Starting phenix.real_space_refine on Fri Oct 23 14:18:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hdo_52070/10_2026/9hdo_52070.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hdo_52070/10_2026/9hdo_52070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hdo_52070/10_2026/9hdo_52070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hdo_52070/10_2026/9hdo_52070.map" model { file = "/net/cci-nas-00/data/ceres_data/9hdo_52070/10_2026/9hdo_52070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hdo_52070/10_2026/9hdo_52070.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 88 5.49 5 Mg 1 5.21 5 S 39 5.16 5 C 6359 2.51 5 N 1772 2.21 5 O 2030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8505 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 43, 'TRANS': 981} Chain: "B" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 7} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "E" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 524 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "F" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' MG': 1, ' ZN': 1, 'D3T': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7304 SG CYS A1130 39.941 75.109 103.457 1.00 61.98 S ATOM 7339 SG CYS A1134 41.843 74.743 106.875 1.00 66.46 S ATOM 7445 SG CYS A1147 42.948 72.572 103.958 1.00 59.35 S Time building chain proxies: 2.14, per 1000 atoms: 0.21 Number of scatterers: 10290 At special positions: 0 Unit cell: (91.68, 143.25, 118.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 39 16.00 P 88 15.00 Mg 1 11.99 O 2030 8.00 N 1772 7.00 C 6359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 260.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A1142 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1147 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1130 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1134 " Number of angles added : 3 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 66.6% alpha, 7.0% beta 36 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.621A pdb=" N LYS A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 331 removed outlier: 3.722A pdb=" N ASP A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LYS A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 370 removed outlier: 3.636A pdb=" N ARG A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.524A pdb=" N TYR A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.064A pdb=" N TYR A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.506A pdb=" N ILE A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 503 removed outlier: 3.572A pdb=" N TYR A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU A 487 " --> pdb=" O ARG A 483 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 537 through 559 removed outlier: 4.186A pdb=" N HIS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 558 " --> pdb=" O HIS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.527A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 621 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.689A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.041A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 800 removed outlier: 4.064A pdb=" N LYS A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Proline residue: A 787 - end of helix Processing helix chain 'A' and resid 805 through 817 Processing helix chain 'A' and resid 817 through 828 Processing helix chain 'A' and resid 833 through 849 removed outlier: 4.047A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 866 through 870 removed outlier: 3.665A pdb=" N GLY A 869 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 885 through 893 removed outlier: 4.192A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 903 removed outlier: 3.594A pdb=" N THR A 902 " --> pdb=" O TRP A 899 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 903 " --> pdb=" O ASN A 900 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 899 through 903' Processing helix chain 'A' and resid 910 through 916 removed outlier: 4.054A pdb=" N TYR A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 961 through 967 removed outlier: 3.733A pdb=" N LEU A 967 " --> pdb=" O TRP A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 982 Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 990 through 994 removed outlier: 3.510A