Starting phenix.real_space_refine on Tue Mar 3 21:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dfw_30666/03_2026/7dfw_30666_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dfw_30666/03_2026/7dfw_30666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dfw_30666/03_2026/7dfw_30666_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dfw_30666/03_2026/7dfw_30666_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dfw_30666/03_2026/7dfw_30666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dfw_30666/03_2026/7dfw_30666.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.009 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 46 5.16 5 C 5195 2.51 5 N 1226 2.21 5 O 1445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7913 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7450 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 50, 'TRANS': 906} Chain: "I" 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: "L" 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: "S" 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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 351 Unusual residues: {'CLR': 6, 'LMT': 1, 'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 14} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.24, per 1000 atoms: 0.28 Number of scatterers: 7913 At special positions: 0 Unit cell: (98.19, 75.279, 135.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 1 15.00 O 1445 8.00 N 1226 7.00 C 5195 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 BETA1-3 " NAG S 2 " - " NAG S 3 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " " NAG S 1 " - " NAG S 2 " 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 I 1 " - " ASN A 497 " " NAG L 1 " - " ASN A 909 " " NAG S 1 " - " ASN A1037 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 318.9 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 60.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 334 through 351 Processing helix chain 'A' and resid 351 through 368 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.919A pdb=" N LEU A 382 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 383 " --> pdb=" O VAL A 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 383' Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.539A pdb=" N HIS A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 4.088A pdb=" N ILE A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.704A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 584 through 607 removed outlier: 3.738A pdb=" N GLN A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 626 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 637 through 647 removed outlier: 4.019A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.673A pdb=" N ARG A 659 " --> pdb=" O SER A 656 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 660 " --> pdb=" O TRP A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 660' Processing helix chain 'A' and resid 665 through 690 removed outlier: 3.610A pdb=" N LEU A 690 " --> pdb=" O PHE A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 724 Proline residue: A 703 - end of helix removed outlier: 3.584A pdb=" N LEU A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASN A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 762 removed outlier: 3.660A pdb=" N ARG A 742 " --> pdb=" O ARG A 738 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Proline residue: A 745 - end of helix removed outlier: 3.720A pdb=" N SER A 751 " --> pdb=" O MET A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 799 removed outlier: 3.701A pdb=" N PHE A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 841 Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 842 through 864 removed outlier: 3.941A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 855 " --> pdb=" O LEU A 851 " (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 Processing helix chain 'A' and resid 882 through 894 removed outlier: 3.657A pdb=" N TYR A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 1004 through 1018 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.576A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1103 removed outlier: 3.738A 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 1130 removed outlier: 4.015A pdb=" N GLU A1111 " --> pdb=" O THR A1107 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A1121 " --> pdb=" O SER A1117 " (cutoff:3.500A) Proline residue: A1122 - end of helix removed outlier: 3.729A pdb=" N CYS A1128 " --> pdb=" O PHE A1124 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A1129 " --> pdb=" O ALA A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1159 removed outlier: 3.546A pdb=" N ASN A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1178 removed outlier: 3.708A pdb=" N GLY A1176 " --> pdb=" O VAL