Starting phenix.real_space_refine on Sat Jul 26 22:24:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j6j_61174/07_2025/9j6j_61174.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j6j_61174/07_2025/9j6j_61174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j6j_61174/07_2025/9j6j_61174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j6j_61174/07_2025/9j6j_61174.map" model { file = "/net/cci-nas-00/data/ceres_data/9j6j_61174/07_2025/9j6j_61174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j6j_61174/07_2025/9j6j_61174.cif" } resolution = 2.86 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5602 2.51 5 N 1486 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8834 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 8834 Classifications: {'peptide': 1127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 1084} Chain breaks: 5 Time building chain proxies: 5.58, per 1000 atoms: 0.63 Number of scatterers: 8834 At special positions: 0 Unit cell: (103.85, 103.85, 107.2, 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 49 16.00 O 1697 8.00 N 1486 7.00 C 5602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 496 " distance=2.06 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 22 sheets defined 7.7% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.538A pdb=" N LEU A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.770A pdb=" N GLN A 438 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.741A pdb=" N SER A 528 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1243 removed outlier: 3.644A pdb=" N TYR A1231 " --> pdb=" O SER A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1257 Processing helix chain 'A' and resid 1274 through 1279 Processing helix chain 'A' and resid 1280 through 1283 removed outlier: 3.746A pdb=" N ILE A1283 " --> pdb=" O PHE A1280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1280 through 1283' Processing helix chain 'A' and resid 1284 through 1291 Processing helix chain 'A' and resid 1308 through 1321 removed outlier: 3.665A pdb=" N LEU A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A1315 " --> pdb=" O ASP A1311 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A1321 " --> pdb=" O GLU A1317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1187 through 1192 removed outlier: 6.755A pdb=" N GLY A1214 " --> pdb=" O ASN A1188 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE A1190 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A1212 " --> pdb=" O PHE A1190 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N HIS A1192 " --> pdb=" O SER A1210 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER A1210 " --> pdb=" O HIS A1192 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLY A1209 " --> pdb=" O SER A1225 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER A1225 " --> pdb=" O GLY A1209 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE A1220 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204 removed outlier: 3.660A pdb=" N GLY A 200 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 236 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL A 226 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 250 removed outlier: 3.933A pdb=" N ASN A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 287 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLU A 273 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR A 285 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 275 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE A 283 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.703A pdb=" N VAL A 364 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 350 " --> pdb=" O CYS A 362 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS A 362 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE A 352 " --> pdb=" O THR A 360 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR A 360 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 373 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 404 Processing sheet with id=AA7, first strand: chain 'A' and resid 441 through 446 removed outlier: 6.888A pdb=" N GLY A 457 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N HIS A 444 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A 455 " --> pdb=" O HIS A 444 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ARG A 446 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG A 453 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ARG A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 463 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU A 487 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET A 465 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 485 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 467 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU A 483 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU A 469 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 499 removed outlier: 5.703A pdb=" N LYS A 518 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA A 532 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 542 through 548 removed outlier: 4.184A pdb=" N ASP A 544 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 592 through 595 Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 642 removed outlier: 3.941A pdb=" N PHE A 642 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 653 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 658 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 661 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER A 671 