pdb=" N ASP A 993 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1006 removed outlier: 3.880A pdb=" N ASP A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1022 removed outlier: 3.576A pdb=" N LEU A1013 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1031 removed outlier: 3.849A pdb=" N ARG A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1043 removed outlier: 3.818A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR A1043 " --> pdb=" O ILE A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.679A pdb=" N GLN A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1076 removed outlier: 3.584A pdb=" N LYS A1071 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1098 through 1110 removed outlier: 3.569A pdb=" N MET A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1139 through 1145 Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 3.544A pdb=" N TRP A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.796A pdb=" N SER A1186 " --> pdb=" O GLU A1183 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N CYS A1188 " --> pdb=" O LYS A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1207 removed outlier: 3.985A pdb=" N THR A1207 " --> pdb=" O THR A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1237 removed outlier: 3.502A pdb=" N TRP A1219 " --> pdb=" O THR A1215 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1258 removed outlier: 4.799A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1266 Processing sheet with id=AA1, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 536 removed outlier: 5.355A pdb=" N LEU A 516 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 536 removed outlier: 5.355A pdb=" N LEU A 516 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 697 through 700 Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 768 478 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2348 1.34 - 1.46: 2762 1.46 - 1.58: 5350 1.58 - 1.70: 169 1.70 - 1.82: 63 Bond restraints: 10692 Sorted by residual: bond pdb=" O3B D3T A1303 " pdb=" PG D3T A1303 " ideal model delta sigma weight residual 1.743 1.632 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C1' D3T A1303 " pdb=" N1 D3T A1303 " ideal model delta sigma weight residual 1.485 1.546 -0.061 2.00e-02 2.50e+03 9.36e+00 bond pdb=" C LEU A 757 " pdb=" N PRO A 758 " ideal model delta sigma weight residual 1.331 1.355 -0.024 7.90e-03 1.60e+04 8.99e+00 bond pdb=" O3A D3T A1303 " pdb=" PB D3T A1303 " ideal model delta sigma weight residual 1.672 1.614 0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" C1' DT E 45 " pdb=" N1 DT E 45 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.14e+00 ... (remaining 10687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 13345 1.91 - 3.82: 1308 3.82 - 5.72: 120 5.72 - 7.63: 15 7.63 - 9.54: 3 Bond angle restraints: 14791 Sorted by residual: angle pdb=" O4' DT B 20 " pdb=" C4' DT B 20 " pdb=" C3' DT B 20 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.64e+01 angle pdb=" C3' DA G 3 " pdb=" O3' DA G 3 " pdb=" P DA G 4 " ideal model delta sigma weight residual 119.70 125.36 -5.66 1.20e+00 6.94e-01 2.22e+01 angle pdb=" CA TYR A 914 " pdb=" CB TYR A 914 " pdb=" CG TYR A 914 " ideal model delta sigma weight residual 113.90 105.49 8.41 1.80e+00 3.09e-01 2.18e+01 angle pdb=" O4' DT B 19 " pdb=" C1' DT B 19 " pdb=" N1 DT B 19 " ideal model delta sigma weight residual 108.00 111.03 -3.03 7.00e-01 2.04e+00 1.88e+01 angle pdb=" C4' DT B 16 " pdb=" O4' DT B 16 " pdb=" C1' DT B 16 " ideal model delta sigma weight residual 110.10 105.77 4.33 1.00e+00 1.00e+00 1.88e+01 ... (remaining 14786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 5922 33.24 - 66.47: 427 66.47 - 99.71: 14 99.71 - 132.95: 0 132.95 - 166.18: 1 Dihedral angle restraints: 6364 sinusoidal: 3324 harmonic: 3040 Sorted by residual: dihedral pdb=" CA SER A 905 " pdb=" C SER A 905 " pdb=" N GLU A 906 " pdb=" CA GLU A 906 " ideal model delta harmonic sigma weight residual 180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA SER A1186 " pdb=" C SER A1186 " pdb=" N CYS A1187 " pdb=" CA CYS A1187 " ideal model delta harmonic sigma weight residual 180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA TRP A1145 " pdb=" C TRP A1145 " pdb=" N ASP A1146 " pdb=" CA ASP A1146 " ideal model delta harmonic sigma weight residual -180.00 -151.23 -28.77 