Starting phenix.real_space_refine on Wed Mar 12 13:50:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7df8_30662/03_2025/7df8_30662_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7df8_30662/03_2025/7df8_30662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7df8_30662/03_2025/7df8_30662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7df8_30662/03_2025/7df8_30662.map" model { file = "/net/cci-nas-00/data/ceres_data/7df8_30662/03_2025/7df8_30662_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7df8_30662/03_2025/7df8_30662_neut_trim.cif" } resolution = 3.03 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= 0.008 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 41 5.16 5 C 4915 2.51 5 N 1171 2.21 5 O 1378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7505 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7148 Classifications: {'peptide': 918} Link IDs: {'PTRANS': 46, 'TRANS': 871} Chain breaks: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Unusual residues: {'CLR': 4, 'LMT': 1, 'NAG': 7} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.97, per 1000 atoms: 0.66 Number of scatterers: 7505 At special positions: 0 Unit cell: (94.429, 77.453, 131.564, 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 41 16.00 O 1378 8.00 N 1171 7.00 C 4915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " distance=2.03 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 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " NAG K 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " NAG R 3 " NAG-ASN " NAG A1301 " - " ASN A 431 " " NAG A1302 " - " ASN A 464 " " NAG A1303 " - " ASN A 506 " " NAG A1304 " - " ASN A 416 " " NAG A1305 " - " ASN A 479 " " NAG A1306 " - " ASN A 927 " " NAG A1307 " - " ASN A1075 " " NAG H 1 " - " ASN A 497 " " NAG K 1 " - " ASN A 909 " " NAG R 1 " - " ASN A1037 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 904.3 milliseconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 58.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.736A pdb=" N LEU A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.697A pdb=" N ILE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 437 through 453 removed outlier: 4.076A pdb=" N GLU A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.659A pdb=" N TYR A 493 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.692A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.516A pdb=" N GLU A 566 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 607 removed outlier: 4.349A pdb=" N ALA A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.626A pdb=" N ILE A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.863A pdb=" N LEU A 633 " --> pdb=" O THR A 629 " (cutoff:3.500A) Proline residue: A 634 - end of helix Processing helix chain 'A' and resid 637 through 647 removed outlier: 3.933A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 690 removed outlier: 3.543A pdb=" N GLY A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 679 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A 688 " --> pdb=" O MET A 684 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 690 " --> pdb=" O PHE A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.733A pdb=" N VAL A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 724 removed outlier: 3.563A pdb=" N PHE A 715 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 743 through 761 Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'A' and resid 766 through 790 removed outlier: 3.530A pdb=" N THR A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 802 removed outlier: 3.557A pdb=" N ARG A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 844 through 864 removed outlier: 4.305A pdb=" N LEU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.603A pdb=" N ALA A 876 " --> pdb=" O GLN A 873 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 877 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 894 removed outlier: 3.637A pdb=" N TYR A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.768A pdb=" N ALA A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 938 removed outlier: 3.620A pdb=" N THR A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 1004 through 1016 removed outlier: 3.549A pdb=" N LEU A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.827A pdb=" N TYR A1062 " --> pdb=" O ASN A1058 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A1063 " --> pdb=" O SER A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1103 removed outlier: 4.055A pdb=" N TYR A1102 " --> pdb=" O THR A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1106 No H-bonds generated for 'chain 'A' and resid 1104 through 1106' Processing helix chain 'A' and resid 1107 through 1118 removed outlier: 3.794A pdb=" N GLU A1111 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1125 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1140 through 1160 Processing helix chain 'A' and resid 1164 through 1176 removed outlier: 3.598A pdb=" N ILE A1169 " --> pdb=" O ALA A1165 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A1170 " --> pdb=" O VAL A1166 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A1176 " --> pdb=" O VAL A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1191 removed outlier: 3.830A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1216 removed outlier: 3.505A pdb=" N MET A1208 " --> pdb=" O ALA A1204 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER A1210 " --> pdb=" O ILE A1206 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA A1211 " --> pdb=" O SER A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1226 Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1240 through 1255 removed outlier: 3.513A pdb=" N LEU A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1266 removed outlier: 3.977A pdb=" N TYR A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA3, first strand: chain 'A' and resid 420 through 423 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 458 removed outlier: 4.119A pdb=" N ARG A 463 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 508 Processing sheet with id=AA6, first strand: chain 'A' and resid 946 through 951 removed outlier: 6.707A pdb=" N TYR A1052 " --> pdb=" O ALA A 947 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET A1050 " --> pdb=" O PRO A 949 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.914A pdb=" N ALA A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 969 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: 2.18 Time building geometry restraints manager: 2.55 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: 2172 1.34 - 1.46: 1551 1.46 - 1.58: 3907 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 7694 Sorted by residual: bond pdb=" C ASP A 378 " pdb=" N PRO A 379 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.11e+00 bond pdb=" C3' LMT A1308 " pdb=" O3' LMT A1308 " ideal model delta sigma weight residual 1.404 1.350 0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" C6' LMT A1308 " pdb=" O6' LMT A1308 " ideal model delta sigma weight residual 1.407 1.356 0.051 2.00e-02 2.50e+03 6.43e+00 bond pdb=" C2B LMT A1308 " pdb=" O2B LMT A1308 " ideal model delta sigma weight residual 1.410 1.362 0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C3B LMT A1308 " pdb=" O3B LMT A1308 " ideal model delta sigma weight residual 1.406 1.358 0.048 2.00e-02 2.50e+03 5.67e+00 ... (remaining 7689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 10139 2.24 - 4.48: 306 4.48 - 6.72: 41 6.72 - 8.97: 10 8.97 - 11.21: 2 Bond angle restraints: 10498 Sorted by residual: angle pdb=" N ASP A 378 " pdb=" CA ASP A 378 " pdb=" C ASP A 378 " ideal model delta sigma weight residual 109.81 121.02 -11.21 2.21e+00 2.05e-01 2.57e+01 angle pdb=" N VAL A 371 " pdb=" CA VAL A 371 " pdb=" C VAL A 371 " ideal model delta sigma weight residual 113.53 109.42 4.11 9.80e-01 1.04e+00 1.76e+01 angle pdb=" CA ASP A 378 " pdb=" C ASP A 378 " pdb=" N PRO A 379 " ideal model delta sigma weight residual 118.44 124.68 -6.24 1.59e+00 3.96e-01 1.54e+01 angle pdb=" N ALA A 744 " pdb=" CA ALA A 744 " pdb=" C ALA A 744 " ideal model delta sigma weight residual 109.81 117.67 -7.86 2.21e+00 2.05e-01 1.26e+01 angle pdb=" N ARG A 801 " pdb=" CA ARG A 801 " pdb=" C ARG A 801 " ideal model delta sigma weight residual 111.33 115.62 -4.29 1.21e+00 6.83e-01 1.26e+01 ... (remaining 10493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 4653 22.77 - 45.55: 275 45.55 - 68.32: 23 68.32 - 91.09: 14 91.09 - 113.87: 5 Dihedral angle restraints: 4970 sinusoidal: 2299 harmonic: 2671 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -156.34 70.34 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CB CYS A 920 " pdb=" SG CYS A 920 " pdb=" SG CYS A 925 " pdb=" CB CYS A 925 " ideal model delta sinusoidal sigma weight