A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1191 removed outlier: 3.851A pdb=" N VAL A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1226 removed outlier: 4.611A pdb=" N SER A1210 " --> pdb=" O ILE A1206 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA A1211 " --> pdb=" O SER A1207 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1217 " --> pdb=" O PHE A1213 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1227 through 1230 Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1240 through 1256 Processing helix chain 'A' and resid 1257 through 1265 removed outlier: 3.626A pdb=" N TYR A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1286 removed outlier: 4.318A pdb=" N GLU A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A1282 " --> pdb=" O LYS A1278 " (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 456 through 457 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: 6.694A pdb=" N MET A1050 " --> pdb=" O PRO A 949 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER A 951 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG A1048 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASN A1037 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing sheet with id=AA7, 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: 6.694A pdb=" N MET A1050 " --> pdb=" O PRO A 949 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER A 951 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG A1048 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 968 through 970 removed outlier: 3.882A pdb=" N LYS A 991 " --> pdb=" O LEU A 969 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1122 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: 1.39 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1203 1.31 - 1.44: 2197 1.44 - 1.57: 4640 1.57 - 1.70: 4 1.70 - 1.83: 71 Bond restraints: 8115 Sorted by residual: bond pdb=" C17 P5S A1308 " pdb=" O19 P5S A1308 " ideal model delta sigma weight residual 1.351 1.406 -0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C3' LMT A1309 " pdb=" O3' LMT A1309 " ideal model delta sigma weight residual 1.404 1.350 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C6B LMT A1309 " pdb=" O6B LMT A1309 " ideal model delta sigma weight residual 1.407 1.353 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C6' LMT A1309 " pdb=" O6' LMT A1309 " ideal model delta sigma weight residual 1.407 1.354 0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C38 P5S A1308 " pdb=" O37 P5S A1308 " ideal model delta sigma weight residual 1.345 1.397 -0.052 2.00e-02 2.50e+03 6.73e+00 ... (remaining 8110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 10943 3.90 - 7.81: 125 7.81 - 11.71: 5 11.71 - 15.62: 1 15.62 - 19.52: 1 Bond angle restraints: 11075 Sorted by residual: angle pdb=" O13 P5S A1308 " pdb=" P12 P5S A1308 " pdb=" O15 P5S A1308 " ideal model delta sigma weight residual 121.25 101.73 19.52 3.00e+00 1.11e-01 4.24e+01 angle pdb=" N ASP A 378 " pdb=" CA ASP A 378 " pdb=" C ASP A 378 " ideal model delta sigma weight residual 109.81 121.79 -11.98 2.21e+00 2.05e-01 2.94e+01 angle pdb=" CA ASP A 378 " pdb=" C ASP A 378 " pdb=" N PRO A 379 " ideal model delta sigma weight residual 118.44 125.35 -6.91 1.59e+00 3.96e-01 1.89e+01 angle pdb=" C LEU A 412 " pdb=" N THR A 413 " pdb=" CA THR A 413 " ideal model delta sigma weight residual 122.78 129.16 -6.38 1.52e+00 4.33e-01 1.76e+01 angle pdb=" CA VAL A 701 " pdb=" C VAL A 701 " pdb=" N VAL A 702 " ideal model delta sigma weight residual 116.60 122.27 -5.67 1.45e+00 4.76e-01 1.53e+01 ... (remaining 11070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 5001 23.11 - 46.21: 281 46.21 - 69.32: 34 69.32 - 92.43: 35 92.43 - 115.53: 7 Dihedral angle restraints: 5358 sinusoidal: 2568 harmonic: 2790 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 -173.82 87.82 1 1.00e+01 1.00e-02 9.23e+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 -18.36 -67.64 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CA PRO A1025 " pdb=" C PRO A1025 " pdb=" N LYS A1026 " pdb=" CA LYS A1026 " ideal model delta harmonic sigma weight residual -180.00 -153.28 -26.72 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 5355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1081 0.062 - 0.125: 208 0.125 - 0.187: 31 0.187 - 0.249: 14 0.249 - 0.312: 5 Chirality restraints: 1339 Sorted by residual: chirality pdb=" C1 NAG S 3 " pdb=" O3 NAG S 2 " pdb=" C2 NAG S 3 " pdb=" O5 NAG S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 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 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB ILE A 996 " pdb=" CA ILE A 996 " pdb=" CG1 ILE A 996 " pdb=" CG2 ILE A 996 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1336 not shown) Planarity restraints: 