Starting phenix.real_space_refine on Sun Oct 25 22:13:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhs_49422/10_2026/9nhs_49422.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhs_49422/10_2026/9nhs_49422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nhs_49422/10_2026/9nhs_49422.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhs_49422/10_2026/9nhs_49422.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nhs_49422/10_2026/9nhs_49422.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhs_49422/10_2026/9nhs_49422.map" } resolution = 4.2 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= 0.038 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 3 6.06 5 P 52 5.49 5 Mg 1 5.21 5 S 97 5.16 5 C 11226 2.51 5 N 3134 2.21 5 O 3505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.02s 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: 18018 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 6075 Classifications: {'peptide': 753} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 717} Chain breaks: 1 Chain: "B" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 541 Classifications: {'RNA': 25} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 14, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 22} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 13} Link IDs: {'rna2p': 2, 'rna3p': 24} Chain: "E" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1215 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 136} Chain: "F" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2100 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 4 Chain: "G" Number of atoms: 7518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7518 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 64, 'TRANS': 889} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7479 SG CYS E 36 41.303 29.583 97.309 1.00142.09 S ATOM 7575 SG CYS E 48 37.426 34.379 79.921 1.00160.72 S ATOM 10084 SG CYS F 302 40.983 72.907 75.707 1.00141.98 S Time building chain proxies: 4.16, per 1000 atoms: 0.23 Number of scatterers: 18018 At special positions: 0 Unit cell: (140.14, 121.03, 141.96, 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 3 29.99 S 97 16.00 P 52 15.00 Mg 1 11.99 O 3505 8.00 N 3134 7.00 C 11226 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: 1.73 Conformation dependent library (CDL) restraints added in 803.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" NE2 HIS E 32 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 22 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 36 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" NE2 HIS E 64 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 54 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 48 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" ND1 HIS F 293 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 302 " 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 23 sheets defined 42.3% alpha, 14.5% beta 22 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 333 through 342 removed outlier: 3.909A pdb=" N VAL A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 387 Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.116A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.686A pdb=" N ARG A 433 " --> pdb=" O ASP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 449 through 467 removed outlier: 3.814A pdb=" N LYS A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 477 removed outlier: 3.770A pdb=" N VAL A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.851A pdb=" N VAL A 504 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.954A pdb=" N ARG A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.660A pdb=" N GLY A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 591 Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.730A pdb=" N VAL A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 634 through 651 removed outlier: 3.828A pdb=" N ILE A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 729 removed outlier: 3.953A pdb=" N ALA A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 842 through 853 Processing helix chain 'A' and resid 867 through 883 removed outlier: 3.546A pdb=" N GLN A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 893 removed outlier: 3.744A pdb=" N ASN A 893 " --> pdb=" O TYR A 890 