Starting phenix.real_space_refine on Sat Oct 24 03:59:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hdr_52073/10_2026/9hdr_52073.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hdr_52073/10_2026/9hdr_52073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hdr_52073/10_2026/9hdr_52073.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hdr_52073/10_2026/9hdr_52073.map" model { file = "/net/cci-nas-00/data/ceres_data/9hdr_52073/10_2026/9hdr_52073.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hdr_52073/10_2026/9hdr_52073.cif" } resolution = 3.1 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 45 5.16 5 C 7563 2.51 5 N 2121 2.21 5 O 2383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 12202 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 10417 Classifications: {'peptide': 1263} Link IDs: {'PTRANS': 50, 'TRANS': 1212} Chain breaks: 1 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 9216 SG CYS A1130 51.619 77.192 102.975 1.00 77.98 S ATOM 9251 SG CYS A1134 53.561 77.153 106.211 1.00128.27 S ATOM 9357 SG CYS A1147 54.699 74.881 103.400 1.00 99.25 S Time building chain proxies: 3.11, per 1000 atoms: 0.25 Number of scatterers: 12202 At special positions: 0 Unit cell: (102.185, 146.115, 117.465, 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 45 16.00 P 88 15.00 Mg 1 11.99 O 2383 8.00 N 2121 7.00 C 7563 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: 1.06 Conformation dependent library (CDL) restraints added in 504.6 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 A1130 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1147 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1134 " Number of angles added : 3 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2438 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 59.6% alpha, 10.8% beta 36 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 212 through 215 removed outlier: 4.535A pdb=" N SER A 215 " --> pdb=" O ALA A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.817A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.760A pdb=" N ASP A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 326 removed outlier: 3.950A pdb=" N LEU A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 326 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 333 through 369 removed outlier: 3.542A pdb=" N ALA A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 removed outlier: 3.645A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.725A pdb=" N TYR A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 removed outlier: 3.545A pdb=" N MET A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.652A pdb=" N ILE A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 503 removed outlier: 3.758A pdb=" N TYR A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU A 487 " --> pdb=" O ARG A 483 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.655A pdb=" N LYS A 501 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 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 553 removed outlier: 3.734A pdb=" N GLN A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.842A pdb=" N LEU A 558 " --> pdb=" O HIS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.876A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.879A pdb=" N ILE A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 removed outlier: 3.502A pdb=" N ASN A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 634 removed outlier: 3.510A pdb=" N TYR A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.889A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.470A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.715A 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 799 removed outlier: 3.833A pdb=" N LYS A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Proline residue: A 787 - end of helix removed outlier: 3.527A pdb=" N ASN A 797 " --> pdb=" O LYS A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 828 removed outlier: 3.559A pdb=" N ASN A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 818 " --> pdb=" O LYS A 814 " (cutoff:3.500A) Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 833 through 849 removed outlier: 4.193A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 847 " --> pdb=" O THR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 removed outlier: 3.513A pdb=" N LEU