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 681 through 686 removed outlier: 3.826A pdb=" N VAL A 683 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 699 " --> pdb=" O HIS A 714 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS A 714 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR A 701 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 710 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A 705 " --> pdb=" O GLU A 708 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 721 through 725 removed outlier: 6.497A pdb=" N GLY A 742 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU A 724 " --> pdb=" O ALA A 740 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA A 740 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 743 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER A 748 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 771 through 778 removed outlier: 6.569A pdb=" N ALA A 788 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE A 774 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 786 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET A 776 " --> pdb=" O TYR A 784 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR A 784 " --> pdb=" O MET A 776 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 783 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 820 through 823 removed outlier: 3.540A pdb=" N VAL A 832 " --> pdb=" O ILE A 842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 861 through 865 removed outlier: 3.811A pdb=" N TYR A 861 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 903 through 910 removed outlier: 6.491A pdb=" N LEU A 919 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 907 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 917 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR A 909 " --> pdb=" O CYS A 915 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS A 915 " --> pdb=" O TYR A 909 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP A 978 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 984 " --> pdb=" O ASP A 978 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER A 945 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLN A 989 " --> pdb=" O SER A 945 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER A 947 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 994 through 1002 removed outlier: 6.657A pdb=" N GLY A1015 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 999 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A1013 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER A1001 " --> pdb=" O TYR A1011 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR A1011 " --> pdb=" O SER A1001 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A1033 " --> pdb=" O VAL A1044 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A1035 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1057 through 1058 removed outlier: 4.061A pdb=" N CYS A1086 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU A1075 " --> pdb=" O THR A1084 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR A1084 " --> pdb=" O GLU A1075 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1100 removed outlier: 6.463A pdb=" N ALA A1117 " --> pdb=" O GLU A1127 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU A1127 " --> pdb=" O ALA A1117 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS A1119 " --> pdb=" O PHE A1125 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE A1125 " --> pdb=" O LYS A1119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1137 through 1142 removed outlier: 6.827A pdb=" N ALA A1151 " --> pdb=" O SER A1138 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A1140 " --> pdb=" O LEU A1149 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A1149 " --> pdb=" O VAL A1140 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE A1142 " --> pdb=" O ASN A1147 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASN A1147 " --> pdb=" O ILE A1142 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN A1161 " --> pdb=" O GLU A1177 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU A1177 " --> pdb=" O GLN A1161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1259 through 1261 267 hydrogen bonds defined for protein. 702 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: 3.59 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2831 1.34 - 1.46: 1436 1.46 - 1.58: 4649 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 8992 Sorted by residual: bond pdb=" N VAL A1292 " pdb=" CA VAL A1292 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.34e+01 bond pdb=" N ARG A1285 " pdb=" CA ARG A1285 " ideal model delta sigma weight residual 1.462 1.495 -0.034 9.50e-03 1.11e+04 1.26e+01 bond pdb=" N MET A1110 " pdb=" CA MET A1110 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.00e-02 1.00e+04 1.05e+01 bond pdb=" N LEU A 497 " pdb=" CA LEU A 497 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.21e-02 6.83e+03 9.75e+00 bond pdb=" N VAL A1291 " pdb=" CA VAL A1291 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.67e+00 ... (remaining 8987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11304 1.71 - 3.43: 731 3.43 - 5.14: 108 5.14 - 6.86: 28 6.86 - 8.57: 6 Bond angle restraints: 12177 Sorted by residual: angle pdb=" C SER A1112 " pdb=" CA SER A1112 " pdb=" CB SER A1112 " ideal model delta sigma weight residual 116.54 107.97 8.57 1.15e+00 7.56e-01 5.56e+01 angle pdb=" N GLU A1290 " pdb=" CA GLU A1290 " pdb=" C GLU A1290 " ideal model delta sigma weight residual 111.28 103.21 8.07 1.09e+00 8.42e-01 5.48e+01 