Starting phenix.real_space_refine on Sat Jul 26 21:06:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dfw_30666/07_2025/7dfw_30666_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dfw_30666/07_2025/7dfw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dfw_30666/07_2025/7dfw_30666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dfw_30666/07_2025/7dfw_30666.map" model { file = "/net/cci-nas-00/data/ceres_data/7dfw_30666/07_2025/7dfw_30666_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dfw_30666/07_2025/7dfw_30666_neut_trim.cif" } resolution = 2.69 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= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.60, per 1000 atoms: 0.83 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: 3.02 Conformation dependent library (CDL) restraints added in 987.2 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: 0.93 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: 2.86 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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: 4.180 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.520 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.046 0.003 TRP A 843 HIS 0.004 0.001 HIS A 400 PHE 0.020 0.002 PHE A1093 TYR 0.015 0.002 TYR A 689 ARG 0.011 0.001 ARG A 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 10) link_NAG-ASN : angle 3.69208 ( 30) link_BETA1-4 : bond 0.00537 ( 4) link_BETA1-4 : angle 1.76874 ( 12) hydrogen bonds : bond 0.15559 ( 388) hydrogen bonds : angle 6.26991 ( 1122) SS BOND : bond 0.00288 ( 5) SS BOND : angle 3.60137 ( 10) link_BETA1-3 : bond 0.00785 ( 1) link_BETA1-3 : angle 3.15780 ( 3) covalent geometry : bond 0.00642 ( 8115) covalent geometry : angle 0.97770 (11075) *********************** 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 : 0.902 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: 1.1020 time to fit residues: 91.4269 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 : 0.868 ------------------------------------------------------------------------------- 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 80 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0050 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 521 HIS A 873 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100774 restraints weight = 11185.405| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.05 r_work: 0.3118 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8135 Z= 0.145 Angle : 0.701 9.630 11130 Z= 0.325 Chirality : 0.044 0.231 1339 Planarity : 0.004 0.040 1333 Dihedral : 13.389 111.841 1853 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.23 % Allowed : 7.01 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.26), residues: 955 helix: 0.08 (0.22), residues: 526 sheet: -0.06 (0.68), residues: 63 loop : -1.76 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 843 HIS 0.003 0.001 HIS A 334 PHE 0.014 0.002 PHE A 791 TYR 0.009 0.001 TYR A 886 ARG 0.003 0.000 ARG A 801 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 10) link_NAG-ASN : angle 3.37195 ( 30) link_BETA1-4 : bond 0.00726 ( 4) link_BETA1-4 : angle 1.96037 ( 12) hydrogen bonds : bond 0.04437 ( 388) hydrogen bonds : angle 4.40809 ( 1122) SS BOND : bond 0.00265 ( 5) SS BOND : angle 1.74842 ( 10) link_BETA1-3 : bond 0.01168 ( 1) link_BETA1-3 : angle 5.14144 ( 3) covalent geometry : bond 0.00331 ( 8115) covalent geometry : angle 0.67039 (11075) *********************** 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 : 0.957 Fit side-chains REVERT: A 450 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.8133 (ttm170) REVERT: A 1236 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8063 (tm-30) outliers start: 10 outliers final: 3 residues processed: 63 average time/residue: 1.3931 time to fit residues: 94.4873 Evaluate side-chains 54 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 82 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.123365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101369 restraints weight = 11352.742| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.07 r_work: 0.3123 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1242 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= 0.128 Angle : 0.643 9.524 11130 Z= 0.297 Chirality : 0.043 0.233 1339 Planarity : 0.004 0.035 1333 Dihedral : 11.960 109.582 1853 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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 (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: -0.25 (0.27), residues: 955 helix: 0.71 (0.23), residues: 528 sheet: 0.10 (0.69), residues: 63 loop : -1.50 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 843 HIS 0.002 0.001 HIS A 521 PHE 0.014 0.001 PHE A 791 TYR 0.008 0.001 TYR A 420 ARG 0.007 0.000 ARG A 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 10) link_NAG-ASN : angle 2.77409 ( 30) link_BETA1-4 : bond 0.00583 ( 4) link_BETA1-4 : angle 1.87784 ( 12) hydrogen bonds : bond 0.04017 ( 388) hydrogen bonds : angle 4.20212 ( 1122) SS BOND : bond 0.00276 ( 5) SS BOND : angle 1.93051 ( 10) link_BETA1-3 : bond 0.01133 ( 1) link_BETA1-3 : angle 5.05319 ( 3) covalent geometry : bond 0.00289 ( 8115) covalent geometry : angle 0.61735 (11075) *********************** 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 71 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8370 (ttp-110) cc_final: 0.8069 (ttm170) REVERT: A 661 MET cc_start: 0.6986 (mmt) cc_final: 0.6446 (mtt) REVERT: A 1236 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8136 (tm-30) outliers start: 10 outliers final: 2 residues processed: 67 average time/residue: 1.0810 time to fit residues: 78.2626 Evaluate side-chains 52 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.123845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102376 restraints weight = 11209.327| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.02 r_work: 0.3132 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1419 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= 0.122 Angle : 0.633 9.365 11130 Z= 0.291 Chirality : 0.042 0.243 1339 Planarity : 0.003 0.034 1333 Dihedral : 11.168 108.809 1850 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.11 % Allowed : 11.19 % 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 (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: 0.08 (0.28), residues: 955 helix: 1.07 (0.24), residues: 521 sheet: 0.20 (0.70), residues: 62 loop : -1.46 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 PHE 0.013 0.001 PHE A 704 TYR 0.013 0.001 TYR A 654 ARG 0.003 0.000 ARG A 463 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 10) link_NAG-ASN : angle 2.57956 ( 30) link_BETA1-4 : bond 0.00601 ( 4) link_BETA1-4 : angle 1.84513 ( 12) hydrogen bonds : bond 0.03762 ( 388) hydrogen bonds : angle 4.11725 ( 1122) SS BOND : bond 0.00330 ( 5) SS BOND : angle 1.81584 ( 10) link_BETA1-3 : bond 0.00935 ( 1) link_BETA1-3 : angle 5.31676 ( 3) covalent geometry : bond 0.00277 ( 8115) covalent geometry : angle 0.60891 (11075) *********************** 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 64 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8304 (ttp-110) cc_final: 0.7977 (ttm170) REVERT: A 598 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: A 661 MET cc_start: 0.6700 (mmt) cc_final: 0.6245 (mtt) REVERT: A 1180 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7978 (mt-10) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 1.2077 time to fit residues: 77.6664 Evaluate side-chains 56 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 598 GLU 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 14 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.120783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099489 restraints weight = 11209.504| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.00 r_work: 0.3088 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8135 Z= 0.190 Angle : 0.690 9.550 11130 Z= 0.319 Chirality : 0.045 0.240 1339 Planarity : 0.004 0.033 1333 Dihedral : 11.103 110.325 1850 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.48 % Allowed : 12.42 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 955 helix: 0.87 (0.23), residues: 539 sheet: 0.12 (0.71), residues: 62 loop : -1.48 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 960 HIS 0.003 0.001 HIS A 521 PHE 0.015 0.002 PHE A 704 TYR 0.011 0.001 TYR A 420 ARG 0.005 0.000 ARG A 801 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 10) link_NAG-ASN : angle 2.80687 ( 30) link_BETA1-4 : bond 0.00463 ( 4) link_BETA1-4 : angle 1.88533 ( 12) hydrogen bonds : bond 0.04650 ( 388) hydrogen bonds : angle 4.23120 ( 1122) SS BOND : bond 0.00392 ( 5) SS BOND : angle 1.94705 ( 10) link_BETA1-3 : bond 0.00733 ( 1) link_BETA1-3 : angle 5.37870 ( 3) covalent geometry : bond 0.00456 ( 8115) covalent geometry : angle 0.66519 (11075) *********************** 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 67 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.8010 (ttm170) REVERT: A 1180 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8027 (mt-10) outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 1.1159 time to fit residues: 75.8737 Evaluate side-chains 59 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 997 THR 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 33 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.123416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102101 restraints weight = 11278.103| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.02 r_work: 0.3130 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1596 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= 0.118 Angle : 0.621 9.419 11130 Z= 0.285 Chirality : 0.042 0.238 1339 Planarity : 0.003 0.037 1333 Dihedral : 10.524 109.156 1850 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.35 % Allowed : 13.41 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 955 helix: 1.11 (0.24), residues: 529 sheet: 0.26 (0.72), residues: 62 loop : -1.41 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 843 HIS 0.002 0.001 HIS A 400 PHE 0.012 0.001 PHE A 791 TYR 0.009 0.001 TYR A 546 ARG 0.004 0.000 ARG A 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 10) link_NAG-ASN : angle 2.53309 ( 30) link_BETA1-4 : bond 0.00540 ( 4) link_BETA1-4 : angle 1.89947 ( 