residual -86.00 -125.37 39.37 1 1.00e+01 1.00e-02 2.18e+01 dihedral pdb=" CA GLU A 381 " pdb=" C GLU A 381 " pdb=" N LEU A 382 " pdb=" CA LEU A 382 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 4967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1035 0.061 - 0.122: 197 0.122 - 0.183: 23 0.183 - 0.244: 12 0.244 - 0.305: 7 Chirality restraints: 1274 Sorted by residual: chirality pdb=" CA ASP A 378 " pdb=" N ASP A 378 " pdb=" C ASP A 378 " pdb=" CB ASP A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C13 CLR A1312 " pdb=" C12 CLR A1312 " pdb=" C14 CLR A1312 " pdb=" C17 CLR A1312 " both_signs ideal model delta sigma weight residual False -2.93 -2.63 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB THR A 377 " pdb=" CA THR A 377 " pdb=" OG1 THR A 377 " pdb=" CG2 THR A 377 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1271 not shown) Planarity restraints: 1282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 3 " -0.336 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG K 3 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG K 3 " -0.047 2.00e-02 2.50e+03 pdb=" N2 NAG K 3 " 0.511 2.00e-02 2.50e+03 pdb=" O7 NAG K 3 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " -0.329 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG A1306 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " -0.057 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " 0.505 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.192 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.292 2.00e-02 2.50e+03 2.45e-01 7.52e+02 pdb=" C7 NAG K 1 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.418 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.015 2.00e-02 2.50e+03 ... (remaining 1279 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 41 2.57 - 3.15: 5990 3.15 - 3.73: 11000 3.73 - 4.32: 15457 4.32 - 4.90: 26240 Nonbonded interactions: 58728 Sorted by model distance: nonbonded pdb=" NH2 ARG A 801 " pdb=" OE1 GLN A 802 " model vdw 1.986 3.120 nonbonded pdb=" OG1 THR A1039 " pdb=" OD1 ASP A1041 " model vdw 2.187 3.040 nonbonded pdb=" OE1 GLU A 624 " pdb=" OG SER A 881 " model vdw 2.188 3.040 nonbonded pdb=" OG SER A1192 " pdb=" OE1 GLU A1203 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR A 407 " pdb=" O6B LMT A1308 " model vdw 2.248 3.040 ... (remaining 58723 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 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'R' } 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: 0.590 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.310 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.006 0.067 7694 Z= 0.388 Angle : 0.880 11.208 10498 Z= 0.435 Chirality : 0.056 0.305 1274 Planarity : 0.017 0.291 1272 Dihedral : 14.527 113.869 3233 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.26 % Allowed : 0.13 % Favored : 99.61 % 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: -4.03 (0.20), residues: 912 helix: -2.75 (0.15), residues: 496 sheet: -1.24 (0.56), residues: 78 loop : -2.63 (0.27), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 953 HIS 0.013 0.002 HIS A1053 PHE 0.037 0.002 PHE A 832 TYR 0.012 0.001 TYR A 546 ARG 0.003 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 425 LEU cc_start: 0.8743 (tp) cc_final: 0.8506 (tp) REVERT: A 517 ASP cc_start: 0.8532 (t0) cc_final: 0.8193 (t0) REVERT: A 543 MET cc_start: 0.7947 (mtp) cc_final: 0.7619 (mtm) REVERT: A 705 LEU cc_start: 0.8308 (tt) cc_final: 0.7661 (mp) REVERT: A 727 ARG cc_start: 0.7302 (mtt-85) cc_final: 0.7081 (mpt-90) REVERT: A 742 ARG cc_start: 0.8706 (ttm-80) cc_final: 0.8491 (ttm-80) REVERT: A 788 MET cc_start: 0.8361 (tpp) cc_final: 0.8138 (tpp) REVERT: A 798 ASP cc_start: 0.8176 (t70) cc_final: 0.7897 (t0) REVERT: A 955 ASP cc_start: 0.7881 (t0) cc_final: 0.7637 (t0) REVERT: A 970 TYR cc_start: 0.8061 (m-80) cc_final: 0.7576 (m-80) REVERT: A 1043 GLN cc_start: 0.6920 (tp-100) cc_final: 0.6693 (tt0) REVERT: A 1050 MET cc_start: 0.9153 (ttt) cc_final: 0.8849 (ttt) outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 0.2115 time to fit residues: 28.6550 Evaluate side-chains 65 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.0030 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.112804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.088886 restraints weight = 11645.426| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.58 r_work: 0.2940 