1343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 3 " -0.346 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG L 3 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG L 3 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG L 3 " 0.535 2.00e-02 2.50e+03 pdb=" O7 NAG L 3 " -0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " -0.335 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A1306 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " -0.050 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.309 2.00e-02 2.50e+03 2.58e-01 8.30e+02 pdb=" C7 NAG A1303 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.198 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.436 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " -0.014 2.00e-02 2.50e+03 ... (remaining 1340 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 317 2.72 - 3.27: 7803 3.27 - 3.81: 12243 3.81 - 4.36: 15987 4.36 - 4.90: 27278 Nonbonded interactions: 63628 Sorted by model distance: nonbonded pdb=" OE1 GLU A 624 " pdb=" OG SER A 881 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP A 534 " pdb=" OG1 THR A 536 " model vdw 2.189 3.040 nonbonded pdb=" O ALA A 365 " pdb=" OH TYR A 689 " model vdw 2.192 3.040 nonbonded pdb=" OE1 GLU A 374 " pdb=" OG SER A 688 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASP A 712 " pdb=" OG1 THR A1219 " model vdw 2.274 3.040 ... (remaining 63623 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 'L' selection = chain 'S' } 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: 3.170 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 0.064 8135 Z= 0.302 Angle : 1.003 19.523 11130 Z= 0.493 Chirality : 0.057 0.312 1339 Planarity : 0.017 0.300 1333 Dihedral : 15.929 115.534 3543 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.21), residues: 955 helix: -2.13 (0.15), residues: 534 sheet: -0.21 (0.67), residues: 62 loop : -2.04 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 421 TYR 0.015 0.002 TYR A 689 PHE 0.020 0.002 PHE A1093 TRP 0.046 0.003 TRP A 843 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00642 ( 8115) covalent geometry : angle 0.97770 (11075) SS BOND : bond 0.00288 ( 5) SS BOND : angle 3.60137 ( 10) hydrogen bonds : bond 0.15559 ( 388) hydrogen bonds : angle 6.26991 ( 1122) link_BETA1-3 : bond 0.00785 ( 1) link_BETA1-3 : angle 3.15780 ( 3) link_BETA1-4 : bond 0.00537 ( 4) link_BETA1-4 : angle 1.76874 ( 12) link_NAG-ASN : bond 0.00477 ( 10) link_NAG-ASN : angle 3.69208 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.7534 (ttp-110) cc_final: 0.7210 (ttm170) REVERT: A 1236 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7763 (tm-30) outliers start: 0 outliers final: 1 residues processed: 77 average time/residue: 0.5270 time to fit residues: 43.4473 Evaluate side-chains 58 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN A 496 ASN A 873 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101090 restraints weight = 11250.051| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.07 r_work: 0.3122 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8135 Z= 0.138 Angle : 0.695 9.935 11130 Z= 0.321 Chirality : 0.044 0.231 1339 Planarity : 0.004 0.039 1333 Dihedral : 13.413 111.957 1853 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.23 % Allowed : 7.13 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.26), residues: 955 helix: 0.11 (0.22), residues: 523 sheet: -0.05 (0.68), residues: 63 loop : -1.74 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.009 0.001 TYR A 886 PHE 0.014 0.001 PHE A 791 TRP 0.015 0.001 TRP A 843 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8115) covalent geometry : angle 0.66382 (11075) SS BOND : bond 0.00235 ( 5) SS BOND : angle 1.69467 ( 10) hydrogen bonds : bond 0.04383 ( 388) hydrogen bonds : angle 4.40806 ( 1122) link_BETA1-3 : bond 0.01100 ( 1) link_BETA1-3 : angle 5.22202 ( 3) link_BETA1-4 : bond 0.00818 ( 4) link_BETA1-4 : angle 1.97567 ( 12) link_NAG-ASN : bond 0.00333 ( 10) link_NAG-ASN : angle 3.34291 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.288 Fit side-chains REVERT: A 450 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.8007 (ttm170) REVERT: A 661 MET cc_start: 0.7018 (mmt) cc_final: 0.6429 (mtt) REVERT: A 1236 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8057 (tm-30) outliers start: 10 outliers final: 3 residues processed: 63 average time/residue: 0.5806 time to fit residues: 39.0950 Evaluate side-chains 55 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 852 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 HIS A 722 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100859 restraints weight = 11228.163| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.07 r_work: 0.3114 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8135 Z= 0.137 Angle : 0.653 9.295 11130 Z= 0.302 