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 38 removed outlier: 3.971A pdb=" N LYS E 38 " --> pdb=" O GLN E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 71 through 78 removed outlier: 4.719A pdb=" N GLN E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 removed outlier: 3.758A pdb=" N LYS E 118 " --> pdb=" O ASP E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 137 through 144 removed outlier: 4.316A pdb=" N LYS E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 110 removed outlier: 3.739A pdb=" N ILE F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS F 90 " --> pdb=" O GLN F 86 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 178 Processing helix chain 'F' and resid 190 through 199 Processing helix chain 'F' and resid 221 through 233 removed outlier: 3.653A pdb=" N MET F 232 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS F 233 " --> pdb=" O ILE F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 260 Processing helix chain 'F' and resid 269 through 279 removed outlier: 4.278A pdb=" N ALA F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 296 removed outlier: 3.540A pdb=" N LEU F 296 " --> pdb=" O ARG F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 301 Processing helix chain 'F' and resid 302 through 323 removed outlier: 3.765A pdb=" N ARG F 317 " --> pdb=" O THR F 313 " (cutoff:3.500A) Proline residue: F 320 - end of helix Processing helix chain 'F' and resid 337 through 350 Processing helix chain 'G' and resid 2 through 10 Processing helix chain 'G' and resid 43 through 48 removed outlier: 3.772A pdb=" N HIS G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 547 Processing helix chain 'G' and resid 550 through 557 removed outlier: 3.778A pdb=" N LEU G 557 " --> pdb=" O ASP G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 578 Processing helix chain 'G' and resid 596 through 605 Processing helix chain 'G' and resid 608 through 622 Processing helix chain 'G' and resid 623 through 635 Processing helix chain 'G' and resid 647 through 657 Processing helix chain 'G' and resid 663 through 681 Processing helix chain 'G' and resid 690 through 696 Processing helix chain 'G' and resid 700 through 721 removed outlier: 5.654A pdb=" N ASP G 709 " --> pdb=" O ARG G 705 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET G 710 " --> pdb=" O GLU G 706 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL G 711 " --> pdb=" O LEU G 707 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG G 712 " --> pdb=" O ASP G 708 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU G 721 " --> pdb=" O ARG G 717 " (cutoff:3.500A) Processing helix chain 'G' and resid 736 through 749 removed outlier: 4.089A pdb=" N ALA G 740 " --> pdb=" O GLU G 736 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 771 removed outlier: 4.460A pdb=" N ARG G 765 " --> pdb=" O GLU G 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 775 through 777 No H-bonds generated for 'chain 'G' and resid 775 through 777' Processing helix chain 'G' and resid 790 through 793 Processing helix chain 'G' and resid 794 through 807 Processing helix chain 'G' and resid 832 through 840 removed outlier: 3.671A pdb=" N GLY G 840 " --> pdb=" O LYS G 836 " (cutoff:3.500A) Processing helix chain 'G' and resid 849 through 860 removed outlier: 3.804A pdb=" N TYR G 853 " --> pdb=" O ALA G 849 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN G 860 " --> pdb=" O ILE G 856 " (cutoff:3.500A) Processing helix chain 'G' and resid 871 through 873 No H-bonds generated for 'chain 'G' and resid 871 through 873' Processing helix chain 'G' and resid 874 through 886 Processing helix chain 'G' and resid 890 through 895 Processing helix chain 'G' and resid 926 through 941 Processing helix chain 'G' and resid 1007 through 1012 Processing helix chain 'G' and resid 1037 through 1049 Processing helix chain 'G' and resid 1077 through 1085 removed outlier: 3.934A pdb=" N LEU G1082 " --> pdb=" O VAL G1078 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS G1084 " --> pdb=" O GLU G1080 " (cutoff:3.500A) Processing helix chain 'G' and resid 1094 through 1106 Processing helix chain 'G' and resid 1107 through 1110 Processing helix chain 'G' and resid 1111 through 1126 Processing helix chain 'G' and resid 1162 through 1166 removed outlier: 3.771A pdb=" N ARG G1166 " --> pdb=" O TYR G1163 " (cutoff:3.500A) Processing helix chain 'G' and resid 1176 through 1180 removed outlier: 4.406A pdb=" N VAL G1180 " --> pdb=" O VAL G1177 " (cutoff:3.500A) Processing helix chain 'G' and resid 1221 through 1230 removed outlier: 3.643A pdb=" N PHE G1230 " --> pdb=" O ILE G1226 " (cutoff:3.500A) Processing helix chain 'G' and resid 1262 through 1266 removed outlier: 3.534A pdb=" N HIS G1265 " --> pdb=" O PHE G1262 " (cutoff:3.500A) Processing helix chain 'G' and resid 1276 through 1295 removed outlier: 3.823A pdb=" N TYR G1292 " --> pdb=" O TYR G1288 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N MET G1293 " --> pdb=" O LEU G1289 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU G1294 " --> pdb=" O THR G1290 " (cutoff:3.500A) Processing helix chain 'G' and resid 1308 through 1326 removed outlier: 3.870A pdb=" N GLN G1312 " --> pdb=" O GLU G1308 " (cutoff:3.500A) Proline residue: G1314 - end of helix removed outlier: 3.718A pdb=" N ILE G1317 " --> pdb=" O ILE G1313 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS G1319 " --> pdb=" O GLY G1315 " (cutoff:3.500A) Processing helix chain 'G' and resid 1356 through 1363 removed outlier: 3.666A pdb=" N VAL G1360 " --> pdb=" O VAL G1356 " (cutoff:3.500A) Processing helix chain 'G' and resid 1378 through 1389 removed outlier: 4.336A pdb=" N ARG G1387 " --> pdb=" O LEU G1383 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN G1389 " --> pdb=" O LEU G1385 " (cutoff:3.500A) Processing helix chain 'G' and resid 1389 through 1394 removed outlier: 3.823A pdb=" N LYS G1393 " --> pdb=" O ASN G1389 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU G1394 " --> pdb=" O ASP G1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1389 through 1394' Processing helix chain 'G' and resid 1394 through 1399 Processing helix chain 'G' and resid 1418 through 1426 Processing helix chain 'G' and resid 1430 through 1438 removed outlier: 3.537A pdb=" N PHE G1438 " --> pdb=" O LYS G1434 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 696 through 703 removed outlier: 4.009A pdb=" N SER A 681 " --> pdb=" O HIS A 703 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS A 680 " --> pdb=" O ASP A 674 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP A 674 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP A 670 " --> pdb=" O ALA A 684 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL A 666 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET A 665 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N TYR A 738 " --> pdb=" O MET A 665 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 667 " --> pdb=" O TYR A 738 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 735 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE A 776 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 737 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL A 778 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG A 739 " --> pdb=" O VAL A 778 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 773 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP A 837 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A 775 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 801 " --> pdb=" O VAL A 818 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP A 152 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 789 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 159 removed outlier: 3.501A pdb=" N LEU A 303 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 296 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.586A pdb=" N LEU A 168 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLU A 239 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN A 170 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 174 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 233 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.651A pdb=" N TYR A 271 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.651A pdb=" N TYR A 271 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 371 Processing sheet with id=AA8, first strand: chain 'A' and resid 399 through 402 Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 498 Processing sheet with id=AB1, first strand: chain 'A' and resid 569 through 570 removed outlier: 7.975A pdb=" N VAL A 569 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 