Starting phenix.real_space_refine on Fri Jan 17 19:52:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7v_38128/01_2025/8x7v_38128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7v_38128/01_2025/8x7v_38128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7v_38128/01_2025/8x7v_38128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7v_38128/01_2025/8x7v_38128.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7v_38128/01_2025/8x7v_38128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7v_38128/01_2025/8x7v_38128.cif" } resolution = 3.01 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 7121 2.51 5 N 1964 2.21 5 O 2029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11202 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7666 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 36, 'TRANS': 939} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 780 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "C" Number of atoms: 2756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2756 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 332} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 6.47, per 1000 atoms: 0.58 Number of scatterers: 11202 At special positions: 0 Unit cell: (97.9, 108.9, 134.2, 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 88 16.00 O 2029 8.00 N 1964 7.00 C 7121 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: 2.45 Conformation dependent library (CDL) restraints added in 1.5 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2674 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 12 sheets defined 45.9% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 58 through 70 removed outlier: 4.331A pdb=" N GLY A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.523A pdb=" N ALA A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 118 through 133 Processing helix chain 'A' and resid 136 through 150 Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.621A pdb=" N ARG A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 321 through 327 removed outlier: 3.771A pdb=" N LYS A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 340 removed outlier: 3.971A pdb=" N TRP A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.759A pdb=" N LEU A 367 " --> pdb=" O PHE A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.907A pdb=" N ASN A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 497 through 511 removed outlier: 3.544A pdb=" N LEU A 501 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 Processing helix chain 'A' and resid 547 through 555 Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 585 through 598 Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.889A pdb=" N LYS A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 640 removed outlier: 4.254A pdb=" N MET A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 654 Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 660 through 674 Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 716 through 728 removed outlier: 3.556A pdb=" N LEU A 720 " --> pdb=" O GLN A 716 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 762 Processing helix chain 'A' and resid 764 through 780 Processing helix chain 'A' and resid 794 through 807 removed outlier: 4.292A pdb=" N HIS A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 4.859A pdb=" N GLN A 827 " --> pdb=" O PRO A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 836 removed outlier: 3.915A pdb=" N VAL A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 862 Processing helix chain 'A' and resid 879 through 893 Processing helix chain 'A' and resid 907 through 920 Proline residue: A 913 - end of helix removed outlier: 3.825A pdb=" N VAL A 920 " --> pdb=" O ASP A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 950 Processing helix chain 'A' and resid 963 through 976 removed outlier: 3.643A pdb=" N GLY A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1005 removed outlier: 3.515A pdb=" N MET A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1050 through 1064 Processing helix chain 'A' and resid 1077 through 1090 removed outlier: 3.684A pdb=" N GLY A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A1082 " --> pdb=" O GLY A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1121 Processing helix chain 'A' and resid 1135 through 1148 removed outlier: 3.524A pdb=" N CYS A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1177 Processing helix chain 'A' and resid 1192 through 1200 removed outlier: 4.444A pdb=" N TYR A1196 " --> pdb=" O GLU A1192 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A1199 " --> pdb=" O ARG A1195 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A1200 " --> pdb=" O TYR A1196 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 99 through 124 Processing helix chain 'C' and resid 154 through 169 removed outlier: 4.159A pdb=" N THR C 158 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing sheet with id=AA1, first strand: chain 'A' and resid 407 through 408 removed outlier: 6.545A pdb=" N VAL A 283 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL A 429 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS A 285 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 320 removed outlier: 3.501A pdb=" N ASP A 362 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 714 removed outlier: 3.749A pdb=" N ARG A 737 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 739 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 736 " --> pdb=" O ASP A 787 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 788 " --> pdb=" O MET A 816 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 815 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY A 845 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 871 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 902 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 931 " --> pdb=" O LEU A 901 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 959 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 986 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A1043 " --> pdb=" O LEU A1013 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N THR A1073 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU A1044 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU A1072 " --> pdb=" O LYS A1102 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU A1101 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1155 through 1156 Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.526A pdb=" N LEU B 80 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 320 through 321 removed outlier: 8.540A pdb=" N ASP C 321 " --> pdb=" O MET C 280 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE C 282 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 276 " --> pdb=" O THR C 571 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 571 " --> pdb=" O LYS C 276 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 278 " --> pdb=" O GLN C 569 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 567 " --> pdb=" O MET C 280 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE C 282 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 565 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS C 547 " --> pdb=" O GLY C 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 291 through 294 removed outlier: 3.859A pdb=" N ALA C 291 " --> pdb=" O CYS C 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 339 through 342 removed outlier: 3.514A pdb=" N THR C 339 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 352 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 361 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU C 373 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP C 363 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 371 " --> pdb=" O ASP C 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 382 through 388 removed outlier: 3.774A pdb=" N ALA C 384 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL C 402 " --> pdb=" O PHE C 398 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL C 403 " --> pdb=" O ASP C 416 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP C 416 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 405 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 426 through 430 removed outlier: 3.773A pdb=" N SER C 426 " --> pdb=" O GLY C 437 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 437 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 455 " --> pdb=" O CYS C 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 465 through 468 removed outlier: 4.213A pdb=" N SER C 465 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 478 " --> pdb=" O SER C 465 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY C 498 " --> pdb=" O GLN C 484 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 486 " --> pdb=" O MET C 496 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET C 496 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 504 through 509 removed outlier: 3.582A pdb=" N TRP C 516 " --> pdb=" O TYR C 528 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 520 " --> pdb=" O PHE C 524 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE C 524 " --> pdb=" O GLY C 520 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 537 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER C 529 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS C 535 " --> pdb=" O SER C 529 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1503 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: 3.93 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3093 1.33 - 1.45: 1871 1.45 - 1.57: 6359 1.57 - 1.69: 0 1.69 - 1.81: 123 Bond restraints: 11446 Sorted by residual: bond pdb=" N PHE A 744 " pdb=" CA PHE A 744 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.29e-02 6.01e+03 8.02e+00 bond pdb=" N ARG A 136 " pdb=" CA ARG A 136 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.31e-02 5.83e+03 6.98e+00 bond pdb=" N LEU A 135 " pdb=" CA LEU A 135 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.05e+00 bond pdb=" N MET A 133 " pdb=" CA MET A 133 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.42e-02 4.96e+03 5.74e+00 bond pdb=" N ARG A 746 " pdb=" CA ARG A 746 " ideal model delta sigma weight residual 1.457 1.485 -0.029 1.31e-02 5.83e+03 4.77e+00 ... (remaining 11441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 15006 1.57 - 3.15: 401 3.15 - 4.72: 70 4.72 - 6.29: 19 6.29 - 7.86: 5 Bond angle restraints: 15501 Sorted by residual: angle pdb=" N GLU B 61 " pdb=" CA GLU B 61 " pdb=" CB GLU B 61 " ideal model delta sigma weight residual 110.30 115.78 -5.48 1.54e+00 4.22e-01 1.27e+01 angle pdb=" C ASP B 60 " pdb=" N GLU B 61 " pdb=" CA GLU B 61 " ideal model delta sigma weight residual 120.68 114.75 5.93 1.70e+00 3.46e-01 1.22e+01 angle pdb=" C PHE A 744 " pdb=" CA PHE A 744 " pdb=" CB PHE A 744 " ideal model delta sigma weight residual 109.52 114.90 -5.38 1.58e+00 4.01e-01 1.16e+01 angle pdb=" CA TRP A1198 " pdb=" CB TRP A1198 " pdb=" CG TRP A1198 " ideal model delta sigma weight residual 113.60 108.07 5.53 1.90e+00 2.77e-01 8.48e+00 angle pdb=" C LYS A 242 " pdb=" N PHE A 243 " pdb=" CA PHE A 243 " ideal model delta sigma weight residual 121.14 116.26 4.88 1.75e+00 3.27e-01 7.76e+00 ... (remaining 15496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 6238 17.08 - 34.16: 507 34.16 - 51.24: 99 51.24 - 68.32: 16 68.32 - 85.40: 11 Dihedral angle restraints: 6871 sinusoidal: 2768 harmonic: 4103 Sorted by residual: dihedral pdb=" CD ARG A 746 " pdb=" NE ARG A 746 " pdb=" CZ ARG A 746 " pdb=" NH1 ARG A 746 " ideal model delta sinusoidal sigma weight residual 0.00 37.62 -37.62 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA TRP A1187 " pdb=" C TRP A1187 " pdb=" N HIS A1188 " pdb=" CA HIS A1188 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLU A 246 " pdb=" C GLU A 246 " pdb=" N GLU A 247 " pdb=" CA GLU A 247 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 6868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1316 0.045 - 0.089: 300 0.089 - 0.134: 117 0.134 - 0.179: 10 0.179 - 0.224: 3 Chirality restraints: 1746 Sorted by residual: chirality pdb=" CA LEU A 135 " pdb=" N LEU A 135 " pdb=" C LEU A 135 " pdb=" CB LEU A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA TRP A1187 " pdb=" N TRP A1187 " pdb=" C TRP A1187 " pdb=" CB TRP A1187 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE C 451 " pdb=" CA ILE C 451 " pdb=" CG1 ILE C 451 " pdb=" CG2 ILE C 451 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 1743 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 746 " 0.662 9.50e-02 1.11e+02 2.97e-01 5.37e+01 pdb=" NE ARG A 746 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 746 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 746 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 746 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 132 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C ASN A 132 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 132 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 133 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 657 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO A 658 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 658 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 658 " -0.026 5.00e-02 4.00e+02 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 110 2.64 - 3.20: 9906 3.20 - 3.77: 16292 3.77 - 4.33: 22037 4.33 - 4.90: 36854 Nonbonded interactions: 85199 Sorted by model distance: nonbonded pdb=" OG SER C 358 " pdb=" OE1 GLN C 374 " model vdw 2.074 3.040 nonbonded pdb=" NH1 ARG C 415 " pdb=" O ASP C 416 " model vdw 2.152 3.120 nonbonded pdb=" NH2 ARG A 513 " pdb=" O ALA A 563 " model vdw 2.185 3.120 nonbonded