12) hydrogen bonds : bond 0.03720 ( 388) hydrogen bonds : angle 4.09679 ( 1122) SS BOND : bond 0.00303 ( 5) SS BOND : angle 1.48023 ( 10) link_BETA1-3 : bond 0.00898 ( 1) link_BETA1-3 : angle 5.39536 ( 3) covalent geometry : bond 0.00269 ( 8115) covalent geometry : angle 0.59686 (11075) *********************** 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 68 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8216 (p0) cc_final: 0.7920 (p0) REVERT: A 450 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7975 (ttm170) REVERT: A 661 MET cc_start: 0.6772 (mmt) cc_final: 0.6320 (mtp) REVERT: A 1180 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7947 (mt-10) outliers start: 11 outliers final: 5 residues processed: 64 average time/residue: 1.1113 time to fit residues: 76.7450 Evaluate side-chains 61 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 997 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.123040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101786 restraints weight = 11293.266| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.00 r_work: 0.3127 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1655 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= 0.127 Angle : 0.628 9.464 11130 Z= 0.289 Chirality : 0.043 0.236 1339 Planarity : 0.003 0.037 1333 Dihedral : 10.298 109.040 1850 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.60 % Allowed : 13.41 % Favored : 84.99 % 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: 0.22 (0.28), residues: 955 helix: 1.14 (0.24), residues: 531 sheet: 0.20 (0.71), residues: 62 loop : -1.36 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 PHE 0.013 0.001 PHE A 704 TYR 0.010 0.001 TYR A 654 ARG 0.003 0.000 ARG A 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 10) link_NAG-ASN : angle 2.51076 ( 30) link_BETA1-4 : bond 0.00534 ( 4) link_BETA1-4 : angle 1.92472 ( 12) hydrogen bonds : bond 0.03840 ( 388) hydrogen bonds : angle 4.06584 ( 1122) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.53922 ( 10) link_BETA1-3 : bond 0.00730 ( 1) link_BETA1-3 : angle 5.31982 ( 3) covalent geometry : bond 0.00293 ( 8115) covalent geometry : angle 0.60439 (11075) *********************** 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 74 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7864 (p0) REVERT: A 450 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7845 (ttm170) REVERT: A 661 MET cc_start: 0.6685 (mmt) cc_final: 0.6233 (mtp) REVERT: A 1026 LYS cc_start: 0.7552 (mmtt) cc_final: 0.6917 (mmmt) REVERT: A 1180 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7903 (mt-10) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 1.0767 time to fit residues: 81.2044 Evaluate side-chains 66 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASP 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 813 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.123214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101897 restraints weight = 11366.991| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.03 r_work: 0.3126 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1708 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= 0.126 Angle : 0.620 9.475 11130 Z= 0.285 Chirality : 0.042 0.239 1339 Planarity : 0.003 0.038 1333 Dihedral : 10.079 109.159 1850 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.60 % Allowed : 13.65 % Favored : 84.75 % 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: 0.27 (0.28), residues: 955 helix: 1.18 (0.24), residues: 536 sheet: 0.20 (0.71), residues: 62 loop : -1.37 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE A 704 TYR 0.006 0.001 TYR A 420 ARG 0.003 0.000 ARG A 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 10) link_NAG-ASN : angle 2.46276 ( 30) link_BETA1-4 : bond 0.00520 ( 4) link_BETA1-4 : angle 1.90156 ( 12) hydrogen bonds : bond 0.03791 ( 388) hydrogen bonds : angle 4.04891 ( 1122) SS BOND : bond 0.00321 ( 5) SS BOND : angle 1.42933 ( 10) link_BETA1-3 : bond 0.00703 ( 1) link_BETA1-3 : angle 5.26301 ( 3) covalent geometry : bond 0.00292 ( 8115) covalent geometry : angle 0.59741 (11075) *********************** 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: 13 poor density : 57 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7940 (p0) REVERT: A 450 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7872 (ttm170) REVERT: A 661 MET cc_start: 0.6714 (mmt) cc_final: 0.6279 (mtp) REVERT: A 1026 LYS cc_start: 0.7547 (mmtt) cc_final: 0.6994 (mmmt) REVERT: A 1129 LEU cc_start: 0.8209 (pp) cc_final: 0.7995 (tp) REVERT: A 1180 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7922 (mt-10) outliers start: 13 outliers final: 11 residues processed: 66 average time/residue: 1.1402 time to fit residues: 80.9328 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 : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 378 ASP 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 1226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.122161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100902 restraints weight = 11498.061| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.02 r_work: 0.3114 