Starting phenix.real_space_refine on Sun Dec 29 19:32:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7v_38128/12_2024/8x7v_38128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7v_38128/12_2024/8x7v_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_38128/12_2024/8x7v_38128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7v_38128/12_2024/8x7v_38128.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7v_38128/12_2024/8x7v_38128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7v_38128/12_2024/8x7v_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.59, per 1000 atoms: 0.59 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: 2.63 Conformation dependent library (CDL) restraints added in 1.6 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: 1.34 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: 4.44 Time building geometry restraints manager: 3.08 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: 0.960 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.050 Find NCS groups from input model: 0.100 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: 0.010 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: 32.510 ------------------------------------------------------------------------------- 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 : 1.280 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: 0.2625 time to fit residues: 67.5140 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 : 1.178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 1.261 Fit side-chains revert: symmetry clash REVERT: A 323 GLU cc_start: 0.7446 (mp0) cc_final: 0.7071 (mp0) REVERT: A 745 PRO cc_start: 0.7423 (Cg_endo) cc_final: 0.7180 (Cg_exo) REVERT: A 838 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.8084 (t0) REVERT: A 863 HIS cc_start: 0.6801 (t70) cc_final: 0.6475 (t70) outliers start: 23 outliers final: 18 residues processed: 155 average time/residue: 0.2367 time to fit residues: 53.1264 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 : 1.284 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 0.042 11446 Z= 0.182 Angle : 0.569 7.940 15501 Z= 0.295 Chirality : 0.042 0.171 1746 Planarity : 0.004 0.040 1965 Dihedral : 4.772 20.510 1515 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 0.33 (0.23), residues: 1396 helix: 1.32 (0.21), residues: 607 sheet: -0.04 (0.32), residues: 280 loop : -0.91 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1198 HIS 0.005 0.001 HIS A 627 PHE 0.024 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 : 1.280 Fit side-chains revert: symmetry clash REVERT: A 745 PRO cc_start: 0.7030 (Cg_endo) cc_final: 0.6803 (Cg_exo) REVERT: A 863 HIS cc_start: 0.6910 (t70) cc_final: 0.6588 (t70) outliers start: 30 outliers final: 19 residues processed: 156 average time/residue: 0.2412 time to fit residues: 54.9024 Evaluate side-chains 146 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 125 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** A1152 ASN A1188 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11446 Z= 0.195 Angle : 0.573 10.135 15501 Z= 0.293 Chirality : 0.042 0.173 1746 Planarity : 0.004 0.040 1965 Dihedral : 4.644 20.592 1515 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.67 % Allowed : 14.55 % Favored : 82.78 % 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: 0.47 (0.23), residues: 1396 helix: 1.49 (0.21), residues: 601 sheet: 0.01 (0.32), residues: 278 loop : -0.86 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 516 HIS 0.006 0.001 HIS A 238 PHE 0.019 0.002 PHE A 243 TYR 0.011 0.001 TYR A 63 ARG 0.006 0.000 ARG C 338 *********************** 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 165 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 745 PRO cc_start: 0.6857 (Cg_endo) cc_final: 0.6603 (Cg_exo) REVERT: A 863 HIS cc_start: 0.6874 (t70) cc_final: 0.6566 (t70) REVERT: A 1086 CYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7313 (t) REVERT: A 1111 CYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5784 (p) REVERT: B 36 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7686 (mt) REVERT: B 109 MET cc_start: 0.7949 (mtp) cc_final: 0.7723 (mtp) REVERT: C 165 ARG cc_start: 0.7612 (mmt90) cc_final: 0.7300 (mmm-85) outliers start: 33 outliers final: 23 residues processed: 152 average time/residue: 0.2214 time to fit residues: 49.6974 Evaluate side-chains 153 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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** A 979 HIS A1152 ASN A1188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11446 Z= 0.152 Angle : 0.534 8.748 15501 Z= 0.274 Chirality : 0.041 0.174 1746 Planarity : 0.004 0.039 1965 Dihedral : 4.440 19.760 1515 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.75 % Allowed : 15.68 % Favored : 81.57 % 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: 0.64 (0.23), residues: 1396 helix: 1.63 (0.21), residues: 602 sheet: 0.04 (0.32), residues: 281 loop : -0.75 (0.27), residues: 513 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 0.023 0.001 PHE A 243 TYR 0.009 0.001 TYR A 63 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 