Chirality : 0.043 0.240 1339 Planarity : 0.004 0.034 1333 Dihedral : 11.790 109.499 1853 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.23 % Allowed : 9.59 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.27), residues: 955 helix: 0.70 (0.23), residues: 534 sheet: 0.15 (0.69), residues: 62 loop : -1.46 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 421 TYR 0.010 0.001 TYR A 420 PHE 0.015 0.002 PHE A 791 TRP 0.013 0.001 TRP A 843 HIS 0.002 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8115) covalent geometry : angle 0.62675 (11075) SS BOND : bond 0.00292 ( 5) SS BOND : angle 1.96675 ( 10) hydrogen bonds : bond 0.04165 ( 388) hydrogen bonds : angle 4.18921 ( 1122) link_BETA1-3 : bond 0.01063 ( 1) link_BETA1-3 : angle 5.12229 ( 3) link_BETA1-4 : bond 0.00629 ( 4) link_BETA1-4 : angle 1.85666 ( 12) link_NAG-ASN : bond 0.00278 ( 10) link_NAG-ASN : angle 2.77173 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.8055 (ttm170) REVERT: A 661 MET cc_start: 0.6993 (mmt) cc_final: 0.6468 (mtt) REVERT: A 1180 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7989 (mt-10) outliers start: 10 outliers final: 2 residues processed: 67 average time/residue: 0.5295 time to fit residues: 38.0646 Evaluate side-chains 54 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 506 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 93 optimal weight: 0.0010 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.123319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101281 restraints weight = 11468.083| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.09 r_work: 0.3124 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8135 Z= 0.124 Angle : 0.636 9.458 11130 Z= 0.292 Chirality : 0.042 0.240 1339 Planarity : 0.003 0.033 1333 Dihedral : 11.272 109.265 1850 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.98 % Allowed : 11.32 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.28), residues: 955 helix: 1.05 (0.24), residues: 521 sheet: 0.21 (0.70), residues: 62 loop : -1.47 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 801 TYR 0.008 0.001 TYR A 546 PHE 0.013 0.001 PHE A1257 TRP 0.017 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8115) covalent geometry : angle 0.61147 (11075) SS BOND : bond 0.00278 ( 5) SS BOND : angle 1.73004 ( 10) hydrogen bonds : bond 0.03847 ( 388) hydrogen bonds : angle 4.14083 ( 1122) link_BETA1-3 : bond 0.00931 ( 1) link_BETA1-3 : angle 5.29375 ( 3) link_BETA1-4 : bond 0.00584 ( 4) link_BETA1-4 : angle 1.85856 ( 12) link_NAG-ASN : bond 0.00255 ( 10) link_NAG-ASN : angle 2.62292 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.8027 (ttm170) REVERT: A 661 MET cc_start: 0.6981 (mmt) cc_final: 0.6475 (mtt) REVERT: A 1180 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8014 (mt-10) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.6459 time to fit residues: 39.8939 Evaluate side-chains 55 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 852 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 93 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.124090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101954 restraints weight = 11398.150| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.10 r_work: 0.3132 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8135 Z= 0.118 Angle : 0.618 9.436 11130 Z= 0.283 Chirality : 0.042 0.242 1339 Planarity : 0.003 0.033 1333 Dihedral : 10.555 108.298 1850 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.60 % Allowed : 12.42 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 955 helix: 1.20 (0.24), residues: 522 sheet: 0.23 (0.70), residues: 62 loop : -1.43 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 801 TYR 0.011 0.001 TYR A 654 PHE 0.012 0.001 PHE A 704 TRP 0.015 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8115) covalent geometry : angle 0.59471 (11075) SS BOND : bond 0.00280 ( 5) SS BOND : angle 1.52348 ( 10) hydrogen bonds : bond 0.03662 ( 388) hydrogen bonds : angle 4.06831 ( 1122) link_BETA1-3 : bond 0.00846 ( 1) link_BETA1-3 : angle 5.35818 ( 3) link_BETA1-4 : bond 0.00556 ( 4) link_BETA1-4 : angle 1.87627 ( 12) link_NAG-ASN : bond 0.00255 ( 10) link_NAG-ASN : angle 2.49674 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.7931 (ttm170) REVERT: A 598 GLU cc_start: 0.8375 (tt0) cc_final: 0.8172 (tt0) REVERT: A 661 MET cc_start: 0.6703 (mmt) cc_final: 0.6279 (mtp) REVERT: A 865 CYS cc_start: 0.8741 (m) cc_final: 0.8486 (p) REVERT: A 1180 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7956 (mt-10) outliers start: 13 outliers final: 5 residues processed: 62 average time/residue: 0.4919 time to fit residues: 32.8207 Evaluate side-chains 58 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 61 optimal weight: 0.0670 chunk 82 