A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 removed outlier: 3.526A pdb=" N GLY A 869 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 884 Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 898 through 902 removed outlier: 3.728A pdb=" N THR A 902 " --> pdb=" O TRP A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 removed outlier: 4.201A pdb=" N TYR A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 961 through 967 removed outlier: 3.836A pdb=" N LEU A 967 " --> pdb=" O TRP A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.531A pdb=" N ILE A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 Processing helix chain 'A' and resid 998 through 1005 Processing helix chain 'A' and resid 1006 through 1008 No H-bonds generated for 'chain 'A' and resid 1006 through 1008' Processing helix chain 'A' and resid 1009 through 1022 removed outlier: 3.507A pdb=" N SER A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1031 removed outlier: 3.542A pdb=" N ARG A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 4.129A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.860A pdb=" N GLN A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1076 removed outlier: 3.692A 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: 4.085A pdb=" N MET A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A1105 " --> pdb=" O ILE A1101 " (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: 3.573A pdb=" N TRP A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1178 Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 4.315A pdb=" N SER A1186 " --> pdb=" O GLU A1183 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS A1188 " --> pdb=" O LYS A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1207 removed outlier: 3.510A pdb=" N ARG A1195 " --> pdb=" O ASP A1191 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A1207 " --> pdb=" O THR A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1238 removed outlier: 3.559A pdb=" N TRP A1219 " --> pdb=" O THR A1215 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A1232 " --> pdb=" O THR A1228 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A1233 " --> pdb=" O MET A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1258 removed outlier: 5.769A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1267 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65 removed outlier: 3.897A pdb=" N LYS A 61 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR A 9 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N CYS A 40 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 11 " --> pdb=" O CYS A 40 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLN A 42 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 13 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 219 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 91 removed outlier: 6.437A pdb=" N LYS A 101 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 89 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET A 99 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG A 91 " --> pdb=" O TYR A 97 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 97 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU A 141 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A 110 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N MET A 143 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 112 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP A 145 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 114 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR A 140 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA5, first strand: chain 'A' and resid 530 through 536 removed outlier: 3.557A pdb=" N ALA A 512 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU A 516 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 536 removed outlier: 3.557A pdb=" N ALA A 512 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU A 516 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 697 through 700 Processing sheet with id=AA8, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AA9, first strand: chain 'A' and resid 765 through 768 531 hydrogen bonds defined for protein. 