angle pdb=" N ASP A 837 " pdb=" CA ASP A 837 " pdb=" C ASP A 837 " ideal model delta sigma weight residual 111.28 103.84 7.44 1.09e+00 8.42e-01 4.66e+01 angle pdb=" N VAL A1113 " pdb=" CA VAL A1113 " pdb=" C VAL A1113 " ideal model delta sigma weight residual 108.96 115.66 -6.70 1.42e+00 4.96e-01 2.23e+01 angle pdb=" N GLU A 495 " pdb=" CA GLU A 495 " pdb=" C GLU A 495 " ideal model delta sigma weight residual 112.04 105.85 6.19 1.44e+00 4.82e-01 1.85e+01 ... (remaining 12172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.20: 4715 18.20 - 36.40: 580 36.40 - 54.60: 104 54.60 - 72.79: 25 72.79 - 90.99: 15 Dihedral angle restraints: 5439 sinusoidal: 2183 harmonic: 3256 Sorted by residual: dihedral pdb=" CA ALA A 564 " pdb=" C ALA A 564 " pdb=" N PHE A 565 " pdb=" CA PHE A 565 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO A 406 " pdb=" C PRO A 406 " pdb=" N GLU A 407 " pdb=" CA GLU A 407 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA HIS A 648 " pdb=" C HIS A 648 " pdb=" N GLN A 649 " pdb=" CA GLN A 649 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 5436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1202 0.084 - 0.167: 194 0.167 - 0.251: 10 0.251 - 0.335: 2 0.335 - 0.418: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CB VAL A1292 " pdb=" CA VAL A1292 " pdb=" CG1 VAL A1292 " pdb=" CG2 VAL A1292 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CA CYS A 496 " pdb=" N CYS A 496 " pdb=" C CYS A 496 " pdb=" CB CYS A 496 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CB ILE A 747 " pdb=" CA ILE A 747 " pdb=" CG1 ILE A 747 " pdb=" CG2 ILE A 747 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1407 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1007 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO A1008 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A1008 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1008 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 594 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.10e+00 pdb=" N PRO A 595 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1109 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C LEU A1109 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A1109 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A1110 " -0.013 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 360 2.70 - 3.25: 8102 3.25 - 3.80: 12852 3.80 - 4.35: 17032 4.35 - 4.90: 29152 Nonbonded interactions: 67498 Sorted by model distance: nonbonded pdb=" O SER A 880 " pdb=" OG1 THR A 881 " model vdw 2.145 3.040 nonbonded pdb=" O LEU A1276 " pdb=" OG SER A1279 " model vdw 2.152 3.040 nonbonded pdb=" OD1 ASP A1038 " pdb=" N GLY A1039 " model vdw 2.154 3.120 nonbonded pdb=" NH2 ARG A 822 " pdb=" O THR A 823 " model vdw 2.154 3.120 nonbonded pdb=" OD1 ASN A 853 " pdb=" NZ LYS A 892 " model vdw 2.158 3.120 ... (remaining 67493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.310 Find NCS groups from input model: 0.090 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.010 0.071 8993 Z= 0.415 Angle : 0.966 8.574 12179 Z= 0.554 Chirality : 0.060 0.418 1410 Planarity : 0.006 0.062 1568 Dihedral : 16.852 90.993 3336 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.10 % 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: -2.90 (0.23), residues: 1115 helix: -1.68 (0.48), residues: 82 sheet: -0.71 (0.24), residues: 473 loop : -3.15 (0.21), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP A1076 HIS 0.008 0.002 HIS A1174 PHE 0.029 0.003 PHE A1158 TYR 0.033 0.003 TYR A1089 ARG 0.014 0.001 ARG A1083 Details of bonding type rmsd hydrogen bonds : bond 0.17035 ( 267) hydrogen bonds : angle 8.08228 ( 702) SS BOND : bond 0.02520 ( 1) SS BOND : angle 3.81510 ( 2) covalent geometry : bond 0.00950 ( 8992) covalent geometry : angle 0.96519 (12177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.915 Fit side-chains REVERT: A 482 ASP cc_start: 0.7846 (p0) cc_final: 0.7617 (t0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 1.6987 time to fit residues: 153.8302 Evaluate side-chains 61 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 40.0000 chunk 45 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.173497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100487 restraints weight = 13123.330| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.52 r_work: 0.2843 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8993 Z= 0.189 Angle : 0.709 7.028 12179 Z= 0.374 Chirality : 0.049 0.224 1410 Planarity : 0.005 0.056 1568 Dihedral : 5.870 22.526 1204 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.02 % Allowed : 12.31 % Favored : 85.67 % 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: -2.61 (0.23), residues: 1115 helix: -1.24 (0.53), residues: 86 sheet: -0.43 (0.24), residues: 474 loop : -3.12 (0.21), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1076 HIS 0.005 0.001 HIS A 423 PHE 0.017 0.002 PHE A 779 TYR 0.014 0.002 TYR A1096 ARG 0.005 0.001 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 267) hydrogen bonds : angle 6.54988 ( 702) SS BOND : bond 0.00795 ( 1) SS BOND : angle 3.77957 ( 2) covalent geometry : bond 0.00457 ( 8992) covalent geometry : angle 0.70761 (12177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 1.044 Fit side-chains REVERT: A 490 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: A 1089 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.7975 (p90) REVERT: A 1152 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: A 1171 GLU cc_start: 0.8070 (mp0) cc_final: 0.7474 (pp20) outliers start: 20 outliers