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7694 Z= 0.170 Angle : 0.627 9.516 10498 Z= 0.294 Chirality : 0.043 0.304 1274 Planarity : 0.005 0.052 1272 Dihedral : 10.838 108.455 1621 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.77 % Allowed : 5.52 % Favored : 93.71 % 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: -1.75 (0.26), residues: 912 helix: -0.49 (0.22), residues: 494 sheet: -1.13 (0.55), residues: 84 loop : -2.07 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 960 HIS 0.007 0.001 HIS A1053 PHE 0.020 0.001 PHE A 930 TYR 0.009 0.001 TYR A 886 ARG 0.002 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7555 (mt) cc_final: 0.7268 (mp) REVERT: A 430 LYS cc_start: 0.8562 (mttm) cc_final: 0.8340 (mttt) REVERT: A 543 MET cc_start: 0.8542 (mtp) cc_final: 0.8307 (mtm) REVERT: A 705 LEU cc_start: 0.8498 (tt) cc_final: 0.7843 (mt) REVERT: A 727 ARG cc_start: 0.7418 (mtt-85) cc_final: 0.7203 (mpt-90) REVERT: A 766 MET cc_start: 0.8305 (mmm) cc_final: 0.7759 (mmt) REVERT: A 955 ASP cc_start: 0.8573 (t0) cc_final: 0.8234 (t0) REVERT: A 970 TYR cc_start: 0.8081 (m-80) cc_final: 0.7705 (m-80) REVERT: A 1252 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8413 (mp) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 0.1846 time to fit residues: 22.1680 Evaluate side-chains 70 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.084041 restraints weight = 12042.718| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.59 r_work: 0.2855 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 7694 Z= 0.457 Angle : 0.716 9.898 10498 Z= 0.339 Chirality : 0.048 0.256 1274 Planarity : 0.004 0.039 1272 Dihedral : 10.613 107.685 1621 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.54 % Allowed : 9.50 % Favored : 88.96 % 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: -1.13 (0.27), residues: 912 helix: 0.06 (0.23), residues: 497 sheet: -1.00 (0.54), residues: 82 loop : -1.84 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 960 HIS 0.003 0.001 HIS A1053 PHE 0.029 0.002 PHE A 930 TYR 0.012 0.002 TYR A 546 ARG 0.002 0.000 ARG A 846 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7566 (mt) cc_final: 0.7272 (mp) REVERT: A 543 MET cc_start: 0.8773 (mtp) cc_final: 0.8536 (mtm) REVERT: A 727 ARG cc_start: 0.7488 (mtt-85) cc_final: 0.7262 (mpt-90) REVERT: A 955 ASP cc_start: 0.8632 (t0) cc_final: 0.8282 (t0) REVERT: A 970 TYR cc_start: 0.8159 (m-80) cc_final: 0.7733 (m-80) REVERT: A 1252 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8469 (mp) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.1623 time to fit residues: 18.9387 Evaluate side-chains 75 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.088225 restraints weight = 11749.350| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.59 r_work: 0.2927 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7694 Z= 0.158 Angle : 0.578 9.517 10498 Z= 0.267 Chirality : 0.041 0.263 1274 Planarity : 0.003 0.032 1272 Dihedral : 9.713 106.130 1621 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.80 % Allowed : 11.42 % Favored : 86.78 % 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: -0.52 (0.28), residues: 912 helix: 0.59 (0.24), residues: 501 sheet: -0.86 (0.55), residues: 84 loop : -1.61 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.006 0.001 HIS A1053 PHE 0.013 0.001 PHE A 704 TYR 0.009 0.001 TYR A 886 ARG 0.001 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7526 (mt) cc_final: 0.7249 (mp) REVERT: A 517 ASP cc_start: 0.8530 (t0) cc_final: 0.8292 (t0) REVERT: A 727 ARG cc_start: 0.7497 (mtt-85) cc_final: 0.7268 (mpt-90) REVERT: A 955 ASP cc_start: 0.8535 (t0) cc_final: 0.8229 (t0) REVERT: A 970 TYR cc_start: 0.8292 (m-80) cc_final: 0.7869 (m-80) REVERT: A 1208 MET cc_start: 0.9142 (tpp) cc_final: 0.8924 (tpt) REVERT: A 1252 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8457 (mp) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.1593 time to fit residues: 19.6452 Evaluate side-chains 78 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 88 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.085583 restraints weight = 11773.165| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.58 r_work: 0.2874 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7694 Z= 0.332 Angle : 0.632 9.758 10498 Z= 0.295 Chirality : 0.044 0.250 1274 Planarity : 0.004 0.031 1272 Dihedral : 9.617 105.897 1621 