_final: 0.7233 (ttm) REVERT: A 232 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8604 (m-10) REVERT: A 464 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8356 (mm-30) REVERT: A 1002 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: A 1006 ARG cc_start: 0.7158 (ttm-80) cc_final: 0.6645 (mmp-170) REVERT: B 99 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9345 (tp) REVERT: B 266 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8721 (tt) outliers start: 37 outliers final: 27 residues processed: 145 average time/residue: 0.1707 time to fit residues: 37.7830 Evaluate side-chains 142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.105787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.084976 restraints weight = 26615.228| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.07 r_work: 0.3324 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9735 Z= 0.169 Angle : 0.656 16.045 13171 Z= 0.310 Chirality : 0.042 0.166 1484 Planarity : 0.004 0.039 1655 Dihedral : 4.472 28.340 1298 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.65 % Allowed : 17.20 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1164 helix: 1.90 (0.20), residues: 682 sheet: -1.41 (0.42), residues: 128 loop : -1.51 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.012 0.001 PHE A 232 TYR 0.018 0.001 TYR A 446 ARG 0.004 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 1.088 Fit side-chains REVERT: A 138 MET cc_start: 0.7524 (ttt) cc_final: 0.7228 (ttm) REVERT: A 232 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8508 (m-10) REVERT: A 248 LEU cc_start: 0.8560 (mm) cc_final: 0.8118 (tp) REVERT: A 464 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8374 (mm-30) REVERT: A 1006 ARG cc_start: 0.7069 (ttm-80) cc_final: 0.5208 (tpt170) REVERT: B 99 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9350 (tp) REVERT: B 110 MET cc_start: 0.8355 (mmt) cc_final: 0.7894 (mmt) REVERT: B 266 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8718 (tt) outliers start: 38 outliers final: 28 residues processed: 144 average time/residue: 0.1744 time to fit residues: 38.2092 Evaluate side-chains 142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 10 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: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.106155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085578 restraints weight = 25982.119| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.04 r_work: 0.3339 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9735 Z= 0.173 Angle : 0.678 16.784 13171 Z= 0.317 Chirality : 0.043 0.186 1484 Planarity : 0.004 0.039 1655 Dihedral : 4.321 27.234 1297 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.07 % Allowed : 17.77 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1164 helix: 1.95 (0.20), residues: 681 sheet: -1.20 (0.43), residues: 126 loop : -1.44 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.013 0.001 PHE A 232 TYR 0.018 0.001 TYR A 446 ARG 0.005 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.7527 (ttt) cc_final: 0.7215 (ttm) REVERT: A 232 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: A 248 LEU cc_start: 0.8582 (mm) cc_final: 0.8067 (tp) REVERT: A 464 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8373 (mm-30) REVERT: A 1002 GLU cc_start: 0.7756 (tp30) cc_final: 0.7202 (tp30) REVERT: A 1006 ARG cc_start: 0.6862 (ttm-80) cc_final: 0.5082 (tpt170) REVERT: A 1145 GLU cc_start: 0.7913 (tt0) cc_final: 0.7480 (tp30) REVERT: B 99 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9345 (tp) REVERT: B 266 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8714 (tt) outliers start: 32 outliers final: 26 residues processed: 144 average time/residue: 0.1780 time to fit residues: 39.0268 Evaluate side-chains 142 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.053 > 50: distance: 75 - 79: 34.998 distance: 80 - 83: 40.579 distance: 81 - 82: 39.317 distance: 81 - 91: 40.957 distance: 83 - 84: 46.290 distance: 84 - 85: 21.413 distance: 84 - 86: 17.594 distance: 85 - 87: 39.640 distance: 86 - 88: 48.559 distance: 88 - 89: 11.194 distance: 92 - 93: 36.515 distance: 92 - 95: 36.313 distance: 93 - 100: 57.167 distance: 100 - 101: 39.043 distance: 101 - 104: 41.133 distance: 105 - 106: 39.200 distance: 105 - 107: 41.077 distance: 108 - 109: 40.805 distance: 109 - 110: 39.441 distance: 109 - 112: 56.252 distance: 110 - 116: 40.203 distance: 112 - 113: 39.153 distance: 112 - 114: 57.755 distance: 113 - 115: 41.333 distance: 117 - 120: 40.662 distance: 118 - 119: 39.838 distance: 118 - 124: 39.170 distance: 120 - 121: 40.597 distance: 121 - 122: 39.561 distance: 121 - 123: 40.982 distance: 124 - 125: 39.935 distance: 125 - 126: 56.603 distance: 126 - 127: 39.015 distance: 127 - 156: 40.313 distance: 128 - 129: 40.380 distance: 130 - 131: 40.534 distance: 131 - 132: 41.019 distance: 131 - 134: 44.314 distance: 132 - 133: 39.357 distance: 132 - 135: 56.551 distance: 133 - 167: 31.457 distance: 135 - 136: 5.892 distance: 136 - 137: 6.373 distance: 136 - 139: 6.015 distance: 137 - 138: 40.567 distance: 137 - 144: 38.881 distance: 139 - 140: 40.587 distance: 140 - 141: 49.128 distance: 141 - 142: 10.692 distance: 141 - 143: 53.707 distance: 145 - 146: 55.994 distance: 145 - 148: 39.995 distance: 146 - 147: 40.413 distance: 146 - 156: 39.034 distance: 147 - 183: 35.399 distance: 148 - 149: 48.919 distance: 149 - 150: 42.882 distance: 149 - 151: 49.598 distance: 150 - 152: 10.201 distance: 152 - 154: 39.307 distance: 157 - 158: 40.183 distance: 158 - 159: 57.043 distance: 158 - 167: 34.341 distance: 159 - 192: 36.715 distance: 161 - 162: 18.387 distance: 161 - 163: 16.695 distance: 162 - 164: 44.910 distance: 163 - 165: 39.785 distance: 164 - 166: 40.490 distance: 165 - 166: 39.913