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.124101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102083 restraints weight = 11265.657| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.09 r_work: 0.3134 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8135 Z= 0.117 Angle : 0.613 9.439 11130 Z= 0.282 Chirality : 0.042 0.239 1339 Planarity : 0.003 0.032 1333 Dihedral : 10.189 107.904 1850 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.11 % Allowed : 13.04 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.28), residues: 955 helix: 1.24 (0.24), residues: 525 sheet: 0.22 (0.71), residues: 62 loop : -1.44 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 421 TYR 0.008 0.001 TYR A 546 PHE 0.012 0.001 PHE A 704 TRP 0.014 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8115) covalent geometry : angle 0.59038 (11075) SS BOND : bond 0.00275 ( 5) SS BOND : angle 1.48697 ( 10) hydrogen bonds : bond 0.03630 ( 388) hydrogen bonds : angle 4.03496 ( 1122) link_BETA1-3 : bond 0.00785 ( 1) link_BETA1-3 : angle 5.29881 ( 3) link_BETA1-4 : bond 0.00556 ( 4) link_BETA1-4 : angle 1.90996 ( 12) link_NAG-ASN : bond 0.00242 ( 10) link_NAG-ASN : angle 2.43720 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7909 (ttm170) REVERT: A 661 MET cc_start: 0.6740 (mmt) cc_final: 0.6312 (mtp) REVERT: A 1180 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7940 (mt-10) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 0.5734 time to fit residues: 39.2594 Evaluate side-chains 62 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 997 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.123952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101907 restraints weight = 11297.604| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.09 r_work: 0.3128 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8135 Z= 0.121 Angle : 0.614 9.454 11130 Z= 0.281 Chirality : 0.042 0.238 1339 Planarity : 0.003 0.034 1333 Dihedral : 10.023 108.208 1850 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.48 % Allowed : 12.92 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.28), residues: 955 helix: 1.21 (0.24), residues: 531 sheet: 0.18 (0.71), residues: 62 loop : -1.37 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.007 0.001 TYR A 546 PHE 0.012 0.001 PHE A 704 TRP 0.013 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8115) covalent geometry : angle 0.59137 (11075) SS BOND : bond 0.00289 ( 5) SS BOND : angle 1.44323 ( 10) hydrogen bonds : bond 0.03690 ( 388) hydrogen bonds : angle 4.02904 ( 1122) link_BETA1-3 : bond 0.00745 ( 1) link_BETA1-3 : angle 5.22383 ( 3) link_BETA1-4 : bond 0.00531 ( 4) link_BETA1-4 : angle 1.90449 ( 12) link_NAG-ASN : bond 0.00243 ( 10) link_NAG-ASN : angle 2.40154 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.7941 (ttm170) REVERT: A 661 MET cc_start: 0.6729 (mmt) cc_final: 0.6315 (mtp) REVERT: A 864 MET cc_start: 0.9160 (ptm) cc_final: 0.8958 (ptp) REVERT: A 1147 MET cc_start: 0.8851 (mtp) cc_final: 0.8632 (mtm) REVERT: A 1180 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7941 (mt-10) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.5166 time to fit residues: 35.9903 Evaluate side-chains 65 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 79 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.123868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.101754 restraints weight = 11408.918| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.10 r_work: 0.3127 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8135 Z= 0.123 Angle : 0.614 9.473 11130 Z= 0.282 Chirality : 0.042 0.238 1339 Planarity : 0.003 0.036 1333 Dihedral : 9.860 108.366 1850 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.48 % Allowed : 13.04 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.28), residues: 955 helix: 1.22 (0.24), residues: 536 sheet: 0.19 (0.71), residues: 62 loop : -1.38 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.007 0.001 TYR A 420 PHE 0.012 0.001 PHE A 704 TRP 0.012 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8115) covalent geometry : angle 0.59209 (11075) SS BOND : bond 0.00304 ( 5) SS BOND : angle 1.45604 ( 10) hydrogen bonds : bond 0.03735 ( 388) hydrogen bonds : angle 4.03016 ( 1122) link_BETA1-3 : bond 0.00664 ( 1) link_BETA1-3 : angle 5.13557 ( 3) link_BETA1-4 : bond 0.00517 ( 4) link_BETA1-4 : angle 1.86980 ( 12) link_NAG-ASN : bond 0.00242 ( 10) link_NAG-ASN : angle 2.37250 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.7928 (ttm170) REVERT: A 661 MET cc_start: 0.6746 (mmt) cc_final: 0.6351 (mtp) REVERT: A 864 MET cc_start: 0.9187 (ptm) cc_final: 0.8984 (ptp) REVERT: A 1129 LEU cc_start: 0.8198 (pp) cc_final: 0.7988 (tp) REVERT: A 1180 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7940 (mt-10) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.4825 time to