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.31 % Allowed : 13.61 % Favored : 84.08 % 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: -0.45 (0.28), residues: 912 helix: 0.64 (0.24), residues: 501 sheet: -0.94 (0.54), residues: 84 loop : -1.54 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.002 0.001 HIS A1053 PHE 0.022 0.002 PHE A 930 TYR 0.009 0.001 TYR A 546 ARG 0.002 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7533 (mt) cc_final: 0.7252 (mp) REVERT: A 517 ASP cc_start: 0.8507 (t0) cc_final: 0.8297 (t0) REVERT: A 727 ARG cc_start: 0.7423 (mtt-85) cc_final: 0.7209 (mpt-90) REVERT: A 955 ASP cc_start: 0.8573 (t0) cc_final: 0.8263 (t0) REVERT: A 970 TYR cc_start: 0.8298 (m-80) cc_final: 0.7821 (m-80) REVERT: A 1252 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8494 (mp) outliers start: 18 outliers final: 15 residues processed: 81 average time/residue: 0.1747 time to fit residues: 20.5640 Evaluate side-chains 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 72 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 31 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.087064 restraints weight = 11694.284| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.60 r_work: 0.2903 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7694 Z= 0.213 Angle : 0.581 9.621 10498 Z= 0.269 Chirality : 0.042 0.247 1274 Planarity : 0.003 0.029 1272 Dihedral : 9.129 104.948 1621 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.31 % Allowed : 14.12 % Favored : 83.57 % 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: -0.21 (0.29), residues: 912 helix: 0.87 (0.24), residues: 501 sheet: -0.82 (0.53), residues: 84 loop : -1.49 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.004 0.001 HIS A1053 PHE 0.014 0.001 PHE A 930 TYR 0.008 0.001 TYR A 546 ARG 0.001 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7534 (mt) cc_final: 0.7253 (mp) REVERT: A 727 ARG cc_start: 0.7421 (mtt-85) cc_final: 0.7197 (mpt-90) REVERT: A 955 ASP cc_start: 0.8535 (t0) cc_final: 0.8237 (t0) REVERT: A 970 TYR cc_start: 0.8301 (m-80) cc_final: 0.7855 (m-80) REVERT: A 1208 MET cc_start: 0.9157 (tpp) cc_final: 0.8930 (tpt) REVERT: A 1252 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8507 (mp) outliers start: 18 outliers final: 9 residues processed: 82 average time/residue: 0.1885 time to fit residues: 22.3671 Evaluate side-chains 79 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 71 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.088946 restraints weight = 11602.525| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.60 r_work: 0.2931 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7694 Z= 0.145 Angle : 0.561 9.548 10498 Z= 0.259 Chirality : 0.040 0.264 1274 Planarity : 0.003 0.027 1272 Dihedral : 8.569 103.804 1621 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.67 % Allowed : 15.15 % Favored : 83.18 % 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: 0.07 (0.29), residues: 912 helix: 1.11 (0.25), residues: 500 sheet: -0.65 (0.54), residues: 84 loop : -1.41 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.006 0.001 HIS A1053 PHE 0.011 0.001 PHE A 930 TYR 0.009 0.001 TYR A 886 ARG 0.001 0.000 ARG A1200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7516 (mt) cc_final: 0.7242 (mp) REVERT: A 727 ARG cc_start: 0.7295 (mtt-85) cc_final: 0.7082 (mpt-90) REVERT: A 894 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8146 (t80) REVERT: A 970 TYR cc_start: 0.8275 (m-80) cc_final: 0.7861 (m-80) REVERT: A 1252 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8488 (mt) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.1552 time to fit residues: 17.1591 Evaluate side-chains 75 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 927 ASN Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 61 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.088498 restraints weight = 11904.035| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.63 r_work: 0.2925 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7694 Z= 0.165 Angle : 0.558 9.591 10498 Z= 0.259 Chirality : 0.041 0.258 1274 Planarity : 0.003 0.027 1272 Dihedral : 8.295 103.005 1621 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.93 % Allowed : 14.63 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 912 helix: 1.19 (0.25), residues: 500 sheet: -0.59 (0.54), residues: 84 loop : -1.35 