1509 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: 2.58 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2412 1.33 - 1.46: 3928 1.46 - 1.58: 6058 1.58 - 1.71: 169 1.71 - 1.84: 71 Bond restraints: 12638 Sorted by residual: bond pdb=" O1G D3T A1303 " pdb=" PG D3T A1303 " ideal model delta sigma weight residual 1.522 1.613 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" O3B D3T A1303 " pdb=" PG D3T A1303 " ideal model delta sigma weight residual 1.743 1.657 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" P DA F 1 " pdb=" OP1 DA F 1 " ideal model delta sigma weight residual 1.480 1.551 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" P DA E 48 " pdb=" O5' DA E 48 " ideal model delta sigma weight residual 1.593 1.624 -0.031 1.00e-02 1.00e+04 9.58e+00 bond pdb=" C1' DT E 28 " pdb=" N1 DT E 28 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.24e+00 ... (remaining 12633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 15920 1.83 - 3.67: 1311 3.67 - 5.50: 161 5.50 - 7.34: 20 7.34 - 9.17: 4 Bond angle restraints: 17416 Sorted by residual: angle pdb=" C4' DT E 40 " pdb=" O4' DT E 40 " pdb=" C1' DT E 40 " ideal model delta sigma weight residual 110.10 105.19 4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" O4' DT B 20 " pdb=" C4' DT B 20 " pdb=" C3' DT B 20 " ideal model delta sigma weight residual 106.00 103.35 2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O4' DT E 39 " pdb=" C1' DT E 39 " pdb=" N1 DT E 39 " ideal model delta sigma weight residual 108.00 111.01 -3.01 7.00e-01 2.04e+00 1.85e+01 angle pdb=" C3' DA G 3 " pdb=" O3' DA G 3 " pdb=" P DA G 4 " ideal model delta sigma weight residual 119.70 124.85 -5.15 1.20e+00 6.94e-01 1.84e+01 angle pdb=" C4' DT B 16 " pdb=" O4' DT B 16 " pdb=" C1' DT B 16 " ideal model delta sigma weight residual 110.10 105.81 4.29 1.00e+00 1.00e+00 1.84e+01 ... (remaining 17411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 7169 35.40 - 70.80: 379 70.80 - 106.20: 15 106.20 - 141.60: 0 141.60 - 177.00: 1 Dihedral angle restraints: 7564 sinusoidal: 3822 harmonic: 3742 Sorted by residual: dihedral pdb=" CA LEU A 949 " pdb=" C LEU A 949 " pdb=" N ASP A 950 " pdb=" CA ASP A 950 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" C4' DA G 3 " pdb=" C3' DA G 3 " pdb=" O3' DA G 3 " pdb=" P DA G 4 " ideal model delta sinusoidal sigma weight residual 220.00 43.00 177.00 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" O4' A D 8 " pdb=" C1' A D 8 " pdb=" N9 A D 8 " pdb=" C4 A D 8 " ideal model delta sinusoidal sigma weight residual -106.00 -154.69 48.69 1 1.70e+01 3.46e-03 1.13e+01 ... (remaining 7561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 1843 0.151 - 0.302: 92 0.302 - 0.452: 4 0.452 - 0.603: 3 0.603 - 0.754: 2 Chirality restraints: 1944 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 3.09 -0.75 2.00e-01 2.50e+01 1.42e+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 9.52e+00 chirality pdb=" P DA B 6 " pdb=" OP1 DA B 6 " pdb=" OP2 DA B 6 " pdb=" O5' DA B 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 8.01e+00 ... (remaining 1941 not shown) Planarity restraints: 1868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 823 " 0.029 2.00e-02 2.50e+03 2.85e-02 1.63e+01 pdb=" CG TYR A 823 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A 823 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 823 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 823 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 823 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 823 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 823 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT E 26 " -0.036 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" N1 DT E 26 " 0.052 2.00e-02 2.50e+03 pdb=" C2 DT E 26 " -0.013 2.00e-02 2.50e+03 pdb=" O2 DT E 26 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DT E 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT E 26 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT E 26 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DT E 26 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT E 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT E 26 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1184 " 0.016 2.00e-02 2.50e+03 2.31e-02 1.06e+01 pdb=" CG TYR A1184 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A1184 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A1184 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1184 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR A1184 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A1184 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A1184 " 0.029 2.00e-02 2.50e+03 ... (remaining 1865 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 98 2.65 - 3.22: 10844 3.22 - 3.78: 18078 3.78 - 4.34: 26548 4.34 - 4.90: 40630 Nonbonded interactions: 96198 Sorted by model distance: nonbonded pdb="MG MG A1301 " pdb=" O2A D3T A1303 " model vdw 2.093 2.170 nonbonded pdb=" O ALA A 601 " pdb="MG MG A1301 " model vdw 2.098 2.170 nonbonded pdb=" OD2 ASP A 702 " pdb="MG MG A1301 " model vdw 2.142 2.170 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A1301 " model vdw 2.191 2.170 nonbonded pdb="MG MG A1301 " pdb=" O2B D3T A1303 " model vdw 2.211 2.170 ... (remaining 96193 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 14.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 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 0.091 12642 Z= 0.492 Angle : 1.071 9.169 17419 Z= 0.686 Chirality : 0.083 0.754 1944 Planarity : 0.010 0.108 1868 Dihedral : 17.641 177.002 5126 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.21), residues: 1259 helix: -0.80 (0.17), residues: 644 sheet: 0.83 (0.47), residues: 103 loop : -0.56 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.004 ARG A1111 TYR 0.051 0.007 TYR A 823 PHE 0.030 0.004 PHE A 366 TRP 0.032 0.005 TRP A1158 HIS 0.009 0.002 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.49 (12638) covalent geometry : angle 1.07086 / 0.69 (17416) hydrogen bonds : bond 0.21098 / 15.06 ( 596) hydrogen bonds : angle 6.53462 / 4.57 ( 1657) metal coordination : bond 0.03178 / 1.60 ( 4) metal coordination : angle 2.58484 / 1.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7314 (mm-30) REVERT: A 99 MET cc_start: 0.7838 (ttp) cc_final: 0.7378 (ttp) REVERT: A 272 MET cc_start: 0.9137 (tpp) cc_final: 0.8698 (tpp) REVERT: A 310 GLU cc_start: 0.9306 (tt0) cc_final: 0.8996 (tp30) REVERT: A 318 THR cc_start: 0.7735 (m) cc_final: 0.7452 (p) REVERT: A 320 GLN cc_start: 0.7397 (tt0) cc_final: 0.7181 (tm-30) REVERT: A 358 LYS cc_start: 0.9234 (mttt) cc_final: 0.8968 (ttpp) REVERT: A 406 GLU cc_start: 0.8485 (tt0) cc_final: 0.8141 (pt0) REVERT: A 421 ASN cc_start: 0.8402 (m-40) cc_final: 0.7899 (t0) REVERT: A 424 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8340 (pm20) REVERT: A 501 LYS cc_start: 0.9304 (tttm) cc_final: 0.9062 (ttpp) REVERT: A 523 ASP cc_start: 0.7195 (m-30) cc_final: 0.6699 (t0) REVERT: A 526 LYS cc_start: 0.7769 (mttt) cc_final: 0.7562 (ttpp) REVERT: A 684 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8642 (mt-10) REVERT: A 692 LYS cc_start: 0.9105 (mttt) cc_final: 0.8749 (mmtm) REVERT: A 736 GLN cc_start: 0.8302 (mt0) cc_final: 0.7975 (mp10) REVERT: A 764 LYS cc_start: 0.9187 (mttt) cc_final: 0.8972 (mtmm) REVERT: A 1182 ASN cc_start: 0.9120 (m-40) cc_final: 0.8570 (t0) REVERT: A 1267 ARG cc_start: 0.8584 (mtt90) cc_final: 0.7988 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1554 time to fit residues: 34.2298 Evaluate side-chains 105 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN A 618 ASN A 865 ASN A 910 HIS A1055 ASN A1066 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.167077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111519 restraints weight = 18630.614| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.18 r_work: 0.3123 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12642 Z= 0.152 Angle : 0.659 6.873 17419 Z= 0.372 Chirality : 0.047 0.362 1944 Planarity : 0.004 0.047 1868 Dihedral : 20.484 176.255 2389 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.52 % Allowed : 4.23 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.23), residues: 1259 helix: 1.12 (0.20), residues: 645 sheet: 0.88 (0.48), residues: 103 loop : -0.05 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 311 TYR 0.014 0.002 TYR A 731 PHE 0.023 0.002 PHE A 994 TRP 0.014 0.001 TRP A1158 HIS 0.029 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (12638) covalent geometry : angle 0.65884 / 0.37 (17416) hydrogen bonds : bond 0.06373 / 4.59 ( 596) hydrogen bonds : angle 4.48955 / 3.10 ( 1657) metal coordination : bond 0.00961 / 0.48 ( 4) metal coordination : angle 1.57101 / 1.