final: 9 residues processed: 81 average time/residue: 1.6595 time to fit residues: 142.1274 Evaluate side-chains 71 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 1089 TYR Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1322 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 3.9990 chunk 94 optimal weight: 0.0030 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 GLN A 800 ASN A 866 ASN A1068 ASN A1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.176762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103628 restraints weight = 13221.677| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.56 r_work: 0.2906 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8993 Z= 0.116 Angle : 0.623 15.792 12179 Z= 0.325 Chirality : 0.046 0.192 1410 Planarity : 0.004 0.053 1568 Dihedral : 5.213 20.694 1204 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 1.61 % Allowed : 15.34 % Favored : 83.05 % 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: -2.30 (0.24), residues: 1115 helix: -0.63 (0.56), residues: 86 sheet: -0.16 (0.25), residues: 449 loop : -2.93 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1256 HIS 0.005 0.001 HIS A 423 PHE 0.014 0.001 PHE A 779 TYR 0.010 0.001 TYR A1096 ARG 0.004 0.000 ARG A1111 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 267) hydrogen bonds : angle 6.01665 ( 702) SS BOND : bond 0.01812 ( 1) SS BOND : angle 5.99761 ( 2) covalent geometry : bond 0.00264 ( 8992) covalent geometry : angle 0.61871 (12177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.977 Fit side-chains REVERT: A 490 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: A 1089 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8191 (p90) outliers start: 16 outliers final: 6 residues processed: 74 average time/residue: 1.4595 time to fit residues: 114.8046 Evaluate side-chains 68 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 1089 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 40.0000 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 0.0470 chunk 39 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.175055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100798 restraints weight = 13049.536| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.71 r_work: 0.2862 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8993 Z= 0.178 Angle : 0.665 15.860 12179 Z= 0.347 Chirality : 0.047 0.183 1410 Planarity : 0.005 0.056 1568 Dihedral : 5.303 20.544 1204 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.93 % Allowed : 16.45 % Favored : 80.63 % 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: -2.32 (0.24), residues: 1115 helix: -0.67 (0.56), residues: 86 sheet: -0.24 (0.24), residues: 471 loop : -2.98 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1256 HIS 0.004 0.001 HIS A 423 PHE 0.016 0.002 PHE A1132 TYR 0.013 0.002 TYR A1096 ARG 0.005 0.001 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 267) hydrogen bonds : angle 5.97350 ( 702) SS BOND : bond 0.01721 ( 1) SS BOND : angle 7.47953 ( 2) covalent geometry : bond 0.00435 ( 8992) covalent geometry : angle 0.65761 (12177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 1.047 Fit side-chains REVERT: A 381 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8189 (tpp80) REVERT: A 490 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8150 (tp30) REVERT: A 496 CYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6934 (p) REVERT: A 833 PHE cc_start: 0.3661 (OUTLIER) cc_final: 0.2346 (t80) REVERT: A 862 MET cc_start: 0.1789 (OUTLIER) cc_final: 0.1473 (mtt) REVERT: A 1089 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7920 (p90) REVERT: A 1152 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8276 (pt0) outliers start: 29 outliers final: 12 residues processed: 83 average time/residue: 1.4416 time to fit residues: 127.3512 Evaluate side-chains 80 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1089 TYR Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1322 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.175782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101727 restraints weight = 12985.937| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.67 r_work: 0.2879 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8993 Z= 0.148 Angle : 0.642 15.343 12179 Z= 0.333 Chirality : 0.046 0.185 1410 Planarity : 0.004 0.054 1568 Dihedral : 5.136 19.272 1204 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.83 % Allowed : 18.16 % Favored : 79.01 % 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: -2.31 (0.24), residues: 1115 helix: -0.50 (0.57), residues: 86 sheet: -0.32 (0.24), residues: 480 loop : -2.95 (0.22), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1256 HIS 0.004 0.001 HIS A 423 PHE 0.012 0.002 PHE A1181 TYR 0.012 0.001 TYR A1096 ARG 0.003 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 267) hydrogen bonds : angle 5.81213 ( 702) SS BOND : bond 0.01495 ( 1) SS BOND : angle 7.31565 ( 2) covalent geometry : bond 0.00359 ( 8992) covalent geometry : angle 0.63508 (12177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.895 Fit side-chains REVERT: A 210 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7877 (pp20) REVERT: A 381 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8307 (tpp80) REVERT: A 490 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: A 534 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: A 593 LEU cc_start: -0.2006 (OUTLIER) cc_final: -0.3532 (mt) REVERT: A 1089 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8026 (p90) REVERT: A 1152 