Starting phenix.real_space_refine on Thu Mar 13 11:22:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dfw_30666/03_2025/7dfw_30666_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dfw_30666/03_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_30666/03_2025/7dfw_30666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dfw_30666/03_2025/7dfw_30666.map" model { file = "/net/cci-nas-00/data/ceres_data/7dfw_30666/03_2025/7dfw_30666_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dfw_30666/03_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-5624/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: 5.66, per 1000 atoms: 0.72 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: 2.56 Conformation dependent library (CDL) restraints added in 977.6 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: 1.01 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: 2.35 Time building geometry restraints manager: 2.87 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: 1.950 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.160 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- 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 8115 Z= 0.412 Angle : 0.978 19.523 11075 Z= 0.486 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 *********************** 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 : 0.890 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: 1.1067 time to fit residues: 91.8860 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 : 0.812 ------------------------------------------------------------------------------- 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 8115 Z= 0.211 Angle : 0.670 9.630 11075 Z= 0.317 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 *********************** 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 : 0.759 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: 1.4170 time to fit residues: 95.5919 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 : 0.929 ------------------------------------------------------------------------------- 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: 0.6980 chunk 74 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 = 0.123387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101304 restraints weight = 11350.151| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.08 r_work: 0.3123 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8115 Z= 0.188 Angle : 0.617 9.447 11075 Z= 0.291 Chirality : 0.043 0.232 1339 Planarity : 0.004 0.035 1333 Dihedral : 11.833 109.390 1853 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.23 % Allowed : 9.35 % Favored : 89.42 % 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: -0.24 (0.27), residues: 955 helix: 0.71 (0.23), residues: 528 sheet: 0.18 (0.69), residues: 62 loop : -1.49 (0.31), residues: 365 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 *********************** 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 69 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.8078 (ttm170) REVERT: A 661 MET cc_start: 0.6987 (mmt) cc_final: 0.6459 (mtt) outliers start: 10 outliers final: 2 residues processed: 65 average time/residue: 1.0245 time to fit residues: 72.2267 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 : 0.935 ------------------------------------------------------------------------------- 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: 0.6980 chunk 80 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 49 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.124209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102144 restraints weight = 11258.684| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.08 r_work: 0.3133 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8115 Z= 0.167 Angle : 0.606 9.439 11075 Z= 0.283 Chirality : 0.042 0.239 1339 Planarity : 0.003 0.033 1333 Dihedral : 11.109 108.576 1850 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: 0.10 (0.28), residues: 955 helix: 1.09 (0.24), residues: 521 sheet: 0.22 (0.71), residues: 62 loop : -1.44 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE A 791 TYR 0.008 0.001 TYR A 546 ARG 0.003 0.000 ARG A 463 *********************** 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 : 0.881 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8010 (ttm170) REVERT: A 598 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: A 661 MET cc_start: 0.6699 (mmt) cc_final: 0.6247 (mtt) REVERT: A 865 CYS cc_start: 0.8755 (m) cc_final: 0.8472 (p) REVERT: A 1180 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7990 (mt-10) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 1.3174 time to fit residues: 84.9032 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 : 0.902 ------------------------------------------------------------------------------- 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: 2.9990 chunk 46 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 61 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.124706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102732 restraints weight = 11201.740| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.07 r_work: 0.3140 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8115 Z= 0.164 Angle : 0.591 9.427 11075 Z= 0.275 Chirality : 0.042 0.238 1339 Planarity : 0.003 0.033 1333 Dihedral : 10.411 107.813 1850 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.72 % Allowed : 12.18 % 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: 0.23 (0.28), residues: 955 helix: 1.20 (0.24), residues: 525 sheet: 0.24 (0.71), residues: 62 loop : -1.42 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE A 704 TYR 0.011 0.001 TYR A 654 ARG 0.003 0.000 ARG A 801 *********************** 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 68 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.7928 (ttm170) REVERT: A 661 MET cc_start: 0.6695 (mmt) cc_final: 0.6277 (mtp) REVERT: A 862 TYR cc_start: 0.8513 (t80) cc_final: 0.8150 (t80) REVERT: A 865 CYS cc_start: 0.8728 (m) cc_final: 0.8481 (p) REVERT: A 1180 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7941 (mt-10) outliers start: 14 outliers final: 4 residues processed: 63 average time/residue: 1.0499 time to fit residues: 71.6543 Evaluate side-chains 57 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.0770 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.125467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103926 restraints weight = 11260.847| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.04 r_work: 0.3154 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8115 Z= 0.149 Angle : 0.578 9.445 11075 Z= 0.269 Chirality : 0.041 0.239 1339 Planarity : 0.003 0.032 1333 Dihedral : 10.008 106.988 1850 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.35 % Allowed : 12.55 % 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: 0.33 (0.28), residues: 955 helix: 1.25 (0.24), residues: 530 sheet: 0.31 (0.72), residues: 62 loop : -1.36 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 843 HIS 0.002 0.001 HIS A 400 PHE 0.011 0.001 PHE A 704 TYR 0.008 0.001 TYR A 546 ARG 0.003 0.000 ARG A 421 *********************** 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 70 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.7917 (ttm170) REVERT: A 661 MET