535 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 534 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N VAL A 598 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE A 536 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 13 through 15 Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'E' and resid 79 through 80 Processing sheet with id=AB5, first strand: chain 'F' and resid 118 through 129 removed outlier: 5.929A pdb=" N TYR F 126 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE F 135 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS F 128 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR F 133 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER F 144 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL F 149 " --> pdb=" O SER F 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 215 through 217 removed outlier: 5.996A pdb=" N MET F 215 " --> pdb=" O TYR F 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 1158 through 1159 removed outlier: 7.128A pdb=" N LEU G1194 " --> pdb=" O LEU G1215 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU G1215 " --> pdb=" O LEU G1194 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA G1196 " --> pdb=" O SER G1213 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER G1213 " --> pdb=" O ALA G1196 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU G1198 " --> pdb=" O ARG G1211 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG G1211 " --> pdb=" O GLU G1198 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 811 through 814 removed outlier: 3.800A pdb=" N VAL G 780 " --> pdb=" O LEU G 823 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 866 through 869 removed outlier: 3.867A pdb=" N ILE G 867 " --> pdb=" O VAL G1145 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL G1145 " --> pdb=" O ILE G 867 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 908 through 912 removed outlier: 7.158A pdb=" N TRP G 920 " --> pdb=" O THR G 911 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N VAL G1065 " --> pdb=" O GLY G1016 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE G1067 " --> pdb=" O PRO G1018 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA G1020 " --> pdb=" O ILE G1067 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU G1069 " --> pdb=" O ALA G1020 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 956 through 961 removed outlier: 3.508A pdb=" N VAL G 968 " --> pdb=" O TYR G 961 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU G 984 " --> pdb=" O LEU G 975 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU G 977 " --> pdb=" O MET G 982 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N MET G 982 " --> pdb=" O LEU G 977 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 1024 through 1026 Processing sheet with id=AC4, first strand: chain 'G' and resid 1233 through 1238 removed outlier: 4.335A pdb=" N SER G1247 " --> pdb=" O ARG G1237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 1407 through 1409 removed outlier: 4.536A pdb=" N CYS G1409 " --> pdb=" O GLY G1415 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY G1415 " --> pdb=" O CYS G1409 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 2.28 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: 4345 1.33 - 1.45: 3835 1.45 - 1.58: 10070 1.58 - 1.70: 102 1.70 - 1.82: 152 Bond restraints: 18504 Sorted by residual: bond pdb=" P A2M B 25 " pdb=" O5' A2M B 25 " ideal model delta sigma weight residual 1.722 1.593 0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" N3 C C 21 " pdb=" C4 C C 21 " ideal model delta sigma weight residual 1.335 1.304 0.031 7.00e-03 2.04e+04 2.01e+01 bond pdb=" C4 C C 23 " pdb=" N4 C C 23 " ideal model delta sigma weight residual 1.335 1.296 0.039 9.00e-03 1.23e+04 1.89e+01 bond pdb=" C4 C C 17 " pdb=" N4 C C 17 " ideal model delta sigma weight residual 1.335 1.296 0.039 9.00e-03 1.23e+04 1.89e+01 bond pdb=" C4 C C 21 " pdb=" N4 C C 21 " ideal model delta sigma weight residual 1.335 1.296 0.039 9.00e-03 1.23e+04 1.84e+01 ... (remaining 18499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.55: 25282 6.55 - 13.10: 35 13.10 - 19.65: 1 19.65 - 26.20: 0 26.20 - 32.75: 2 Bond angle restraints: 25320 Sorted by residual: angle pdb=" O3' U B 24 " pdb=" P A2M B 25 " pdb=" O5' A2M B 25 " ideal