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 6361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1480 0.136 - 0.273: 148 0.273 - 0.409: 4 0.409 - 0.546: 1 0.546 - 0.682: 5 Chirality restraints: 1638 Sorted by residual: chirality pdb=" P DA F 1 " pdb=" OP1 DA F 1 " pdb=" OP2 DA F 1 " pdb=" O5' DA F 1 " both_signs ideal model delta sigma weight residual True 2.34 3.02 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" P DT E 25 " pdb=" OP1 DT E 25 " pdb=" OP2 DT E 25 " pdb=" O5' DT E 25 " both_signs ideal model delta sigma weight residual True 2.34 -3.01 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" P DA G 1 " pdb=" OP1 DA G 1 " pdb=" OP2 DA G 1 " pdb=" O5' DA G 1 " both_signs ideal model delta sigma weight residual True 2.34 2.95 -0.62 2.00e-01 2.50e+01 9.54e+00 ... (remaining 1635 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 824 " 0.266 9.50e-02 1.11e+02 1.20e-01 1.02e+01 pdb=" NE ARG A 824 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 824 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 824 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 824 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1227 " 0.015 2.00e-02 2.50e+03 2.20e-02 9.69e+00 pdb=" CG TYR A1227 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A1227 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A1227 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A1227 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A1227 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A1227 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR A1227 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 522 " -0.258 9.50e-02 1.11e+02 1.16e-01 9.26e+00 pdb=" NE ARG A 522 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 522 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 522 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 522 " -0.003 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 43 2.63 - 3.20: 8541 3.20 - 3.76: 15402 3.76 - 4.33: 22769 4.33 - 4.90: 34346 Nonbonded interactions: 81101 Sorted by model distance: nonbonded pdb=" O ALA A 601 " pdb="MG MG A1301 " model vdw 2.062 2.170 nonbonded pdb="MG MG A1301 " pdb=" O2A D3T A1303 " model vdw 2.119 2.170 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A1301 " model vdw 2.136 2.170 nonbonded pdb="MG MG A1301 " pdb=" O1G D3T A1303 " model vdw 2.180 2.170 nonbonded pdb="MG MG A1301 " pdb=" O2B D3T A1303 " model vdw 2.189 2.170 ... (remaining 81096 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.250 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.008 0.111 10696 Z= 0.519 Angle : 1.163 9.540 14794 Z= 0.784 Chirality : 0.093 0.682 1638 Planarity : 0.010 0.120 1540 Dihedral : 19.042 166.184 4384 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.11 % Allowed : 0.64 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1023 helix: -1.26 (0.16), residues: 594 sheet: 0.23 (0.68), residues: 46 loop : -0.44 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG A 824 TYR 0.038 0.005 TYR A 914 PHE 0.021 0.004 PHE A 273 TRP 0.026 0.004 TRP A1158 HIS 0.015 0.002 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.52 (10692) covalent geometry : angle 1.16202 / 0.78 (14791) hydrogen bonds : bond 0.24288 / 15.94 ( 542) hydrogen bonds : angle 6.87692 / 5.04 ( 1537) metal coordination : bond 0.01965 / 0.90 ( 4) metal coordination : angle 4.01813 / 1.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 298 LYS cc_start: 0.7761 (tptt) cc_final: 0.7551 (tppt) REVERT: A 310 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7375 (mm-30) REVERT: A 358 LYS cc_start: 0.7639 (mttt) cc_final: 0.7298 (ttpt) REVERT: A 363 ARG cc_start: 0.7378 (mtt180) cc_final: 0.7154 (mtp180) REVERT: A 375 ARG cc_start: 0.7350 (ttt90) cc_final: 0.6809 (tpm170) REVERT: A 379 ARG cc_start: 0.7668 (ttt-90) cc_final: 0.6926 (mmm160) REVERT: A 424 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7364 (mm-30) REVERT: A 444 GLU cc_start: 0.7531 (tt0) cc_final: 0.7183 (mp0) REVERT: A 468 LYS cc_start: 0.7746 (mttt) cc_final: 0.7475 (mmtp) REVERT: A 591 ASP cc_start: 0.7548 (t0) cc_final: 0.7229 (OUTLIER) REVERT: A 692 LYS cc_start: 0.7847 (mttt) cc_final: 0.7644 (mmmt) REVERT: A 737 LYS cc_start: 0.6598 (mttt) cc_final: 0.5962 (tmmt) REVERT: A 765 ARG cc_start: 0.8744 (ptt90) cc_final: 0.8374 (ptt-90) REVERT: A 863 GLN cc_start: 0.8136 (mt0) cc_final: 0.7354 (mm110) REVERT: A 921 GLU cc_start: 0.7240 (tt0) cc_final: 0.6959 (tm-30) REVERT: A 948 LYS cc_start: 0.7763 (mttt) cc_final: 0.7086 (mmtm) REVERT: A 972 LYS cc_start: 0.8016 (tttt) cc_final: 0.7798 (mppt) REVERT: A 1082 LYS cc_start: 0.7855 (mttt) cc_final: 0.7351 (mmpt) REVERT: A 1162 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7235 (mtt180) REVERT: A 1239 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7246 (mm-30) REVERT: A 1249 LYS cc_start: 0.7904 (mttt) cc_final: 0.7398 (tptp) REVERT: A 1267 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7729 (tpt170) outliers start: 1 outliers final: 2 residues processed: 117 average time/residue: 0.8238 time to fit residues: 101.7330 Evaluate side-chains 86 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 802 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 106, 38] chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.4648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 GLN A 389 GLN A 553 GLN A 554 HIS A 618 ASN A 851 GLN A1055 ASN A1127 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.186060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.142028 restraints weight = 11243.769| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.36 r_work: 0.3647 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10696 Z= 0.171 Angle : 0.708 6.532 14794 Z= 0.407 Chirality : 0.048 0.321 1638 Planarity : 0.005 0.047 1540 Dihedral : 21.897 163.287 2134 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.96 % Allowed : 5.84 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1023 helix: 1.42 (0.20), residues: 599 sheet: 0.24 (0.66), residues: 46 loop : -0.03 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 588 TYR 0.013 0.002 TYR A 731 PHE 0.018 0.002 PHE A1240 TRP 0.014 0.001 TRP A 799 HIS 0.003 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.17 (10692) covalent geometry : angle 0.70753 / 0.41 (14791) hydrogen bonds : bond 0.07511 / 4.90 ( 542) hydrogen bonds : angle 4.30323 / 3.14 ( 1537) metal coordination : bond 0.00729 / 0.30 ( 4) metal coordination : angle 2.28227 / 1.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 375 ARG cc_start: 0.7256 (ttt90) cc_final: 0.6884 (tpm170) REVERT: A 379 ARG cc_start: 0.7551 (ttt-90) cc_final: 0.7140 (mmm160) REVERT: A 468 LYS cc_start: 0.8066 (mttt) cc_final: 0.7787 (mmtp) REVERT: A 737 LYS cc_start: 0.6584 (mttt) cc_final: 0.6241 (tmmt) REVERT: A 863 GLN cc_start: 0.7935 (mt0) cc_final: 0.7620 (mm110) REVERT: A 948 LYS cc_start: 0.7997 (mttt) cc_final: 0.7522 (mmtm) REVERT: A 1163 ASP cc_start: 0.6805 (m-30) cc_final: 0.6573 (m-30) REVERT: A 1165 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6974 (mm-30) outliers start: 9 outliers final: 3 residues processed: 105 average time/residue: 0.7661 time to fit residues: 84.9716 Evaluate side-chains 76 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 1165 GLU Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [5, 49, 91, 73, 36, 31, 16, 71, 12, 44, 102] chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 73 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.0050 chunk 102 optimal weight: 30.0000 overall best weight: 0.4852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A 710 ASN A 851 GLN A1113 HIS A1127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.188247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.144115 restraints weight = 11395.505| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.40 r_work: 0.3692 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10696 Z= 0.145 Angle : 0.600 6.365 14794 Z= 0.349 Chirality : 0.042 0.304 1638 Planarity : 0.004 0.040 1540 Dihedral : 21.849 164.128 2132 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.49 % Allowed : 8.71 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.26), residues: 1023 helix: 1.89 (0.21), residues: 599 sheet: 0.24 (0.63), residues: 46 loop : -0.06 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 311 TYR 0.012 0.001 TYR A1189 PHE 0.013 0.002 PHE A 367 TRP 0.025 0.001 TRP A 799 HIS 0.003 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (10692) covalent geometry : angle 0.59918 / 0.35 (14791) hydrogen bonds : bond 0.06085 / 3.95 ( 542) hydrogen bonds : angle 3.89892 / 2.86 ( 1537) metal coordination : bond 0.00555 / 0.24 ( 4) metal coordination : angle 2.22110 / 1.