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.7309 (ttp) cc_final: 0.6624 (ttp) REVERT: A 272 MET cc_start: 0.8437 (tpp) cc_final: 0.8210 (tpp) REVERT: A 318 THR cc_start: 0.7700 (m) cc_final: 0.7422 (p) REVERT: A 526 LYS cc_start: 0.8195 (mttt) cc_final: 0.7932 (mmmm) REVERT: A 1238 ASP cc_start: 0.7892 (t0) cc_final: 0.7684 (t0) outliers start: 6 outliers final: 3 residues processed: 118 average time/residue: 0.1392 time to fit residues: 22.5001 Evaluate side-chains 99 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [39, 112, 40, 8, 31, 11, 110, 95, 87, 106, 127] chunk 39 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 HIS A 230 HIS A 443 GLN A 553 GLN A 865 ASN A1066 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.164636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.108587 restraints weight = 18817.726| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.62 r_work: 0.3069 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12642 Z= 0.195 Angle : 0.634 9.421 17419 Z= 0.354 Chirality : 0.046 0.372 1944 Planarity : 0.005 0.045 1868 Dihedral : 20.614 178.712 2389 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.78 % Allowed : 5.61 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1259 helix: 1.32 (0.21), residues: 643 sheet: 0.96 (0.48), residues: 103 loop : -0.18 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 311 TYR 0.017 0.002 TYR A1227 PHE 0.020 0.002 PHE A 367 TRP 0.014 0.002 TRP A1145 HIS 0.021 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (12638) covalent geometry : angle 0.63335 / 0.35 (17416) hydrogen bonds : bond 0.06010 / 4.34 ( 596) hydrogen bonds : angle 4.21404 / 2.93 ( 1657) metal coordination : bond 0.02162 / 1.08 ( 4) metal coordination : angle 2.87787 / 2.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.7341 (ttp) cc_final: 0.6551 (ttp) REVERT: A 269 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: A 272 MET cc_start: 0.8484 (tpp) cc_final: 0.8233 (tpp) REVERT: A 307 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7633 (ttp80) REVERT: A 318 THR cc_start: 0.7758 (m) cc_final: 0.7472 (p) REVERT: A 526 LYS cc_start: 0.8076 (mttt) cc_final: 0.7832 (mmmm) outliers start: 9 outliers final: 5 residues processed: 99 average time/residue: 0.1316 time to fit residues: 18.2340 Evaluate side-chains 94 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [42, 91, 56, 67, 50, 33, 14, 59, 23, 72, 65] chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 ASN A1066 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.166066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109778 restraints weight = 18646.862| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.22 r_work: 0.3112 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12642 Z= 0.136 Angle : 0.544 6.613 17419 Z= 0.307 Chirality : 0.041 0.339 1944 Planarity : 0.004 0.045 1868 Dihedral : 20.492 179.380 2389 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.60 % Allowed : 6.04 % Favored : 93.35 % 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: 1.21 (0.23), residues: 1259 helix: 1.56 (0.21), residues: 641 sheet: 0.91 (0.48), residues: 103 loop : -0.11 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.013 0.001 TYR A1227 PHE 0.013 0.001 PHE A 367 TRP 0.012 0.001 TRP A1145 HIS 0.016 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (12638) covalent geometry : angle 0.54289 / 0.31 (17416) hydrogen bonds : bond 0.04865 / 3.50 ( 596) hydrogen bonds : angle 3.95123 / 2.75 ( 1657) metal coordination : bond 0.01700 / 0.85 ( 4) metal coordination : angle 2.93219 / 2.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7474 (ttp) cc_final: 0.6651 (ttp) REVERT: A 269 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 272 MET cc_start: 0.8645 (tpp) cc_final: 0.8343 (tpp) REVERT: A 307 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7634 (ttp80) REVERT: A 318 THR cc_start: 0.7781 (m) cc_final: 0.7490 (p) REVERT: A 526 LYS cc_start: 0.8134 (mttt) cc_final: 0.7899 (mmmm) REVERT: A 1042 THR cc_start: 0.8935 (m) cc_final: 0.8656 (t) outliers start: 7 outliers final: 6 residues processed: 100 average time/residue: 0.1310 time to fit residues: 18.1757 Evaluate side-chains 97 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [51, 101, 3, 14, 78, 1, 99, 129, 121, 109, 13] chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A 865 ASN A1066 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106090 restraints weight = 18719.451| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.12 