model delta sigma weight residual 104.00 71.25 32.75 1.90e+00 2.77e-01 2.97e+02 angle pdb=" C3' U B 24 " pdb=" O3' U B 24 " pdb=" P A2M B 25 " ideal model delta sigma weight residual 119.70 106.56 13.14 1.20e+00 6.94e-01 1.20e+02 angle pdb=" O3' U B 24 " pdb=" P A2M B 25 " pdb=" OP2 A2M B 25 " ideal model delta sigma weight residual 108.00 139.91 -31.91 3.00e+00 1.11e-01 1.13e+02 angle pdb=" O5' G B 5 " pdb=" C5' G B 5 " pdb=" C4' G B 5 " ideal model delta sigma weight residual 109.40 116.50 -7.10 8.00e-01 1.56e+00 7.88e+01 angle pdb=" O5' U C 16 " pdb=" C5' U C 16 " pdb=" C4' U C 16 " ideal model delta sigma weight residual 109.40 102.98 6.42 8.00e-01 1.56e+00 6.43e+01 ... (remaining 25315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.63: 10496 20.63 - 41.26: 719 41.26 - 61.90: 130 61.90 - 82.53: 50 82.53 - 103.16: 4 Dihedral angle restraints: 11399 sinusoidal: 5174 harmonic: 6225 Sorted by residual: dihedral pdb=" C5' U B 1 " pdb=" C4' U B 1 " pdb=" C3' U B 1 " pdb=" O3' U B 1 " ideal model delta sinusoidal sigma weight residual 147.00 84.84 62.16 1 8.00e+00 1.56e-02 8.00e+01 dihedral pdb=" O4' U B 1 " pdb=" C4' U B 1 " pdb=" C3' U B 1 " pdb=" C2' U B 1 " ideal model delta sinusoidal sigma weight residual 24.00 -28.27 52.27 1 8.00e+00 1.56e-02 5.82e+01 dihedral pdb=" C4' U B 1 " pdb=" C3' U B 1 " pdb=" C2' U B 1 " pdb=" C1' U B 1 " ideal model delta sinusoidal sigma weight residual -35.00 10.28 -45.28 1 8.00e+00 1.56e-02 4.44e+01 ... (remaining 11396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2732 0.131 - 0.262: 135 0.262 - 0.393: 13 0.393 - 0.524: 1 0.524 - 0.654: 2 Chirality restraints: 2883 Sorted by residual: chirality pdb=" C3' A2M B 25 " pdb=" C4' A2M B 25 " pdb=" O3' A2M B 25 " pdb=" C2' A2M B 25 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" P U B 24 " pdb=" OP1 U B 24 " pdb=" OP2 U B 24 " pdb=" O5' U B 24 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 2880 not shown) Planarity restraints: 3073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 325 " 0.316 2.00e-02 2.50e+03 1.94e-01 7.56e+02 pdb=" CG TYR A 325 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 325 " -0.144 2.00e-02 2.50e+03 pdb=" CD2 TYR A 325 " -0.140 2.00e-02 2.50e+03 pdb=" CE1 TYR A 325 " -0.143 2.00e-02 2.50e+03 pdb=" CE2 TYR A 325 " -0.170 2.00e-02 2.50e+03 pdb=" CZ TYR A 325 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 325 " 0.334 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 22 " -0.327 2.00e-02 2.50e+03 1.63e-01 5.97e+02 pdb=" N1 U C 22 " 0.050 2.00e-02 2.50e+03 pdb=" C2 U C 22 " 0.133 2.00e-02 2.50e+03 pdb=" O2 U C 22 " 0.072 2.00e-02 2.50e+03 pdb=" N3 U C 22 " 0.061 2.00e-02 2.50e+03 pdb=" C4 U C 22 " -0.035 2.00e-02 2.50e+03 pdb=" O4 U C 22 " -0.243 2.00e-02 2.50e+03 pdb=" C5 U C 22 " 0.129 2.00e-02 2.50e+03 pdb=" C6 U C 22 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 5 " -0.220 2.00e-02 2.50e+03 1.03e-01 3.19e+02 pdb=" N9 G B 5 " -0.003 2.00e-02 2.50e+03 pdb=" C8 G B 5 " 0.116 2.00e-02 2.50e+03 pdb=" N7 G B 5 " 0.124 2.00e-02 2.50e+03 pdb=" C5 G B 5 " 0.050 2.00e-02 2.50e+03 pdb=" C6 G B 5 " -0.041 2.00e-02 2.50e+03 pdb=" O6 G B 5 " -0.169 2.00e-02 2.50e+03 pdb=" N1 G B 5 " -0.029 2.00e-02 2.50e+03 pdb=" C2 G B 5 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G B 5 " 0.119 2.00e-02 2.50e+03 pdb=" N3 G B 5 " 0.015 2.00e-02 2.50e+03 pdb=" C4 G B 5 " 0.043 2.00e-02 2.50e+03 ... (remaining 3070 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 89 2.44 - 3.05: 11570 3.05 - 3.67: 28844 3.67 - 4.28: 40872 4.28 - 4.90: 65195 Nonbonded interactions: 146570 Sorted by model distance: nonbonded pdb=" OP1 U C 16 " pdb="MG MG A 901 " model vdw 1.821 2.170 nonbonded pdb=" OD2 ASP A 740 " pdb="MG MG A 901 " model vdw 1.852 2.170 nonbonded pdb=" OD2 ASP A 670 " pdb="MG MG A 901 " model vdw 1.938 2.170 nonbonded pdb=" OD1 ASP A 670 " pdb="MG MG A 901 " model vdw 1.990 2.170 nonbonded pdb=" O3' U B 24 " pdb=" C5' A2M B 25 " model vdw 2.012 2.752 ... (remaining 146565 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 group one per residue 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: 2.840 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.250 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 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 : 0.011 1.030 18512 Z= 0.531 Angle : 1.170 