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.006 0.001 HIS A1053 PHE 0.013 0.001 PHE A 930 TYR 0.008 0.001 TYR A 886 ARG 0.001 0.000 ARG A1136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7510 (mt) cc_final: 0.7231 (mp) REVERT: A 517 ASP cc_start: 0.8554 (t0) cc_final: 0.8346 (t0) REVERT: A 894 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8163 (t80) REVERT: A 970 TYR cc_start: 0.8280 (m-80) cc_final: 0.7880 (m-80) REVERT: A 1252 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8522 (mp) outliers start: 15 outliers final: 11 residues processed: 78 average time/residue: 0.1727 time to fit residues: 19.6884 Evaluate side-chains 80 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.111572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087364 restraints weight = 11879.140| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.62 r_work: 0.2907 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7694 Z= 0.220 Angle : 0.585 9.797 10498 Z= 0.271 Chirality : 0.043 0.348 1274 Planarity : 0.003 0.026 1272 Dihedral : 8.211 101.815 1621 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.93 % Allowed : 15.02 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 912 helix: 1.16 (0.25), residues: 500 sheet: -0.59 (0.54), residues: 84 loop : -1.31 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.005 0.001 HIS A1053 PHE 0.017 0.001 PHE A 930 TYR 0.008 0.001 TYR A 546 ARG 0.001 0.000 ARG A1241 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7507 (mt) cc_final: 0.7228 (mp) REVERT: A 517 ASP cc_start: 0.8438 (t0) cc_final: 0.8237 (t0) REVERT: A 894 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8279 (t80) REVERT: A 970 TYR cc_start: 0.8294 (m-80) cc_final: 0.7883 (m-80) REVERT: A 1252 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8542 (mp) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 0.1590 time to fit residues: 19.0122 Evaluate side-chains 81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 85 optimal weight: 6.9990 chunk 42 optimal weight: 0.0000 chunk 64 optimal weight: 0.0470 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.4682 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.114266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.090125 restraints weight = 11914.006| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.64 r_work: 0.2954 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7694 Z= 0.130 Angle : 0.536 9.629 10498 Z= 0.249 Chirality : 0.040 0.346 1274 Planarity : 0.003 0.028 1272 Dihedral : 7.751 99.887 1621 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.41 % Allowed : 15.79 % Favored : 82.80 % 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: 0.31 (0.29), residues: 912 helix: 1.31 (0.25), residues: 500 sheet: -0.57 (0.53), residues: 84 loop : -1.31 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.007 0.001 HIS A1053 PHE 0.010 0.001 PHE A 930 TYR 0.009 0.001 TYR A 654 ARG 0.001 0.000 ARG A 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.7488 (mt) cc_final: 0.7211 (mp) REVERT: A 894 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8215 (t80) REVERT: A 970 TYR cc_start: 0.8292 (m-80) cc_final: 0.7925 (m-80) REVERT: A 1252 LEU cc_start: 0.8719 (tp) cc_final: 0.8471 (mt) outliers start: 11 outliers final: 9 residues processed: 78 average time/residue: 0.1477 time to fit residues: 17.4825 Evaluate side-chains 77 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 15 optimal weight: 8.9990 chunk 47 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.113052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.088883 restraints weight = 11743.235| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.62 r_work: 0.2937 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7694 Z= 0.168 Angle : 0.553 9.689 10498 Z= 0.259 Chirality : 0.041 0.317 1274 Planarity : 0.003 0.026 1272 Dihedral : 7.659 99.021 1621 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.67 % Allowed : 16.17 % Favored : 82.16 % 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: 0.38 (0.29), residues: 912 helix: 1.31 (0.25), residues: 500 sheet: -0.24 (0.55), residues: 74 loop : -1.24 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.006 0.001 HIS A1053 PHE 0.014 0.001 PHE A 930 TYR 0.009 0.001 TYR A 886 ARG 0.001 0.000 ARG A 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.47 seconds wall clock time: 65 minutes 9.50 seconds (3909.50 seconds total)