169 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 745 PRO cc_start: 0.6795 (Cg_endo) cc_final: 0.6558 (Cg_exo) REVERT: A 863 HIS cc_start: 0.6875 (t70) cc_final: 0.6573 (t70) REVERT: A 1086 CYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7310 (t) REVERT: A 1111 CYS cc_start: 0.6080 (OUTLIER) cc_final: 0.5682 (p) REVERT: B 36 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7616 (mt) REVERT: C 165 ARG cc_start: 0.7516 (mmt90) cc_final: 0.7211 (mmm-85) outliers start: 34 outliers final: 20 residues processed: 156 average time/residue: 0.2367 time to fit residues: 54.4447 Evaluate side-chains 153 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 313 PHE 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 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 1152 ASN 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 282 ILE Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 549 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11446 Z= 0.166 Angle : 0.556 9.520 15501 Z= 0.284 Chirality : 0.041 0.182 1746 Planarity : 0.004 0.040 1965 Dihedral : 4.388 19.615 1515 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.31 % Allowed : 15.93 % Favored : 80.76 % 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: 1.61 (0.21), residues: 603 sheet: 0.08 (0.32), residues: 280 loop : -0.70 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 516 HIS 0.007 0.001 HIS A 238 PHE 0.021 0.001 PHE A 243 TYR 0.011 0.001 TYR A 63 ARG 0.005 0.000 ARG C 338 *********************** 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 173 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.5730 (ptm) cc_final: 0.5454 (ttp) REVERT: A 745 PRO cc_start: 0.6787 (Cg_endo) cc_final: 0.6547 (Cg_exo) REVERT: A 863 HIS cc_start: 0.6845 (t70) cc_final: 0.6572 (t70) REVERT: A 1086 CYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7344 (t) REVERT: A 1111 CYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5668 (p) REVERT: B 36 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7617 (mt) REVERT: C 165 ARG cc_start: 0.7522 (mmt90) cc_final: 0.7216 (mmm-85) outliers start: 41 outliers final: 25 residues processed: 158 average time/residue: 0.2271 time to fit residues: 52.6828 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 : 1.349 ------------------------------------------------------------------------------- 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 402 GLU 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 696 ASP 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 1152 ASN 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 525 LEU Chi-restraints excluded: chain C residue 549 ASP 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 15 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 114 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 11446 Z= 0.147 Angle : 0.541 11.234 15501 Z= 0.274 Chirality : 0.041 0.186 1746 Planarity : 0.004 0.039 1965 Dihedral : 4.294 19.074 1515 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.59 % Allowed : 16.90 % Favored : 80.52 % 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: 0.71 (0.23), residues: 1396 helix: 1.61 (0.21), residues: 603 sheet: 0.11 (0.32), residues: 273 loop : -0.63 (0.27), residues: 520 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 0.020 0.001 PHE A 243 TYR 0.012 0.001 TYR A 732 ARG 0.006 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 167 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.5693 (ptm) cc_final: 0.5441 (ttp) REVERT: A 745 PRO cc_start: 0.6643 (Cg_endo) cc_final: 0.6409 (Cg_exo) REVERT: A 863 HIS cc_start: 0.6833 (t70) cc_final: 0.6569 (t70) REVERT: A 1086 CYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7311 (t) REVERT: A 1111 CYS cc_start: 0.5997 (OUTLIER) cc_final: 0.5611 (p) REVERT: C 165 ARG cc_start: 0.7508 (mmt90) cc_final: 0.7210 (mmm-85) outliers start: 32 outliers final: 20 residues processed: 156 average time/residue: 0.2282 time to fit residues: 53.3576 Evaluate side-chains 154 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 402 GLU 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 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 95 THR Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 566 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** A1152 ASN A1188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11446 Z= 0.364 Angle : 0.697 10.309 15501 Z= 0.357 Chirality : 0.046 0.185 1746 Planarity : 0.005 0.042 1965 Dihedral : 4.889 23.093 1515 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.40 % Allowed : 17.14 % Favored : 79.47 % 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: 0.21 (0.22), residues: 1396 helix: 1.21 (0.21), residues: 602 sheet: 0.03 (0.32), residues: 272 loop : -1.01 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 516 HIS 0.009 0.002 HIS A 627 PHE 0.028 0.002 PHE A 404 TYR 0.019 0.002 TYR C 568 ARG 0.006 0.001 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 172 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.5880 (ptm) cc_final: 0.5581 (ttp) REVERT: A 674 