32.753 25320 Z= 0.801 Chirality : 0.066 0.654 2883 Planarity : 0.011 0.194 3073 Dihedral : 14.722 103.161 7369 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.48 % Allowed : 1.81 % Favored : 97.71 % Cbeta Deviations : 0.05 % 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: -0.91 (0.18), residues: 2097 helix: -0.17 (0.19), residues: 750 sheet: -0.28 (0.31), residues: 274 loop : -0.94 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 433 TYR 0.334 0.006 TYR A 325 PHE 0.091 0.005 PHE A 259 TRP 0.133 0.008 TRP G 657 HIS 0.010 0.001 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.43 (18504) covalent geometry : angle 1.16966 / 0.80 (25320) hydrogen bonds : bond 0.18945 / 12.28 ( 724) hydrogen bonds : angle 7.41946 / 5.13 ( 2019) metal coordination : bond 0.44116 / 22.44 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 265 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7422 (mmt) cc_final: 0.6373 (mmp) REVERT: A 272 PHE cc_start: 0.7589 (m-10) cc_final: 0.7334 (m-10) REVERT: A 535 VAL cc_start: 0.8765 (t) cc_final: 0.8464 (t) REVERT: A 589 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7579 (mmp80) REVERT: A 713 MET cc_start: 0.7791 (mmp) cc_final: 0.7348 (mmm) REVERT: E 1 MET cc_start: 0.6698 (mpp) cc_final: 0.6177 (mpp) REVERT: E 78 LEU cc_start: 0.8719 (mt) cc_final: 0.8316 (mt) REVERT: E 86 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: F 147 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.7964 (t70) REVERT: F 166 TYR cc_start: 0.8741 (m-80) cc_final: 0.8149 (m-80) REVERT: F 284 TYR cc_start: 0.7407 (m-10) cc_final: 0.6865 (m-80) REVERT: G 554 ILE cc_start: 0.6010 (mt) cc_final: 0.5438 (mt) REVERT: G 648 LEU cc_start: 0.9017 (pt) cc_final: 0.8402 (tp) REVERT: G 695 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7834 (mpt180) REVERT: G 783 ARG cc_start: 0.3953 (ppt170) cc_final: 0.3416 (tmm160) REVERT: G 853 TYR cc_start: 0.8036 (m-10) cc_final: 0.7832 (m-10) REVERT: G 870 LEU cc_start: 0.8584 (mm) cc_final: 0.8351 (tp) REVERT: G 1173 ASP cc_start: 0.7053 (t0) cc_final: 0.6852 (t0) REVERT: G 1341 TRP cc_start: 0.6989 (m100) cc_final: 0.6625 (m100) outliers start: 9 outliers final: 1 residues processed: 272 average time/residue: 0.1467 time to fit residues: 60.1410 Evaluate side-chains 214 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 210 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 212, 77] chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.0370 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A 602 ASN A 673 HIS A 701 ASN A 716 ASN A 753 HIS A 789 GLN E 47 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN F 231 GLN F 257 ASN G 683 GLN G 817 ASN G 941 HIS G1002 HIS G1171 GLN G1265 HIS G1312 GLN ** G1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.087786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.076363 restraints weight = 106361.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.078138 restraints weight = 63610.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.079399 restraints weight = 43998.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.080278 restraints weight = 33336.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.080939 restraints weight = 26950.409| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18512 Z= 0.157 Angle : 0.661 8.585 25320 Z= 0.354 Chirality : 0.045 0.234 2883 Planarity : 0.006 0.089 3073 Dihedral : 12.035 97.032 3125 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.22 % 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: -0.76 (0.18), residues: 2097 helix: 0.08 (0.19), residues: 769 sheet: -0.50 (0.30), residues: 280 loop : -0.87 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 647 TYR 0.026 0.002 TYR A 325 PHE 0.020 0.002 PHE F 253 TRP 0.014 0.001 TRP G 657 HIS 0.012 0.001 HIS E 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (18504) covalent geometry : angle 0.66145 / 0.35 (25320) hydrogen bonds : bond 0.05060 / 3.36 ( 724) hydrogen bonds : angle 5.86366 / 4.06 ( 2019) metal coordination : bond 0.01779 / 0.97 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 260 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7241 (mmt) cc_final: 0.6554 (mmp) REVERT: A 391 ILE cc_start: 0.8298 (mm) cc_final: 0.8070 (mt) REVERT: A 608 GLU cc_start: 0.8825 (pt0) cc_final: 0.8008 (pp20) REVERT: A 693 MET cc_start: 0.8943 (mmm) cc_final: 0.8031 (tpt) REVERT: A 780 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8188 (pptt) REVERT: E 1 MET cc_start: 0.6975 (mpp) cc_final: 0.6596 (mpp) REVERT: E 78 LEU cc_start: 0.8670 (mt) cc_final: 0.8231 (mt) REVERT: F 166 TYR cc_start: 0.8741 (m-80) cc_final: 0.8229 (m-80) REVERT: F 284 TYR cc_start: 0.7321 (m-10) cc_final: 0.6632 (m-80) REVERT: G 40 MET cc_start: 0.9219 (mmt) cc_final: 0.8796 (mmm) REVERT: G 49 MET cc_start: 0.5143 (mmm) cc_final: 0.4470 (mmp) REVERT: G 554 ILE cc_start: 0.5999 (mt) cc_final: 0.5756 (mt) REVERT: G 564 MET cc_start: 0.8337 (pmm) cc_final: 0.8110 (pmm) REVERT: G 783 ARG cc_start: 0.3996 (ppt170) cc_final: 0.3350 (tmm160) REVERT: G 988 MET cc_start: 0.8803 (mmp) cc_final: 0.8554 (mmm) REVERT: G 1081 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7600 (mp) REVERT: G 1173 ASP cc_start: 0.6904 (t0) cc_final: 0.6697 (t0) REVERT: G 1283 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7838 (mp) outliers start: 4 outliers final: 0 residues processed: 263 average time/residue: 0.1334 time to fit residues: 54.3294 Evaluate side-chains 202 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [39, 104, 195, 209, 124, 205, 191, 31, 174, 176, 53] chunk 39 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 195 optimal weight: 30.0000 chunk 209 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 176 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 GLN A 573 HIS ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN A 859 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 HIS F 142 GLN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.082642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.071588 restraints weight = 111539.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073210 restraints weight = 67870.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.074370 restraints weight = 47656.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.075190 restraints weight = 36562.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.075804 restraints weight = 29850.356| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 18512 Z= 0.286 Angle : 0.770 14.452 25320 Z= 0.409 Chirality : 0.047 0.213 2883 Planarity : 0.006 0.058 3073 Dihedral : 12.163 85.601 3125 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.16 % Allowed : 4.26 % Favored : 95.59 % 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: -1.12 (0.18), residues: 2097 helix: -0.25 (0.18), residues: 771 sheet: -0.59 (0.30), residues: 277 loop : -1.09 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 819 TYR 0.030 0.002 TYR A 325 PHE 0.031 0.003 PHE G 754 TRP 0.013 0.002 TRP G 732 HIS 0.010 0.002 HIS G1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.29 (18504) covalent geometry : angle 0.76984 / 0.41 (25320) hydrogen bonds : bond 0.05632 / 3.63 ( 724) hydrogen bonds : angle 5.95632 / 4.14 ( 2019) metal coordination : bond 0.00934 / 0.49 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.8412 (p0) cc_final: 0.8200 (p0) REVERT: A 267 MET cc_start: 0.7672 (mmt) cc_final: 0.6969 (mmp) REVERT: A 372 MET cc_start: 0.7938 (mmt) cc_final: 0.7643 (mmt) REVERT: A 385 LYS cc_start: 0.9119 (mptt) cc_final: 0.8804 (mmtt) REVERT: E 78 LEU cc_start: 0.8632 (mt) cc_final: 0.8259 (mt) REVERT: E 86 ARG cc_start: 0.8214 (ttp-110) cc_final: 0.7898 (mtm-85) REVERT: F 127 CYS cc_start: 0.7767 (p) cc_final: 0.6981 (p) REVERT: F 166 TYR cc_start: 0.8949 (m-80) cc_final: 0.8461 (m-80) REVERT: F 284 TYR cc_start: 0.7621 (m-10) cc_final: 0.7041 (m-80) REVERT: G 40 MET cc_start: 0.9289 (mmt) cc_final: 0.8894 (mmm) REVERT: G 564 MET cc_start: 0.8369 (pmm) cc_final: 0.8133 (pmm) REVERT: G 853 TYR cc_start: 0.8345 (m-10) cc_final: 0.8124 (m-10) REVERT: G 988 MET cc_start: 0.8852 (mmp) cc_final: 0.8542 (mmm) REVERT: G 1081 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7739 (mp) REVERT: G 1173 ASP cc_start: 0.7443 (t0) cc_final: 0.7222 (t0) REVERT: G 1283 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8116 (mp) outliers start: 3 outliers final: 1 residues processed: 251 average time/residue: 0.1388 time to fit residues: 53.4847 Evaluate side-chains 193 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [180, 1, 177, 155, 20, 92, 123, 171, 192, 108, 83] chunk 180 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 92 optimal weight: 0.3980 chunk 123 optimal weight: 20.0000 chunk 171 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS A 859 ASN E 34 GLN E 77 GLN E 121 HIS F 142 GLN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1429 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.084060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.072918 restraints weight = 108782.