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.433 Fit side-chains REVERT: A 311 ARG cc_start: 0.6850 (mtt-85) cc_final: 0.6630 (mtt-85) REVERT: A 375 ARG cc_start: 0.7186 (ttt90) cc_final: 0.6893 (tpm170) REVERT: A 379 ARG cc_start: 0.7455 (ttt-90) cc_final: 0.7127 (mmm160) REVERT: A 468 LYS cc_start: 0.7962 (mttt) cc_final: 0.7722 (mmtp) REVERT: A 737 LYS cc_start: 0.6450 (mttt) cc_final: 0.5923 (tmmt) REVERT: A 863 GLN cc_start: 0.8055 (mt0) cc_final: 0.7736 (mm110) REVERT: A 948 LYS cc_start: 0.7839 (mttt) cc_final: 0.7392 (mmtm) REVERT: A 1223 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8311 (mtm) outliers start: 14 outliers final: 3 residues processed: 87 average time/residue: 0.7190 time to fit residues: 66.5718 Evaluate side-chains 74 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [47, 1, 92, 58, 70, 97, 33, 83, 9, 96, 36] chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A 581 ASN A 659 GLN A 851 GLN A1032 GLN A1127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.185340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.140831 restraints weight = 11350.211| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.36 r_work: 0.3647 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10696 Z= 0.168 Angle : 0.643 7.959 14794 Z= 0.364 Chirality : 0.043 0.303 1638 Planarity : 0.005 0.042 1540 Dihedral : 21.854 160.906 2132 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.59 % Allowed : 10.31 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1023 helix: 1.69 (0.21), residues: 599 sheet: 0.20 (0.64), residues: 46 loop : -0.23 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1267 TYR 0.017 0.002 TYR A1232 PHE 0.014 0.002 PHE A 367 TRP 0.020 0.002 TRP A 799 HIS 0.005 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (10692) covalent geometry : angle 0.64189 / 0.36 (14791) hydrogen bonds : bond 0.06911 / 4.51 ( 542) hydrogen bonds : angle 4.02885 / 2.95 ( 1537) metal coordination : bond 0.00524 / 0.20 ( 4) metal coordination : angle 2.70943 / 1.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 375 ARG cc_start: 0.7212 (ttt90) cc_final: 0.6924 (tpm170) REVERT: A 379 ARG cc_start: 0.7472 (ttt-90) cc_final: 0.7202 (mmm160) REVERT: A 468 LYS cc_start: 0.8071 (mttt) cc_final: 0.7781 (mmtp) REVERT: A 734 ASN cc_start: 0.6722 (OUTLIER) cc_final: 0.6475 (p0) REVERT: A 737 LYS cc_start: 0.6499 (mttt) cc_final: 0.6003 (tmmt) REVERT: A 754 MET cc_start: 0.7510 (mtt) cc_final: 0.7292 (mtm) REVERT: A 853 ARG cc_start: 0.8367 (ptm160) cc_final: 0.8057 (ptp-170) REVERT: A 863 GLN cc_start: 0.8016 (mt0) cc_final: 0.7757 (mm110) REVERT: A 948 LYS cc_start: 0.7936 (mttt) cc_final: 0.7591 (mmtm) REVERT: A 1223 MET cc_start: 0.8709 (mtm) cc_final: 0.8448 (mtm) outliers start: 15 outliers final: 6 residues processed: 82 average time/residue: 0.7302 time to fit residues: 63.7210 Evaluate side-chains 76 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1129 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [100, 68, 74, 40, 13, 43, 36, 15, 24, 97, 55] chunk 100 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN A 421 ASN A 443 GLN A 851 GLN A1032 GLN A1127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.186214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.142501 restraints weight = 11288.810| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.31 r_work: 0.3674 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10696 Z= 0.146 Angle : 0.585 6.145 14794 Z= 0.337 Chirality : 0.041 0.292 1638 Planarity : 0.004 0.044 1540 Dihedral : 21.777 161.937 2132 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.59 % Allowed : 10.73 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.26), residues: 1023 helix: 1.81 (0.21), residues: 599 sheet: 0.33 (0.64), residues: 46 loop : -0.24 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.013 0.002 TYR A1189 PHE 0.014 0.002 PHE A 367 TRP 0.026 0.001 TRP A 799 HIS 0.003 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (10692) covalent geometry : angle 0.58413 / 0.34 (14791) hydrogen bonds : bond 0.06210 / 4.05 ( 542) hydrogen bonds : angle 3.92732 / 2.88 ( 1537) metal coordination : bond 0.00564 / 0.22 ( 4) metal coordination : angle 2.35697 / 1.