r_work: 0.3041 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12642 Z= 0.259 Angle : 0.654 7.981 17419 Z= 0.359 Chirality : 0.046 0.344 1944 Planarity : 0.005 0.047 1868 Dihedral : 20.583 179.871 2389 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.95 % Allowed : 7.34 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1259 helix: 1.23 (0.20), residues: 645 sheet: 0.77 (0.47), residues: 108 loop : -0.36 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 483 TYR 0.021 0.002 TYR A 731 PHE 0.019 0.002 PHE A 367 TRP 0.017 0.002 TRP A1145 HIS 0.017 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.26 (12638) covalent geometry : angle 0.65242 / 0.36 (17416) hydrogen bonds : bond 0.06386 / 4.58 ( 596) hydrogen bonds : angle 4.20177 / 2.93 ( 1657) metal coordination : bond 0.02835 / 1.42 ( 4) metal coordination : angle 3.74344 / 2.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7567 (ttp) cc_final: 0.6761 (ttp) REVERT: A 272 MET cc_start: 0.8633 (tpp) cc_final: 0.8321 (tpp) REVERT: A 318 THR cc_start: 0.7927 (m) cc_final: 0.7635 (p) REVERT: A 526 LYS cc_start: 0.8143 (mttt) cc_final: 0.7864 (mmmm) REVERT: A 1189 TYR cc_start: 0.8083 (m-80) cc_final: 0.7866 (m-80) outliers start: 11 outliers final: 10 residues processed: 94 average time/residue: 0.1304 time to fit residues: 17.2537 Evaluate side-chains 94 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [94, 33, 6, 49, 28, 104, 25, 59, 79, 41, 123] chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 ASN A 865 ASN A1182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.166068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.110092 restraints weight = 18510.045| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.08 r_work: 0.3119 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12642 Z= 0.118 Angle : 0.522 6.533 17419 Z= 0.295 Chirality : 0.039 0.304 1944 Planarity : 0.004 0.050 1868 Dihedral : 20.289 175.631 2389 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.86 % Allowed : 8.46 % Favored : 90.67 % 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: 1.27 (0.24), residues: 1259 helix: 1.65 (0.21), residues: 641 sheet: 0.91 (0.47), residues: 108 loop : -0.15 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 747 TYR 0.012 0.001 TYR A1227 PHE 0.011 0.001 PHE A 367 TRP 0.011 0.001 TRP A 573 HIS 0.016 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (12638) covalent geometry : angle 0.52046 / 0.29 (17416) hydrogen bonds : bond 0.04402 / 3.17 ( 596) hydrogen bonds : angle 3.82985 / 2.67 ( 1657) metal coordination : bond 0.01429 / 0.71 ( 4) metal coordination : angle 3.18835 / 2.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7497 (ttp) cc_final: 0.6634 (ttp) REVERT: A 272 MET cc_start: 0.8677 (tpp) cc_final: 0.8369 (tpp) REVERT: A 284 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: A 318 THR cc_start: 0.7799 (m) cc_final: 0.7517 (p) REVERT: A 382 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8343 (mtmt) REVERT: A 526 LYS cc_start: 0.8061 (mttt) cc_final: 0.7789 (mmmm) REVERT: A 1042 THR cc_start: 0.8981 (m) cc_final: 0.8705 (t) REVERT: A 1189 TYR cc_start: 0.7892 (m-80) cc_final: 0.7609 (m-80) outliers start: 10 outliers final: 5 residues processed: 98 average time/residue: 0.1278 time to fit residues: 17.5194 Evaluate side-chains 95 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [50, 15, 59, 101, 71, 127, 82, 45, 54, 24, 96] chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 0.0030 chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 96 optimal weight: 0.2980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A 865 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.167144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111735 restraints weight = 18663.983| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.11 r_work: 0.3140 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12642 Z= 0.111 Angle : 0.494 6.772 17419 Z= 0.281 Chirality : 0.039 0.256 1944 Planarity : 0.004 0.050 1868 Dihedral : 19.996 162.638 2389 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.69 % Allowed : 8.72 % Favored : 90.59 % 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: 1.48 (0.24), residues: 1259 helix: 1.88 (0.21), residues: 645 sheet: 0.94 (0.48), residues: 115 loop : -0.13 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 747 TYR 0.009 0.001 TYR A1227 PHE 0.009 0.001 PHE A 367 TRP 0.009 0.001 TRP A1145 HIS 0.011 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (12638) covalent geometry : angle 0.49211 / 0.28 (17416) hydrogen bonds : bond 0.03837 / 2.74 ( 596) hydrogen bonds : angle 3.65734 / 2.55 ( 1657) metal coordination : bond 0.01246 / 0.62 ( 4) metal coordination : angle 2.94028 / 2.