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1724 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= 0.143 Angle : 0.640 9.506 11130 Z= 0.295 Chirality : 0.043 0.238 1339 Planarity : 0.003 0.037 1333 Dihedral : 10.039 109.691 1850 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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 (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 (0.28), residues: 955 helix: 1.12 (0.23), residues: 539 sheet: 0.18 (0.71), residues: 62 loop : -1.39 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 960 HIS 0.002 0.001 HIS A 334 PHE 0.013 0.001 PHE A 704 TYR 0.007 0.001 TYR A 546 ARG 0.003 0.000 ARG A 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 10) link_NAG-ASN : angle 2.51595 ( 30) link_BETA1-4 : bond 0.00491 ( 4) link_BETA1-4 : angle 1.92118 ( 12) hydrogen bonds : bond 0.04059 ( 388) hydrogen bonds : angle 4.07899 ( 1122) SS BOND : bond 0.00351 ( 5) SS BOND : angle 1.60739 ( 10) link_BETA1-3 : bond 0.00644 ( 1) link_BETA1-3 : angle 5.19868 ( 3) covalent geometry : bond 0.00339 ( 8115) covalent geometry : angle 0.61677 (11075) *********************** 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 72 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7820 (ttm170) REVERT: A 661 MET cc_start: 0.6602 (mmt) cc_final: 0.6144 (mtp) REVERT: A 1026 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7031 (mmmt) REVERT: A 1129 LEU cc_start: 0.8178 (pp) cc_final: 0.7965 (tp) REVERT: A 1180 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7946 (mt-10) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 1.1440 time to fit residues: 82.2871 Evaluate side-chains 68 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR 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 1226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 69 optimal weight: 0.0470 chunk 93 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.123101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101887 restraints weight = 11285.066| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.02 r_work: 0.3125 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8135 Z= 0.128 Angle : 0.629 9.474 11130 Z= 0.289 Chirality : 0.042 0.239 1339 Planarity : 0.003 0.037 1333 Dihedral : 9.819 109.535 1850 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.72 % Allowed : 13.65 % 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 (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: 0.29 (0.28), residues: 955 helix: 1.21 (0.24), residues: 535 sheet: 0.08 (0.70), residues: 64 loop : -1.36 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE A 704 TYR 0.008 0.001 TYR A 546 ARG 0.003 0.000 ARG A 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 10) link_NAG-ASN : angle 2.42565 ( 30) link_BETA1-4 : bond 0.00504 ( 4) link_BETA1-4 : angle 1.87108 ( 12) hydrogen bonds : bond 0.03823 ( 388) hydrogen bonds : angle 4.04089 ( 1122) SS BOND : bond 0.00306 ( 5) SS BOND : angle 1.43375 ( 10) link_BETA1-3 : bond 0.00662 ( 1) link_BETA1-3 : angle 5.12391 ( 3) covalent geometry : bond 0.00299 ( 8115) covalent geometry : angle 0.60727 (11075) ********************** 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 71 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.7852 (ttm170) REVERT: A 661 MET cc_start: 0.6649 (mmt) cc_final: 0.6208 (mtp) REVERT: A 959 ASP cc_start: 0.8672 (p0) cc_final: 0.8391 (p0) REVERT: A 1180 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7933 (mt-10) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 1.1436 time to fit residues: 82.5151 Evaluate side-chains 66 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR 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 1226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.123546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101576 restraints weight = 11422.895| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.11 r_work: 0.3124 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1815 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= 0.117 Angle : 0.614 10.177 11130 Z= 0.283 Chirality : 0.041 0.239 1339 Planarity : 0.003 0.037 1333 Dihedral : 9.550 109.013 1850 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.35 % Allowed : 14.02 % 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 (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: 0.32 (0.28), residues: 955 helix: 1.21 (0.24), residues: 535 sheet: 0.08 (0.70), residues: 64 loop : -1.29 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.004 0.001 HIS A 334 PHE 0.012 0.001 PHE A 704 TYR 0.008 0.001 TYR A 546 ARG 0.003 0.000 ARG A 421 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 10) link_NAG-ASN : angle 2.32013 ( 30) link_BETA1-4 : bond 0.00506 ( 4) link_BETA1-4 : angle 1.83611 ( 12) hydrogen bonds : bond 0.03649 ( 388) hydrogen bonds : angle 3.99941 ( 1122) SS BOND : bond 0.00286 ( 5) SS BOND : angle 1.40399 ( 10) link_BETA1-3 : bond 0.00603 ( 1) link_BETA1-3 : angle 4.99985 ( 3) covalent geometry : bond 0.00270 ( 8115) covalent geometry : angle 0.59323 (11075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5575.75 seconds wall clock time: 97 minutes 39.29 seconds (5859.29 seconds total)