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.438 Fit side-chains REVERT: A 375 ARG cc_start: 0.7188 (ttt90) cc_final: 0.6920 (tpm170) REVERT: A 468 LYS cc_start: 0.8024 (mttt) cc_final: 0.7745 (mmtp) REVERT: A 734 ASN cc_start: 0.6758 (OUTLIER) cc_final: 0.6487 (p0) REVERT: A 737 LYS cc_start: 0.6531 (mttt) cc_final: 0.5995 (tmmt) REVERT: A 754 MET cc_start: 0.7419 (mtt) cc_final: 0.7166 (mtm) REVERT: A 853 ARG cc_start: 0.8402 (ptm160) cc_final: 0.8089 (ptp-170) REVERT: A 863 GLN cc_start: 0.7938 (mt0) cc_final: 0.7723 (mm-40) REVERT: A 948 LYS cc_start: 0.7915 (mttt) cc_final: 0.7599 (mmtm) REVERT: A 1162 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.5961 (mtp180) REVERT: A 1223 MET cc_start: 0.8649 (mtm) cc_final: 0.8304 (mtm) outliers start: 15 outliers final: 4 residues processed: 79 average time/residue: 0.7335 time to fit residues: 61.7425 Evaluate side-chains 72 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [58, 66, 104, 83, 20, 61, 96, 92, 97, 0, 35] chunk 58 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN A 443 GLN A 851 GLN A1032 GLN A1127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.187010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.142075 restraints weight = 11359.001| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.40 r_work: 0.3672 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10696 Z= 0.135 Angle : 0.561 6.277 14794 Z= 0.323 Chirality : 0.039 0.254 1638 Planarity : 0.004 0.045 1540 Dihedral : 21.668 165.945 2132 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.91 % Allowed : 11.16 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.26), residues: 1023 helix: 1.93 (0.21), residues: 598 sheet: 0.40 (0.64), residues: 46 loop : -0.28 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 379 TYR 0.012 0.001 TYR A 731 PHE 0.014 0.001 PHE A 367 TRP 0.034 0.001 TRP A 799 HIS 0.003 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (10692) covalent geometry : angle 0.56048 / 0.32 (14791) hydrogen bonds : bond 0.05717 / 3.73 ( 542) hydrogen bonds : angle 3.83850 / 2.81 ( 1537) metal coordination : bond 0.00486 / 0.20 ( 4) metal coordination : angle 2.35567 / 1.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.337 Fit side-chains REVERT: A 284 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: A 310 GLU cc_start: 0.7021 (tt0) cc_final: 0.6775 (tm-30) REVERT: A 375 ARG cc_start: 0.7092 (ttt90) cc_final: 0.6778 (tpm170) REVERT: A 379 ARG cc_start: 0.7217 (mmm-85) cc_final: 0.6697 (mmm160) REVERT: A 468 LYS cc_start: 0.8011 (mttt) cc_final: 0.7696 (mmtp) REVERT: A 734 ASN cc_start: 0.6693 (OUTLIER) cc_final: 0.6423 (p0) REVERT: A 737 LYS cc_start: 0.6634 (mttt) cc_final: 0.6061 (tmmt) REVERT: A 863 GLN cc_start: 0.7994 (mt0) cc_final: 0.7710 (mm-40) REVERT: A 948 LYS cc_start: 0.7917 (mttt) cc_final: 0.7535 (mmtm) REVERT: A 1162 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.5953 (mtp180) REVERT: A 1223 MET cc_start: 0.8647 (mtm) cc_final: 0.8378 (mtm) outliers start: 18 outliers final: 5 residues processed: 83 average time/residue: 0.7675 time to fit residues: 67.5411 Evaluate side-chains 75 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [88, 77, 89, 45, 78, 86, 81, 76, 97, 2, 102] chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN A 443 GLN A 851 GLN A1032 GLN A1127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.186978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.142513 restraints weight = 11221.601| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.37 r_work: 0.3656 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10696 Z= 0.136 Angle : 0.557 6.207 14794 Z= 0.320 Chirality : 0.039 0.268 1638 Planarity : 0.004 0.045 1540 Dihedral : 21.596 165.237 2132 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.81 % Allowed : 11.58 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.26), residues: 1023 helix: 1.91 (0.21), residues: 604 sheet: 0.39 (0.63), residues: 46 loop : -0.33 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 379 TYR 0.012 0.001 TYR A 731 PHE 0.015 0.001 PHE A 367 TRP 0.039 0.001 TRP A 799 HIS 0.003 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (10692) covalent geometry : angle 0.55644 / 0.32 (14791) hydrogen bonds : bond 0.05752 / 3.75 ( 542) hydrogen bonds : angle 3.84850 / 2.82 ( 1537) metal coordination : bond 0.00633 / 0.24 ( 4) metal coordination : angle 2.31923 