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.6032 (mt0) REVERT: A 745 PRO cc_start: 0.7130 (Cg_endo) cc_final: 0.6862 (Cg_exo) REVERT: A 863 HIS cc_start: 0.6731 (t70) cc_final: 0.6509 (t-90) REVERT: A 1086 CYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7519 (t) REVERT: A 1111 CYS cc_start: 0.6456 (OUTLIER) cc_final: 0.5911 (p) REVERT: C 165 ARG cc_start: 0.7692 (mmt90) cc_final: 0.7385 (mmm-85) REVERT: C 464 MET cc_start: 0.7115 (mmp) cc_final: 0.6837 (mmp) outliers start: 42 outliers final: 28 residues processed: 160 average time/residue: 0.2528 time to fit residues: 60.9927 Evaluate side-chains 161 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 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 674 GLN 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 948 VAL Chi-restraints excluded: chain A residue 960 ASN 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 1152 ASN Chi-restraints excluded: chain A residue 1187 TRP 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 549 ASP 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 117 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2272 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= 0.186 Angle : 0.595 11.393 15501 Z= 0.302 Chirality : 0.042 0.177 1746 Planarity : 0.004 0.040 1965 Dihedral : 4.613 21.292 1515 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.67 % Allowed : 17.46 % Favored : 79.87 % 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 (0.23), residues: 1396 helix: 1.40 (0.21), residues: 602 sheet: -0.02 (0.32), residues: 280 loop : -0.84 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 115 HIS 0.009 0.001 HIS A 238 PHE 0.020 0.001 PHE A 243 TYR 0.010 0.001 TYR C 568 ARG 0.007 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 167 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 GLN cc_start: 0.6356 (OUTLIER) cc_final: 0.5890 (mt0) REVERT: A 745 PRO cc_start: 0.6929 (Cg_endo) cc_final: 0.6659 (Cg_exo) REVERT: A 863 HIS cc_start: 0.6719 (t70) cc_final: 0.6499 (t-90) REVERT: A 1086 CYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7285 (t) REVERT: A 1111 CYS cc_start: 0.6054 (OUTLIER) cc_final: 0.5476 (p) REVERT: C 165 ARG cc_start: 0.7571 (mmt90) cc_final: 0.7258 (mmm-85) outliers start: 33 outliers final: 26 residues processed: 154 average time/residue: 0.2386 time to fit residues: 54.3153 Evaluate side-chains 159 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 674 GLN Chi-restraints excluded: chain A residue 743 ILE 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 549 ASP 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 81 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11446 Z= 0.185 Angle : 0.593 11.336 15501 Z= 0.299 Chirality : 0.042 0.172 1746 Planarity : 0.004 0.040 1965 Dihedral : 4.497 21.051 1515 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.59 % Allowed : 17.30 % Favored : 80.11 % 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: 0.43 (0.23), residues: 1396 helix: 1.37 (0.21), residues: 604 sheet: -0.04 (0.32), residues: 274 loop : -0.77 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 115 HIS 0.009 0.001 HIS A 238 PHE 0.021 0.001 PHE A 243 TYR 0.011 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 170 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.5882 (mt0) REVERT: A 745 PRO cc_start: 0.6937 (Cg_endo) cc_final: 0.6641 (Cg_exo) REVERT: A 863 HIS cc_start: 0.6715 (t70) cc_final: 0.6496 (t-90) REVERT: A 1086 CYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7300 (t) REVERT: A 1111 CYS cc_start: 0.6113 (OUTLIER) cc_final: 0.5601 (p) REVERT: C 165 ARG cc_start: 0.7582 (mmt90) cc_final: 0.7273 (mmm-85) outliers start: 32 outliers final: 27 residues processed: 156 average time/residue: 0.2138 time to fit residues: 49.6013 Evaluate side-chains 162 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 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 674 GLN Chi-restraints excluded: chain A residue 743 ILE 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 549 ASP 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 34 optimal weight: 0.0040 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.4540 r_free = 0.4540 target = 0.198621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.151576 restraints weight = 12273.612| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 2.97 r_work: 0.4035 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2402 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= 0.161 Angle : 0.574 11.300 15501 Z= 0.288 Chirality : 0.042 0.218 1746 Planarity : 0.004 0.039 1965 Dihedral : 4.356 20.236 1515 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.75 % Allowed : 17.30 % Favored : 79.95 % 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: 0.53 (0.23), residues: 1396 helix: 1.46 (0.21), residues: 604 sheet: -0.01 (0.32), residues: 276 loop : -0.71 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 115 HIS 0.009 0.001 HIS A 238 PHE 0.020 0.001 PHE A 243 TYR 0.009 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: 2476.81 seconds wall clock time: 46 minutes 28.37 seconds (2788.37 seconds total)