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8251 (pt0) outliers start: 28 outliers final: 15 residues processed: 78 average time/residue: 1.4073 time to fit residues: 116.9902 Evaluate side-chains 79 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1089 TYR Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1246 LYS Chi-restraints excluded: chain A residue 1322 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 82 optimal weight: 0.0070 chunk 42 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.177472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105516 restraints weight = 12819.583| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.91 r_work: 0.2921 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8993 Z= 0.111 Angle : 0.598 14.106 12179 Z= 0.310 Chirality : 0.045 0.166 1410 Planarity : 0.004 0.053 1568 Dihedral : 4.854 21.054 1204 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.62 % Allowed : 18.57 % Favored : 78.81 % 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: -2.16 (0.24), residues: 1115 helix: -0.27 (0.59), residues: 86 sheet: -0.15 (0.24), residues: 460 loop : -2.85 (0.22), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1256 HIS 0.005 0.001 HIS A 423 PHE 0.011 0.001 PHE A1213 TYR 0.009 0.001 TYR A1096 ARG 0.003 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 267) hydrogen bonds : angle 5.56182 ( 702) SS BOND : bond 0.01307 ( 1) SS BOND : angle 6.91551 ( 2) covalent geometry : bond 0.00256 ( 8992) covalent geometry : angle 0.59135 (12177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7886 (pp20) REVERT: A 381 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8363 (tpp80) REVERT: A 438 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: A 469 GLU cc_start: 0.8373 (tp30) cc_final: 0.8020 (tt0) REVERT: A 490 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8145 (tp30) REVERT: A 593 LEU cc_start: -0.2493 (OUTLIER) cc_final: -0.3888 (mt) REVERT: A 833 PHE cc_start: 0.3645 (OUTLIER) cc_final: 0.2482 (t80) REVERT: A 1089 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.8084 (p90) REVERT: A 1152 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8126 (pt0) outliers start: 26 outliers final: 13 residues processed: 78 average time/residue: 1.4549 time to fit residues: 120.6515 Evaluate side-chains 80 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1089 TYR Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1322 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 19 optimal weight: 0.2980 chunk 108 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 86 optimal weight: 0.0020 chunk 10 optimal weight: 2.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.178143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104781 restraints weight = 13119.146| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.07 r_work: 0.2977 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8993 Z= 0.098 Angle : 0.580 13.177 12179 Z= 0.300 Chirality : 0.045 0.156 1410 Planarity : 0.004 0.054 1568 Dihedral : 4.661 21.485 1204 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.02 % Allowed : 19.68 % Favored : 78.30 % 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: -2.05 (0.24), residues: 1115 helix: -0.07 (0.60), residues: 86 sheet: -0.07 (0.25), residues: 461 loop : -2.82 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1256 HIS 0.004 0.001 HIS A 423 PHE 0.012 0.001 PHE A1213 TYR 0.007 0.001 TYR A 188 ARG 0.005 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.03197 ( 267) hydrogen bonds : angle 5.36470 ( 702) SS BOND : bond 0.01130 ( 1) SS BOND : angle 6.68227 ( 2) covalent geometry : bond 0.00221 ( 8992) covalent geometry : angle 0.57381 (12177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 2.317 Fit side-chains REVERT: A 210 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7880 (pp20) REVERT: A 438 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: A 490 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8136 (tp30) REVERT: A 534 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: A 593 LEU cc_start: -0.3239 (OUTLIER) cc_final: -0.4504 (mt) REVERT: A 833 PHE cc_start: 0.3735 (OUTLIER) cc_final: 0.2483 (t80) REVERT: A 862 MET cc_start: 0.0823 (mtt) cc_final: 0.0468 (mtt) REVERT: A 1171 GLU cc_start: 0.7941 (mp0) cc_final: 0.7615 (mp0) outliers start: 20 outliers final: 9 residues processed: 80 average time/residue: 2.4654 time to fit residues: 209.6264 Evaluate side-chains 75 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1140 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.0170 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 35 optimal weight: 0.0270 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 783 HIS A1323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.177815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103981 restraints weight = 13159.725| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.08 r_work: 0.2971 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8993 Z= 0.106 Angle : 0.591 13.443 12179 Z= 0.305 Chirality : 0.045 0.158 1410 Planarity : 0.004 0.054 1568 Dihedral : 4.622 21.584 1204 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.42 % Allowed : 19.27 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.25), residues: 1115 helix: -0.04 (0.60), residues: 86 sheet: 0.01 (0.25), residues: 460 loop : -2.76 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1256 HIS 0.004 0.001 HIS A 423 PHE 0.012 0.001 PHE A 779 TYR 0.009 0.001 TYR A 188 ARG 0.006 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 