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.509 Fit side-chains REVERT: A 99 MET cc_start: 0.7361 (ttp) cc_final: 0.6465 (ttp) REVERT: A 269 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: A 272 MET cc_start: 0.8653 (tpp) cc_final: 0.8330 (tpp) REVERT: A 284 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: A 361 GLU cc_start: 0.8256 (tp30) cc_final: 0.8024 (mm-30) REVERT: A 382 LYS cc_start: 0.8646 (mtpp) cc_final: 0.8357 (mtmt) REVERT: A 526 LYS cc_start: 0.8080 (mttt) cc_final: 0.7846 (mmmm) outliers start: 8 outliers final: 3 residues processed: 100 average time/residue: 0.1362 time to fit residues: 19.1021 Evaluate side-chains 92 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [19, 102, 86, 107, 42, 63, 26, 106, 24, 51, 50] chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 86 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A 746 ASN A 865 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.167131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111940 restraints weight = 18634.924| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.10 r_work: 0.3143 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12642 Z= 0.111 Angle : 0.496 7.487 17419 Z= 0.281 Chirality : 0.038 0.172 1944 Planarity : 0.004 0.050 1868 Dihedral : 19.908 149.722 2389 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.69 % Allowed : 9.76 % Favored : 89.55 % 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 (0.24), residues: 1259 helix: 1.89 (0.21), residues: 652 sheet: 1.03 (0.48), residues: 115 loop : -0.10 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.011 0.001 TYR A1227 PHE 0.009 0.001 PHE A 367 TRP 0.009 0.001 TRP A 573 HIS 0.010 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (12638) covalent geometry : angle 0.49478 / 0.28 (17416) hydrogen bonds : bond 0.03781 / 2.70 ( 596) hydrogen bonds : angle 3.60117 / 2.52 ( 1657) metal coordination : bond 0.01290 / 0.64 ( 4) metal coordination : angle 2.85591 / 2.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.432 Fit side-chains REVERT: A 99 MET cc_start: 0.7416 (ttp) cc_final: 0.6557 (ttp) REVERT: A 272 MET cc_start: 0.8657 (tpp) cc_final: 0.8342 (tpp) REVERT: A 284 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: A 318 THR cc_start: 0.7748 (m) cc_final: 0.7540 (p) REVERT: A 382 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8353 (mtmt) outliers start: 8 outliers final: 7 residues processed: 96 average time/residue: 0.1260 time to fit residues: 17.2516 Evaluate side-chains 92 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 986 GLN Chi-restraints excluded: chain A residue 1216 MET Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [99, 82, 62, 116, 130, 24, 17, 79, 29, 102, 128] chunk 99 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 128 optimal weight: 50.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A 865 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.164284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108827 restraints weight = 18574.832| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.12 r_work: 0.3084 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12642 Z= 0.195 Angle : 0.562 8.663 17419 Z= 0.312 Chirality : 0.042 0.153 1944 Planarity : 0.004 0.047 1868 Dihedral : 20.000 144.825 2389 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.69 % Allowed : 10.02 % Favored : 89.29 % 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: 1.37 (0.24), residues: 1259 helix: 1.71 (0.21), residues: 644 sheet: 1.20 (0.49), residues: 108 loop : -0.16 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 809 TYR 0.018 0.002 TYR A1227 PHE 0.016 0.001 PHE A 367 TRP 0.012 0.001 TRP A1145 HIS 0.009 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (12638) covalent geometry : angle 0.56010 / 0.31 (17416) hydrogen bonds : bond 0.05038 / 3.62 ( 596) hydrogen bonds : angle 3.80062 / 2.66 ( 1657) metal coordination : bond 0.02411 / 1.21 ( 4) metal coordination : angle 3.30103 / 2.