pdb=" OE2 GLU C 541 " pdb=" OH TYR C 568 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 642 " pdb=" OD1 ASP A 644 " model vdw 2.199 3.040 ... (remaining 85194 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 : 0.003 0.037 11446 Z= 0.217 Angle : 0.646 7.863 15501 Z= 0.342 Chirality : 0.044 0.224 1746 Planarity : 0.008 0.297 1965 Dihedral : 13.389 85.402 4197 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.08 % Allowed : 0.32 % Favored : 99.60 % 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: 0.16 (0.22), residues: 1396 helix: 1.05 (0.21), residues: 602 sheet: -0.09 (0.31), residues: 285 loop : -0.81 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 115 HIS 0.009 0.001 HIS A 627 PHE 0.031 0.002 PHE A 243 TYR 0.011 0.002 TYR C 420 ARG 0.005 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 745 PRO cc_start: 0.7357 (Cg_endo) cc_final: 0.7109 (Cg_exo) REVERT: A 912 MET cc_start: 0.7428 (mtm) cc_final: 0.7108 (mtp) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2541 time to fit residues: 65.2592 Evaluate side-chains 128 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS A 629 HIS ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A 979 HIS A1188 HIS C 487 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.203198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.161339 restraints weight = 12214.009| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 2.50 r_work: 0.4013 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 11446 Z= 0.489 Angle : 0.819 10.277 15501 Z= 0.421 Chirality : 0.051 0.200 1746 Planarity : 0.006 0.044 1965 Dihedral : 5.359 28.746 1515 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.86 % Allowed : 9.86 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1396 helix: 0.82 (0.20), residues: 601 sheet: -0.13 (0.31), residues: 275 loop : -1.17 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 516 HIS 0.011 0.002 HIS A 627 PHE 0.027 0.003 PHE A 335 TYR 0.023 0.003 TYR C 528 ARG 0.008 0.001 ARG C 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 323 GLU cc_start: 0.7442 (mp0) cc_final: 0.7028 (mp0) REVERT: A 745 PRO cc_start: 0.7359 (Cg_endo) cc_final: 0.7106 (Cg_exo) REVERT: A 838 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8192 (t0) REVERT: A 863 HIS cc_start: 0.7065 (t70) cc_final: 0.6642 (t70) outliers start: 23 outliers final: 18 residues processed: 155 average time/residue: 0.2362 time to fit residues: 52.6758 Evaluate side-chains 150 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1022 ASP Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 495 HIS Chi-restraints excluded: chain C residue 549 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 107 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A 838 ASN ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN A1188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.207872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.164806 restraints weight = 12041.933| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.84 r_work: 0.4100 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11446 Z= 0.177 Angle : 0.565 7.941 15501 Z= 0.293 Chirality : 0.042 0.171 1746 Planarity : 0.004 0.039 1965 Dihedral : 4.755 20.421 1515 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.43 % Allowed : 13.02 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1396 helix: 1.34 (0.21), residues: 607 sheet: -0.03 (0.32), residues: 280 loop : -0.89 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1198 HIS 0.005 0.001 HIS A1012 PHE 0.025 0.001 PHE A 243 TYR 0.012 0.001 TYR A 63 ARG 0.004 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 745 PRO cc_start: 0.6935 (Cg_endo) cc_final: 0.6697 (Cg_exo) REVERT: A 863 HIS cc_start: 0.7140 (t70) cc_final: 0.6714 (t70) outliers start: 30 outliers final: 19 residues processed: 156 average time/residue: 0.2338 time to fit residues: 53.4253 Evaluate side-chains 147 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1152 ASN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 426 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS A 502 HIS A 838 ASN ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.204946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.163754 restraints weight = 12072.145| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.50 r_work: 0.4063 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11446 Z= 0.257 Angle : 0.617 8.174 15501 Z= 0.316 Chirality : 0.044 0.194 1746 Planarity : 0.004 0.043 1965 Dihedral : 4.802 21.633 1515 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.07 % Allowed : 14.87 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1396 helix: 1.31 (0.21), residues: 607 sheet: -0.05 (0.32), residues: 276 loop : -0.99 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 516 HIS 0.007 0.001 HIS A 627 PHE 0.018 0.002 PHE A 243 TYR 0.013 0.002 TYR A 63 ARG 0.004 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 745 PRO cc_start: 0.7096 (Cg_endo) cc_final: 0.6817 (Cg_exo) REVERT: A 863 HIS cc_start: 0.7114 (t70) cc_final: 0.6725 (t70) REVERT: A 1086 CYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7764 (t) REVERT: A 1111 CYS cc_start: 0.6322 (OUTLIER) cc_final: 0.5701 (p) REVERT: A 1122 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6826 (mtt90) REVERT: B 36 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7761 (mt) REVERT: B 109 MET cc_start: 0.7880 (mtp) cc_final: 0.7648 (mtp) REVERT: C 165 ARG cc_start: 0.7863 (mmt90) cc_final: 0.7530 (mmm-85) outliers start: 38 outliers final: 25 residues processed: 155 average time/residue: 0.2419 time to fit residues: 55.2043 Evaluate side-chains 158 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1111 CYS Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 549 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 32 optimal weight: 0.0570 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 137 optimal weight: 0.0370 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 838 ASN ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS A1152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.210094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.167315 restraints weight = 12175.300| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 2.80 r_work: 0.4207 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11446 Z= 0.133 Angle : 0.513 7.886 15501 Z= 0.263 Chirality : 0.040 0.171 1746 Planarity : 0.004 0.037 1965 Dihedral : 4.330 19.326 1515 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.10 % Allowed : 16.65 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.23), residues: 1396 helix: 1.64 (0.21), residues: 603 sheet: 0.10 (0.32), residues: 283 loop : -0.71 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 668 HIS 0.007 0.001 HIS A 238 PHE 0.021 0.001 PHE A 243 TYR 0.007 0.001 TYR C 420 ARG 0.005 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 406 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6731 (mt) REVERT: A 534 MET cc_start: 0.6298 (ttp) cc_final: 0.6001 (ptm) REVERT: A 745 PRO cc_start: 0.6672 (Cg_endo) cc_final: 0.6424 (Cg_exo) REVERT: A 863 HIS cc_start: 0.7108 (t70) cc_final: 0.6706 (t70) REVERT: A 1086 CYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7654 (t) REVERT: A 1111 CYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5657 (p) REVERT: B 109 MET cc_start: 0.7836 (mtp) cc_final: 0.7607 (mtp) REVERT: C 165 ARG cc_start: 0.7652 (mmt90) cc_final: 0.7329 (mmm-85) outliers start: 26 outliers final: 12 residues processed: 154 average time/residue: 0.2606 time to fit residues: 59.0911 Evaluate side-chains 148 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1111 CYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 489 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.0570 chunk 134 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 HIS A1152 ASN A1188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.209703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.166668 restraints weight = 12003.277| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.75 r_work: 0.4123 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11446 Z= 0.162 Angle : 0.543 9.212 15501 Z= 0.276 Chirality : 0.041 0.234 1746 Planarity : 0.004 0.039 1965 Dihedral : 4.285 19.413 1515 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.83 % Allowed : 16.49 % Favored : 80.68 % 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: 0.73 (0.23), residues: 1396 helix: 1.67 (0.21), residues: 603 sheet: 0.09 (0.32), residues: 273 loop : -0.66 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 516 HIS 0.006 0.001 HIS A 238 PHE 0.020 0.001 PHE A 243 TYR 0.010 0.001 TYR A 732 ARG 0.006 0.000 ARG A 872 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.6258 (ttp) cc_final: 0.5940 (ptm) REVERT: A 745 PRO cc_start: 0.6710 (Cg_endo) cc_final: 0.6462 (Cg_exo) REVERT: A 863 HIS cc_start: 0.7096 (t70) cc_final: 0.6740 (t70) REVERT: A 1086 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7704 (t) REVERT: A 1111 CYS cc_start: 0.6164 (OUTLIER) cc_final: 0.5674 (p) REVERT: A 1123 HIS cc_start: 0.6562 (OUTLIER) cc_final: 0.6349 (t-90) REVERT: B 109 MET cc_start: 0.7886 (mtp) cc_final: 0.7668 (mtp) REVERT: C 165 ARG cc_start: 0.7697 (mmt90) cc_final: 0.7367 (mmm-85) REVERT: C 479 MET cc_start: 0.7578 (mmm) cc_final: 0.7104 (mmm) outliers start: 35 outliers final: 20 residues processed: 160 average time/residue: 0.2157 time to fit residues: 51.3285 Evaluate side-chains 155 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1111 CYS Chi-restraints excluded: chain A residue 1123 HIS Chi-restraints excluded: chain A residue 1152 ASN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 566 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 17 optimal weight: 0.1980 chunk 124 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.200756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.153072 restraints weight = 12486.211| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 3.07 r_work: 0.3988 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 11446 Z= 0.156 Angle : 0.543 11.154 15501 Z= 0.274 Chirality : 0.041 0.205 1746 Planarity : 0.004 0.038 1965 Dihedral : 4.232 19.112 1515 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.67 % Allowed : 16.90 % Favored : 80.44 % 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: 0.74 (0.23), residues: 1396 helix: 1.63 (0.21), residues: 604 sheet: 0.14 (0.32), residues: 273 loop : -0.61 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 516 HIS 0.008 0.001 HIS A 238 PHE 0.021 0.001 PHE A 243 TYR 0.011 0.001 TYR C 354 ARG 0.007 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 240 MET cc_start: 0.3650 (ptm) cc_final: 0.3382 (ptp) REVERT: A 534 MET cc_start: 0.6581 (ttp) cc_final: 0.6141 (ptm) REVERT: A 745 PRO cc_start: 0.6647 (Cg_endo) cc_final: 0.6385 (Cg_exo) REVERT: A 798 MET cc_start: 0.7397 (tpp) cc_final: 0.7051 (mmt) REVERT: A 863 HIS cc_start: 0.7166 (t70) cc_final: 0.6531 (t-90) REVERT: A 1086 CYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7887 (t) REVERT: A 1111 CYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5581 (p) REVERT: B 109 MET cc_start: 0.7312 (mtp) cc_final: 0.7099 (mtp) REVERT: C 165 ARG cc_start: 0.7160 (mmt90) cc_final: 0.6814 (mmm-85) outliers start: 33 outliers final: 22 residues processed: 161 average time/residue: 0.2258 time to fit residues: 54.3410 Evaluate side-chains 160 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1111 CYS Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 570 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 130 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.0370 chunk 131 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.197452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.149935 restraints weight = 12475.937| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.00 r_work: 0.4052 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11446 Z= 0.169 Angle : 0.550 9.799 15501 Z= 0.279 Chirality : 0.041 0.192 1746 Planarity : 0.004 0.037 1965 Dihedral : 4.239 19.224 1515 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.99 % Allowed : 16.73 % Favored : 80.27 % 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: 0.72 (0.23), residues: 1396 helix: 1.60 (0.21), residues: 604 sheet: 0.13 (0.32), residues: 273 loop : -0.59 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 115 HIS 0.007 0.001 HIS A 238 PHE 0.020 0.001 PHE A 243 TYR 0.010 0.001 TYR C 568 ARG 0.006 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.3692 (ptm) cc_final: 0.3414 (ptp) REVERT: A 534 MET cc_start: 0.6360 (ttp) cc_final: 0.5965 (ptm) REVERT: A 674 GLN cc_start: 0.5443 (OUTLIER) cc_final: 0.5006 (mt0) REVERT: A 745 PRO cc_start: 0.6629 (Cg_endo) cc_final: 0.6362 (Cg_exo) REVERT: A 798 MET cc_start: 0.7493 (tpp) cc_final: 0.7182 (mmt) REVERT: A 863 HIS cc_start: 0.7105 (t70) cc_final: 0.6553 (t-90) REVERT: A 1086 CYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7798 (t) REVERT: A 1111 CYS cc_start: 0.6212 (OUTLIER) cc_final: 0.5598 (p) REVERT: C 165 ARG cc_start: 0.7276 (mmt90) cc_final: 0.6920 (mmm-85) outliers start: 37 outliers final: 28 residues processed: 162 average time/residue: 0.2088 time to fit residues: 50.5824 Evaluate side-chains 164 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 674 GLN Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1111 CYS Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 570 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.197674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.150581 restraints weight = 12343.682| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.01 r_work: 0.3950 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11446 Z= 0.207 Angle : 0.584 11.704 