fit residues: 34.6129 Evaluate side-chains 64 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 58 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.125402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103287 restraints weight = 11328.784| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.11 r_work: 0.3149 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8135 Z= 0.102 Angle : 0.590 9.427 11130 Z= 0.270 Chirality : 0.041 0.239 1339 Planarity : 0.003 0.033 1333 Dihedral : 9.501 107.513 1850 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.48 % Allowed : 13.41 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.29), residues: 955 helix: 1.35 (0.24), residues: 530 sheet: 0.27 (0.71), residues: 62 loop : -1.32 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.009 0.001 TYR A 546 PHE 0.011 0.001 PHE A 704 TRP 0.026 0.001 TRP A 843 HIS 0.002 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8115) covalent geometry : angle 0.57043 (11075) SS BOND : bond 0.00234 ( 5) SS BOND : angle 1.23962 ( 10) hydrogen bonds : bond 0.03341 ( 388) hydrogen bonds : angle 3.95846 ( 1122) link_BETA1-3 : bond 0.00674 ( 1) link_BETA1-3 : angle 4.98264 ( 3) link_BETA1-4 : bond 0.00533 ( 4) link_BETA1-4 : angle 1.81665 ( 12) link_NAG-ASN : bond 0.00254 ( 10) link_NAG-ASN : angle 2.21693 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8322 (ttp-110) cc_final: 0.7908 (ttm170) REVERT: A 661 MET cc_start: 0.6681 (mmt) cc_final: 0.6325 (mtp) REVERT: A 864 MET cc_start: 0.9157 (ptm) cc_final: 0.8946 (ptp) REVERT: A 865 CYS cc_start: 0.8709 (m) cc_final: 0.8473 (p) REVERT: A 1180 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7923 (mt-10) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.4794 time to fit residues: 34.1309 Evaluate side-chains 63 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101142 restraints weight = 11326.054| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.01 r_work: 0.3116 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8135 Z= 0.151 Angle : 0.641 9.535 11130 Z= 0.297 Chirality : 0.043 0.242 1339 Planarity : 0.004 0.034 1333 Dihedral : 9.671 109.024 1850 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.60 % Allowed : 13.53 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.28), residues: 955 helix: 1.17 (0.24), residues: 540 sheet: 0.16 (0.71), residues: 62 loop : -1.39 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.008 0.001 TYR A 483 PHE 0.013 0.001 PHE A 791 TRP 0.026 0.001 TRP A 843 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8115) covalent geometry : angle 0.61991 (11075) SS BOND : bond 0.00355 ( 5) SS BOND : angle 1.61783 ( 10) hydrogen bonds : bond 0.04112 ( 388) hydrogen bonds : angle 4.06795 ( 1122) link_BETA1-3 : bond 0.00419 ( 1) link_BETA1-3 : angle 4.94452 ( 3) link_BETA1-4 : bond 0.00509 ( 4) link_BETA1-4 : angle 1.90504 ( 12) link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 2.38389 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.7842 (ttm170) REVERT: A 661 MET cc_start: 0.6679 (mmt) cc_final: 0.6274 (mtp) REVERT: A 1026 LYS cc_start: 0.7662 (mmtt) cc_final: 0.7017 (mmmt) REVERT: A 1147 MET cc_start: 0.8726 (mtp) cc_final: 0.8505 (mtm) REVERT: A 1180 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7937 (mt-10) outliers start: 13 outliers final: 12 residues processed: 64 average time/residue: 0.5324 time to fit residues: 36.4274 Evaluate side-chains 67 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 1164 ASN Chi-restraints excluded: chain A residue 1226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101611 restraints weight = 11358.664| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.02 r_work: 0.3123 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8135 Z= 0.136 Angle : 0.623 9.492 11130 Z= 0.288 Chirality : 0.042 0.241 1339 Planarity : 0.003 0.034 1333 Dihedral : 9.562 109.323 1850 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.48 % Allowed : 13.90 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.28), residues: 955 helix: 1.18 (0.23), residues: 540 sheet: 0.12 (0.71), residues: 62 loop : -1.35 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 801 TYR 0.008 0.001 TYR A 546 PHE 0.012 0.001 PHE A 704 TRP 0.025 0.001 TRP A 843 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8115) covalent geometry : angle 0.60247 (11075) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.44681 ( 10) hydrogen bonds : bond 0.03890 ( 388) hydrogen bonds : angle 4.05149 ( 1122) link_BETA1-3 : bond 0.00510 ( 1) link_BETA1-3 : angle 4.84024 ( 3) link_BETA1-4 : bond 0.00485 ( 4) link_BETA1-4 : angle 1.84503 ( 12) link_NAG-ASN : bond 0.00236 ( 10) link_NAG-ASN : angle 2.32828 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2568.62 seconds wall clock time: 44 minutes 28.59 seconds (2668.59 seconds total)