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.367 Fit side-chains REVERT: A 284 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: A 310 GLU cc_start: 0.6993 (tt0) cc_final: 0.6770 (tm-30) REVERT: A 375 ARG cc_start: 0.7161 (ttt90) cc_final: 0.6872 (tpm170) REVERT: A 468 LYS cc_start: 0.7982 (mttt) cc_final: 0.7653 (mmtm) REVERT: A 734 ASN cc_start: 0.6722 (OUTLIER) cc_final: 0.6431 (p0) REVERT: A 737 LYS cc_start: 0.6706 (mttt) cc_final: 0.6123 (tmmt) REVERT: A 853 ARG cc_start: 0.8481 (ptp-170) cc_final: 0.7433 (ppt90) REVERT: A 863 GLN cc_start: 0.8025 (mt0) cc_final: 0.7735 (mm-40) REVERT: A 948 LYS cc_start: 0.7934 (mttt) cc_final: 0.7567 (mmtm) REVERT: A 1162 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6097 (mtp180) REVERT: A 1223 MET cc_start: 0.8664 (mtm) cc_final: 0.8407 (mtm) outliers start: 17 outliers final: 8 residues processed: 84 average time/residue: 0.7315 time to fit residues: 65.4492 Evaluate side-chains 80 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [15, 106, 54, 16, 91, 42, 0, 87, 45, 58, 12] chunk 15 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN A 443 GLN A 581 ASN A1032 GLN A1127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.186437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141441 restraints weight = 11144.497| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.39 r_work: 0.3639 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10696 Z= 0.148 Angle : 0.578 6.204 14794 Z= 0.330 Chirality : 0.040 0.264 1638 Planarity : 0.004 0.046 1540 Dihedral : 21.574 165.566 2132 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.38 % Allowed : 12.11 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1023 helix: 1.86 (0.21), residues: 604 sheet: 0.39 (0.64), residues: 46 loop : -0.33 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 379 TYR 0.013 0.002 TYR A 731 PHE 0.015 0.001 PHE A 367 TRP 0.036 0.002 TRP A 799 HIS 0.003 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (10692) covalent geometry : angle 0.57690 / 0.33 (14791) hydrogen bonds : bond 0.06074 / 3.98 ( 542) hydrogen bonds : angle 3.90083 / 2.86 ( 1537) metal coordination : bond 0.00587 / 0.22 ( 4) metal coordination : angle 2.24137 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.358 Fit side-chains REVERT: A 310 GLU cc_start: 0.6977 (tt0) cc_final: 0.6715 (tm-30) REVERT: A 375 ARG cc_start: 0.7219 (ttt90) cc_final: 0.6911 (tpm170) REVERT: A 468 LYS cc_start: 0.7986 (mttt) cc_final: 0.7649 (mmtm) REVERT: A 734 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6436 (p0) REVERT: A 737 LYS cc_start: 0.6758 (mttt) cc_final: 0.6132 (tmmt) REVERT: A 853 ARG cc_start: 0.8526 (ptp-170) cc_final: 0.7447 (ppt90) REVERT: A 863 GLN cc_start: 0.8100 (mt0) cc_final: 0.7747 (mm-40) REVERT: A 948 LYS cc_start: 0.7981 (mttt) cc_final: 0.7603 (mmtm) REVERT: A 1162 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6113 (mtp180) REVERT: A 1223 MET cc_start: 0.8690 (mtm) cc_final: 0.8428 (mtm) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.7237 time to fit residues: 62.4600 Evaluate side-chains 80 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [105, 57, 85, 25, 88, 41, 37, 77, 34, 81, 18] chunk 105 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN A 443 GLN A1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.185322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140249 restraints weight = 11177.980| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 1.42 r_work: 0.3625 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10696 Z= 0.161 Angle : 0.603 6.594 14794 Z= 0.343 Chirality : 0.041 0.253 1638 Planarity : 0.005 0.047 1540 Dihedral : 21.517 165.266 2132 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.49 % Allowed : 12.01 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.26), residues: 1023 helix: 1.70 (0.21), residues: 605 sheet: 0.38 (0.64), residues: 46 loop : -0.36 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 379 TYR 0.014 0.002 TYR A 731 PHE 0.016 0.002 PHE A 367 TRP 0.042 0.002 TRP A 799 HIS 0.004 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (10692) covalent geometry : angle 0.60245 / 0.34 (14791) hydrogen bonds : bond 0.06563 / 4.27 ( 542) hydrogen bonds : angle 3.99892 / 2.92 ( 1537) metal coordination : bond 0.00539 / 0.21 ( 4) metal coordination : angle 2.28918 / 1.