cc_start: 0.6687 (mmt) cc_final: 0.6268 (mtp) REVERT: A 862 TYR cc_start: 0.8542 (t80) cc_final: 0.8169 (t80) REVERT: A 865 CYS cc_start: 0.8741 (m) cc_final: 0.8481 (p) REVERT: A 1180 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7910 (mt-10) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 1.0617 time to fit residues: 76.7604 Evaluate side-chains 62 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1226 VAL 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: 0.2980 chunk 58 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 0.0070 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 67 optimal weight: 0.0270 overall best weight: 0.1414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106893 restraints weight = 11320.247| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.11 r_work: 0.3204 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8115 Z= 0.121 Angle : 0.553 9.362 11075 Z= 0.255 Chirality : 0.040 0.241 1339 Planarity : 0.003 0.034 1333 Dihedral : 9.380 104.055 1850 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.98 % Allowed : 12.92 % 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: 0.48 (0.29), residues: 955 helix: 1.31 (0.24), residues: 539 sheet: 0.38 (0.71), residues: 62 loop : -1.26 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 843 HIS 0.003 0.000 HIS A 400 PHE 0.009 0.001 PHE A 704 TYR 0.006 0.001 TYR A 886 ARG 0.003 0.000 ARG A 421 *********************** 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 71 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8261 (ttp-110) cc_final: 0.7881 (ttm170) REVERT: A 661 MET cc_start: 0.6586 (mmt) cc_final: 0.6257 (mtp) REVERT: A 862 TYR cc_start: 0.8493 (t80) cc_final: 0.8138 (t80) REVERT: A 864 MET cc_start: 0.8964 (ptm) cc_final: 0.8746 (ptp) REVERT: A 865 CYS cc_start: 0.8682 (m) cc_final: 0.8476 (p) REVERT: A 1180 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7760 (mt-10) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 1.0909 time to fit residues: 81.5637 Evaluate side-chains 60 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.5980 chunk 26 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 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 = 0.3547 r_free = 0.3547 target = 0.124830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103283 restraints weight = 11315.224| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.05 r_work: 0.3147 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8115 Z= 0.186 Angle : 0.593 9.466 11075 Z= 0.274 Chirality : 0.042 0.240 1339 Planarity : 0.003 0.028 1333 Dihedral : 9.486 105.651 1850 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.11 % Allowed : 13.65 % 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: 0.44 (0.29), residues: 955 helix: 1.36 (0.24), residues: 530 sheet: 0.28 (0.71), residues: 62 loop : -1.33 (0.33), residues: 363 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 0.008 0.001 TYR A 420 ARG 0.005 0.000 ARG A 421 *********************** 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 68 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8278 (ttp-110) cc_final: 0.7842 (ttm170) REVERT: A 661 MET cc_start: 0.6589 (mmt) cc_final: 0.6224 (mtp) REVERT: A 862 TYR cc_start: 0.8527 (t80) cc_final: 0.8161 (t80) REVERT: A 865 CYS cc_start: 0.8629 (m) cc_final: 0.8400 (p) REVERT: A 1180 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7869 (mt-10) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 1.1365 time to fit residues: 81.7862 Evaluate side-chains 64 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.121846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100355 restraints weight = 11495.033| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.05 r_work: 0.3103 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8115 Z= 0.267 Angle : 0.640 9.572 11075 Z= 0.300 Chirality : 0.044 0.241 1339 Planarity : 0.004 0.027 1333 Dihedral : 9.916 109.216 1850 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.23 % Allowed : 13.90 % 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: 0.23 (0.28), residues: 955 helix: 1.13 (0.23), residues: 540 sheet: 0.20 (0.72), residues: 62 loop : -1.39 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 960 HIS 0.005 0.001 HIS A 334 PHE 0.014 0.002 PHE A 704 TYR 0.010 0.001 TYR A 420 ARG 0.005 0.000 ARG A 421 *********************** 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: 10 poor density : 59 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.7940 (ttm170) REVERT: A 661 MET cc_start: 0.6724 (mmt) cc_final: 0.6332 (mtp) REVERT: A 894 PHE cc_start: 0.8607 (m-80) cc_final: 0.8308 (m-80) REVERT: A 1180 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7978 (mt-10) outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 1.1453 time to fit residues: 81.1949 Evaluate side-chains 65 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.123500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101487 restraints weight = 11273.921| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.10 r_work: 0.3125 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8115 Z= 0.176 Angle : 0.593 9.466 11075 Z= 0.277 Chirality : 0.041 0.239 1339 Planarity : 0.003 0.028 1333 Dihedral : 9.614 108.804 1850 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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: 0.36 (0.28), residues: 955 helix: 1.25 (0.24), residues: 537 sheet: 0.20 (0.72), residues: 62 loop : -1.32 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 843 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE A 704 TYR 0.009 0.001 TYR A 546 ARG 0.006 0.000 ARG A 421 ********************** 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: 11 poor density : 60 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.7948 (ttm170) REVERT: A 661 MET cc_start: 0.6724 (mmt) cc_final: 0.6351 (mtp) REVERT: A 894 PHE cc_start: 0.8541 (m-80) cc_final: 0.8223 (m-80) REVERT: A 1026 LYS cc_start: 0.7473 (mmtt) cc_final: 0.6961 (mmmt) REVERT: A 1180 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7952 (mt-10) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 1.4718 time to fit residues: 110.0898 Evaluate side-chains 65 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 0.0030 chunk 49 optimal weight: 0.0070 chunk 93 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.3408 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.125884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103762 restraints weight = 11399.311| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.13 r_work: 0.3159 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8115 Z= 0.139 Angle : 0.568 9.982 11075 Z= 0.264 Chirality : 0.040 0.239 1339 Planarity : 0.003 0.027 1333 Dihedral : 9.096 107.022 1850 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.11 % Allowed : 14.51 % Favored : 84.38 % 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: 0.49 (0.29), residues: 955 helix: 1.40 (0.24), residues: 529 sheet: 0.31 (0.71), residues: 62 loop : -1.30 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 843 HIS 0.002 0.000 HIS A 400 PHE 0.011 0.001 PHE A 704 TYR 0.008 0.001 TYR A 546 ARG 0.006 0.000 ARG A 421 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5294.25 seconds wall clock time: 92 minutes 9.80 seconds (5529.80 seconds total)