15501 Z= 0.295 Chirality : 0.042 0.187 1746 Planarity : 0.004 0.039 1965 Dihedral : 4.356 20.042 1515 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.99 % Allowed : 16.57 % Favored : 80.44 % 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: 0.62 (0.23), residues: 1396 helix: 1.52 (0.21), residues: 604 sheet: 0.05 (0.32), residues: 275 loop : -0.63 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 115 HIS 0.008 0.001 HIS A 238 PHE 0.020 0.002 PHE A 243 TYR 0.013 0.001 TYR A 63 ARG 0.006 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.3681 (ptm) cc_final: 0.3405 (ptp) REVERT: A 534 MET cc_start: 0.6366 (ttp) cc_final: 0.5991 (ptm) REVERT: A 674 GLN cc_start: 0.5413 (OUTLIER) cc_final: 0.4984 (mt0) REVERT: A 745 PRO cc_start: 0.6703 (Cg_endo) cc_final: 0.6411 (Cg_exo) REVERT: A 798 MET cc_start: 0.7467 (tpp) cc_final: 0.7150 (mmt) REVERT: A 863 HIS cc_start: 0.7072 (t70) cc_final: 0.6482 (t-90) REVERT: A 1086 CYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7874 (t) REVERT: A 1111 CYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5648 (p) REVERT: C 165 ARG cc_start: 0.7211 (mmt90) cc_final: 0.6850 (mmm-85) outliers start: 37 outliers final: 27 residues processed: 156 average time/residue: 0.2209 time to fit residues: 51.5402 Evaluate side-chains 161 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 674 GLN Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1111 CYS Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 570 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 75 optimal weight: 0.0870 chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.201229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.154008 restraints weight = 12346.177| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.02 r_work: 0.4021 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11446 Z= 0.165 Angle : 0.567 11.823 15501 Z= 0.283 Chirality : 0.041 0.178 1746 Planarity : 0.004 0.038 1965 Dihedral : 4.248 19.325 1515 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.67 % Allowed : 16.90 % Favored : 80.44 % 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: 0.68 (0.23), residues: 1396 helix: 1.54 (0.21), residues: 604 sheet: 0.09 (0.32), residues: 275 loop : -0.58 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 115 HIS 0.008 0.001 HIS A 238 PHE 0.021 0.001 PHE A 243 TYR 0.010 0.001 TYR A 63 ARG 0.007 0.000 ARG C 415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.3657 (ptm) cc_final: 0.3386 (ptp) REVERT: A 534 MET cc_start: 0.6318 (ttp) cc_final: 0.5954 (ptm) REVERT: A 674 GLN cc_start: 0.5340 (OUTLIER) cc_final: 0.4885 (mt0) REVERT: A 745 PRO cc_start: 0.6614 (Cg_endo) cc_final: 0.6331 (Cg_exo) REVERT: A 798 MET cc_start: 0.7414 (tpp) cc_final: 0.7133 (mmt) REVERT: A 863 HIS cc_start: 0.7066 (t70) cc_final: 0.6525 (t-90) REVERT: A 1086 CYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7840 (t) REVERT: A 1111 CYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5601 (p) REVERT: C 165 ARG cc_start: 0.7171 (mmt90) cc_final: 0.6816 (mmm-85) outliers start: 33 outliers final: 28 residues processed: 154 average time/residue: 0.2177 time to fit residues: 49.7078 Evaluate side-chains 165 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 674 GLN Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain A residue 941 GLN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1086 CYS Chi-restraints excluded: chain A residue 1111 CYS Chi-restraints excluded: chain A residue 1198 TRP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 570 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 133 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 863 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.198476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.151524 restraints weight = 12319.520| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 3.00 r_work: 0.4014 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11446 Z= 0.179 Angle : 0.578 12.048 15501 Z= 0.289 Chirality : 0.042 0.216 1746 Planarity : 0.004 0.038 1965 Dihedral : 4.262 19.664 1515 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.67 % Allowed : 17.14 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1396 helix: 1.53 (0.21), residues: 604 sheet: 0.08 (0.33), residues: 275 loop : -0.58 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 115 HIS 0.008 0.001 HIS A 238 PHE 0.022 0.001 PHE A 243 TYR 0.011 0.001 TYR A 63 ARG 0.007 0.000 ARG C 415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6095.07 seconds wall clock time: 110 minutes 3.79 seconds (6603.79 seconds total)