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.367 Fit side-chains REVERT: A 99 MET cc_start: 0.7398 (ttp) cc_final: 0.6559 (ttp) REVERT: A 272 MET cc_start: 0.8661 (tpp) cc_final: 0.8332 (tpp) REVERT: A 318 THR cc_start: 0.7718 (m) cc_final: 0.7500 (p) REVERT: A 382 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8362 (mtmt) REVERT: A 747 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7722 (mmp80) REVERT: A 910 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.7493 (m90) REVERT: A 1189 TYR cc_start: 0.8205 (m-80) cc_final: 0.7872 (m-80) outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 0.1192 time to fit residues: 15.5947 Evaluate side-chains 87 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [41, 32, 111, 16, 54, 90, 5, 114, 45, 62, 126] chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 111 optimal weight: 0.0010 chunk 16 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 126 optimal weight: 40.0000 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A 746 ASN A 865 ASN A1182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.166014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.110972 restraints weight = 18579.546| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.16 r_work: 0.3112 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12642 Z= 0.123 Angle : 0.515 9.823 17419 Z= 0.289 Chirality : 0.039 0.151 1944 Planarity : 0.004 0.049 1868 Dihedral : 19.890 140.034 2389 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.60 % Allowed : 10.28 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.24), residues: 1259 helix: 1.82 (0.21), residues: 643 sheet: 1.22 (0.49), residues: 108 loop : -0.10 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.013 0.001 TYR A1227 PHE 0.010 0.001 PHE A 367 TRP 0.010 0.001 TRP A 573 HIS 0.008 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (12638) covalent geometry : angle 0.51375 / 0.29 (17416) hydrogen bonds : bond 0.04171 / 2.99 ( 596) hydrogen bonds : angle 3.68034 / 2.57 ( 1657) metal coordination : bond 0.01656 / 0.83 ( 4) metal coordination : angle 3.03987 / 2.17 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.432 Fit side-chains REVERT: A 99 MET cc_start: 0.7390 (ttp) cc_final: 0.6538 (ttp) REVERT: A 272 MET cc_start: 0.8663 (tpp) cc_final: 0.8343 (tpp) REVERT: A 284 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7706 (m-80) REVERT: A 318 THR cc_start: 0.7747 (m) cc_final: 0.7533 (p) REVERT: A 382 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8388 (mtmt) REVERT: A 747 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7587 (mmp80) REVERT: A 910 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7473 (m90) REVERT: A 1189 TYR cc_start: 0.8109 (m-80) cc_final: 0.7776 (m-80) outliers start: 7 outliers final: 4 residues processed: 88 average time/residue: 0.1287 time to fit residues: 16.1304 Evaluate side-chains 88 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: [36, 111, 64, 47, 73, 122, 115, 84, 1, 53, 100] chunk 36 optimal weight: 0.4980 chunk 111 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 115 optimal weight: 0.0040 chunk 84 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.167653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113077 restraints weight = 18643.527| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.42 r_work: 0.3138 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12642 Z= 0.107 Angle : 0.491 10.873 17419 Z= 0.277 Chirality : 0.038 0.154 1944 Planarity : 0.004 0.051 1868 Dihedral : 19.722 136.149 2389 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.69 % Allowed : 10.10 % Favored : 89.21 % 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: 1.61 (0.24), residues: 1259 helix: 1.94 (0.21), residues: 650 sheet: 1.17 (0.49), residues: 108 loop : -0.06 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.010 0.001 TYR A1227 PHE 0.008 0.001 PHE A 367 TRP 0.009 0.001 TRP A1158 HIS 0.005 0.001 HIS A 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (12638) covalent geometry : angle 0.49012 / 0.28 (17416) hydrogen bonds : bond 0.03612 / 2.60 ( 596) hydrogen bonds : angle 3.54520 / 2.48 ( 1657) metal coordination : bond 0.01205 / 0.60 ( 4) metal coordination : angle 2.81349 / 2.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3884.26 seconds wall clock time: 66 minutes 59.72 seconds (4019.72 seconds total)