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.413 Fit side-chains REVERT: A 310 GLU cc_start: 0.7032 (tt0) cc_final: 0.6828 (tm-30) REVERT: A 375 ARG cc_start: 0.7233 (ttt90) cc_final: 0.6887 (tpm170) REVERT: A 468 LYS cc_start: 0.8022 (mttt) cc_final: 0.7677 (mmtm) REVERT: A 734 ASN cc_start: 0.6743 (OUTLIER) cc_final: 0.6399 (p0) REVERT: A 737 LYS cc_start: 0.6840 (mttt) cc_final: 0.6157 (tmmt) REVERT: A 853 ARG cc_start: 0.8543 (ptp-170) cc_final: 0.7436 (ppt-90) REVERT: A 863 GLN cc_start: 0.8097 (mt0) cc_final: 0.7772 (mm-40) REVERT: A 948 LYS cc_start: 0.7986 (mttt) cc_final: 0.7636 (mmtm) REVERT: A 1162 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6124 (mtp180) REVERT: A 1223 MET cc_start: 0.8723 (mtm) cc_final: 0.8466 (mtm) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 0.7033 time to fit residues: 61.4949 Evaluate side-chains 80 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [62, 11, 54, 64, 3, 36, 89, 42, 70, 104, 59] chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN A 443 GLN A1127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.186059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141211 restraints weight = 11023.569| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.41 r_work: 0.3644 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10696 Z= 0.149 Angle : 0.580 6.463 14794 Z= 0.332 Chirality : 0.040 0.247 1638 Planarity : 0.004 0.047 1540 Dihedral : 21.444 166.636 2132 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.17 % Allowed : 12.54 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.26), residues: 1023 helix: 1.77 (0.21), residues: 605 sheet: 0.47 (0.63), residues: 46 loop : -0.32 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 379 TYR 0.013 0.002 TYR A 731 PHE 0.015 0.001 PHE A 367 TRP 0.037 0.002 TRP A 799 HIS 0.003 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (10692) covalent geometry : angle 0.57893 / 0.33 (14791) hydrogen bonds : bond 0.06142 / 4.00 ( 542) hydrogen bonds : angle 3.93993 / 2.89 ( 1537) metal coordination : bond 0.00547 / 0.21 ( 4) metal coordination : angle 2.09915 / 0.98 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.412 Fit side-chains REVERT: A 375 ARG cc_start: 0.7145 (ttt90) cc_final: 0.6843 (tpm170) REVERT: A 468 LYS cc_start: 0.7994 (mttt) cc_final: 0.7677 (mmtm) REVERT: A 734 ASN cc_start: 0.6742 (OUTLIER) cc_final: 0.6418 (p0) REVERT: A 737 LYS cc_start: 0.6833 (mttt) cc_final: 0.6186 (tmmt) REVERT: A 853 ARG cc_start: 0.8526 (ptp-170) cc_final: 0.7405 (ppt-90) REVERT: A 863 GLN cc_start: 0.8027 (mt0) cc_final: 0.7683 (mm-40) REVERT: A 948 LYS cc_start: 0.7974 (mttt) cc_final: 0.7632 (mmtm) REVERT: A 1162 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6154 (mtp180) REVERT: A 1223 MET cc_start: 0.8690 (mtm) cc_final: 0.8378 (mtm) outliers start: 11 outliers final: 7 residues processed: 79 average time/residue: 0.7581 time to fit residues: 63.7725 Evaluate side-chains 80 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [31, 23, 105, 27, 88, 51, 94, 71, 13, 47, 4] chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A1127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.185738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.140932 restraints weight = 11144.764| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.37 r_work: 0.3650 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10696 Z= 0.151 Angle : 0.585 6.386 14794 Z= 0.335 Chirality : 0.040 0.252 1638 Planarity : 0.005 0.048 1540 Dihedral : 21.380 166.530 2132 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.17 % Allowed : 12.43 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.26), residues: 1023 helix: 1.74 (0.21), residues: 605 sheet: 0.51 (0.64), residues: 46 loop : -0.33 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 379 TYR 0.013 0.002 TYR A 731 PHE 0.016 0.002 PHE A 367 TRP 0.041 0.002 TRP A 799 HIS 0.004 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (10692) covalent geometry : angle 0.58457 / 0.33 (14791) hydrogen bonds : bond 0.06268 / 4.08 ( 542) hydrogen bonds : angle 3.96476 / 2.90 ( 1537) metal coordination : bond 0.00543 / 0.21 ( 4) metal coordination : angle 2.05911 / 0.97 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5193.91 seconds wall clock time: 88 minutes 51.69 seconds (5331.69 seconds total)