267) hydrogen bonds : angle 5.31644 ( 702) SS BOND : bond 0.01143 ( 1) SS BOND : angle 6.77651 ( 2) covalent geometry : bond 0.00247 ( 8992) covalent geometry : angle 0.58464 (12177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7832 (pp20) REVERT: A 438 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7705 (mt0) REVERT: A 469 GLU cc_start: 0.8352 (tp30) cc_final: 0.8001 (tt0) REVERT: A 490 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8127 (tp30) REVERT: A 534 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 833 PHE cc_start: 0.3723 (OUTLIER) cc_final: 0.2510 (t80) REVERT: A 1152 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8013 (pt0) outliers start: 24 outliers final: 13 residues processed: 78 average time/residue: 1.4712 time to fit residues: 121.8689 Evaluate side-chains 76 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1140 VAL Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1237 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.174121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099504 restraints weight = 13128.771| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.04 r_work: 0.2895 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8993 Z= 0.197 Angle : 0.686 16.135 12179 Z= 0.354 Chirality : 0.047 0.180 1410 Planarity : 0.004 0.060 1568 Dihedral : 5.141 21.883 1204 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.32 % Allowed : 19.58 % Favored : 78.10 % 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: -2.10 (0.24), residues: 1115 helix: -0.37 (0.57), residues: 86 sheet: -0.18 (0.24), residues: 480 loop : -2.80 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1256 HIS 0.004 0.001 HIS A1192 PHE 0.016 0.002 PHE A1132 TYR 0.015 0.002 TYR A 188 ARG 0.004 0.000 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 267) hydrogen bonds : angle 5.62085 ( 702) SS BOND : bond 0.01713 ( 1) SS BOND : angle 7.74234 ( 2) covalent geometry : bond 0.00490 ( 8992) covalent geometry : angle 0.67934 (12177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7859 (pp20) REVERT: A 437 LYS cc_start: 0.8680 (tptt) cc_final: 0.8380 (tppt) REVERT: A 438 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: A 490 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: A 534 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 776 MET cc_start: 0.3365 (OUTLIER) cc_final: 0.3091 (ptp) REVERT: A 833 PHE cc_start: 0.3450 (OUTLIER) cc_final: 0.2571 (t80) outliers start: 23 outliers final: 13 residues processed: 76 average time/residue: 1.3569 time to fit residues: 109.7778 Evaluate side-chains 77 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 776 MET Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 983 GLU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.174416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102061 restraints weight = 13091.961| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.83 r_work: 0.2867 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8993 Z= 0.174 Angle : 0.670 15.642 12179 Z= 0.346 Chirality : 0.046 0.184 1410 Planarity : 0.004 0.058 1568 Dihedral : 5.073 20.559 1204 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.12 % Allowed : 20.18 % Favored : 77.70 % 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: -2.17 (0.24), residues: 1115 helix: -0.40 (0.57), residues: 86 sheet: -0.27 (0.24), residues: 491 loop : -2.85 (0.23), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1256 HIS 0.003 0.001 HIS A 423 PHE 0.014 0.002 PHE A1181 TYR 0.012 0.001 TYR A 188 ARG 0.004 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 267) hydrogen bonds : angle 5.55931 ( 702) SS BOND : bond 0.01633 ( 1) SS BOND : angle 7.53677 ( 2) covalent geometry : bond 0.00430 ( 8992) covalent geometry : angle 0.66345 (12177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7935 (pp20) REVERT: A 469 GLU cc_start: 0.8455 (tp30) cc_final: 0.8129 (tt0) REVERT: A 490 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8069 (tp30) REVERT: A 534 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 833 PHE cc_start: 0.3549 (OUTLIER) cc_final: 0.2323 (t80) REVERT: A 862 MET cc_start: 0.0920 (mtt) cc_final: 0.0585 (mtt) outliers start: 21 outliers final: 13 residues processed: 73 average time/residue: 1.4222 time to fit residues: 110.9680 Evaluate side-chains 74 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 chunk 89 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.177352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.103315 restraints weight = 13172.250| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.08 r_work: 0.2960 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8993 Z= 0.111 Angle : 0.613 13.858 12179 Z= 0.314 Chirality : 0.045 0.172 1410 Planarity : 0.004 0.056 1568 Dihedral : 4.695 21.261 1204 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.12 % Allowed : 20.28 % Favored : 77.60 % 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: -1.96 (0.24), residues: 1115 helix: -0.10 (0.59), residues: 86 sheet: -0.03 (0.24), residues: 465 loop : -2.73 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1256 HIS 0.004 0.001 HIS A 423 PHE 0.011 0.001 PHE A 409 TYR 0.008 0.001 TYR A1096 ARG 0.004 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 267) hydrogen bonds : angle 5.31143 ( 702) SS BOND : bond 0.01245 ( 1) SS BOND : angle 6.94681 ( 2) covalent geometry : bond 0.00262 ( 8992) covalent geometry : angle 0.60649 (12177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7486.93 seconds wall clock time: 131 minutes 7.10 seconds (7867.10 seconds total)