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.074647 restraints weight = 65409.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.075862 restraints weight = 45295.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.076738 restraints weight = 34176.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.077273 restraints weight = 27615.246| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18512 Z= 0.156 Angle : 0.636 10.225 25320 Z= 0.336 Chirality : 0.044 0.186 2883 Planarity : 0.005 0.059 3073 Dihedral : 12.058 86.245 3125 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.11 % Allowed : 2.45 % Favored : 97.45 % 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: -0.92 (0.18), residues: 2097 helix: 0.04 (0.18), residues: 764 sheet: -0.73 (0.29), residues: 274 loop : -1.00 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 231 TYR 0.016 0.001 TYR A 325 PHE 0.023 0.002 PHE F 253 TRP 0.039 0.002 TRP G 693 HIS 0.006 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (18504) covalent geometry : angle 0.63631 / 0.34 (25320) hydrogen bonds : bond 0.04211 / 2.79 ( 724) hydrogen bonds : angle 5.58308 / 3.88 ( 2019) metal coordination : bond 0.00443 / 0.24 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7752 (mmt) cc_final: 0.6896 (mmm) REVERT: A 385 LYS cc_start: 0.9042 (mptt) cc_final: 0.8712 (mmtt) REVERT: A 610 ILE cc_start: 0.9628 (mt) cc_final: 0.9357 (mt) REVERT: A 614 CYS cc_start: 0.8083 (m) cc_final: 0.7815 (m) REVERT: A 638 ILE cc_start: 0.7744 (tt) cc_final: 0.7514 (tt) REVERT: A 827 ILE cc_start: 0.8244 (mt) cc_final: 0.7945 (mt) REVERT: E 1 MET cc_start: 0.7438 (mpp) cc_final: 0.7193 (mpp) REVERT: E 78 LEU cc_start: 0.8780 (mt) cc_final: 0.8239 (mt) REVERT: E 86 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7820 (mtm-85) REVERT: F 127 CYS cc_start: 0.7646 (p) cc_final: 0.6858 (p) REVERT: F 166 TYR cc_start: 0.8922 (m-80) cc_final: 0.8443 (m-80) REVERT: F 284 TYR cc_start: 0.7517 (m-10) cc_final: 0.6802 (m-10) REVERT: G 40 MET cc_start: 0.9251 (mmt) cc_final: 0.8953 (mmm) REVERT: G 47 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7658 (mtt90) REVERT: G 49 MET cc_start: 0.5473 (mmm) cc_final: 0.5090 (mmm) REVERT: G 564 MET cc_start: 0.8436 (pmm) cc_final: 0.8199 (pmm) REVERT: G 853 TYR cc_start: 0.8325 (m-10) cc_final: 0.8071 (m-10) REVERT: G 988 MET cc_start: 0.8866 (mmp) cc_final: 0.8549 (mmm) outliers start: 2 outliers final: 0 residues processed: 265 average time/residue: 0.1380 time to fit residues: 56.6257 Evaluate side-chains 194 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [186, 164, 105, 3, 68, 39, 122, 72, 184, 86, 168] chunk 186 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 39 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 184 optimal weight: 0.0370 chunk 86 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 HIS A 673 HIS A 859 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 HIS F 142 GLN G 681 GLN ** G1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1391 GLN ** G1425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.085060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.073835 restraints weight = 106786.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.075540 restraints weight = 64038.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.076767 restraints weight = 44561.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.077635 restraints weight = 33813.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.078262 restraints weight = 27360.372| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18512 Z= 0.132 Angle : 0.617 10.650 25320 Z= 0.323 Chirality : 0.044 0.187 2883 Planarity : 0.005 0.053 3073 Dihedral : 11.967 86.873 3125 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.05 % Allowed : 1.76 % Favored : 98.19 % 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 (0.18), residues: 2097 helix: 0.16 (0.19), residues: 765 sheet: -0.62 (0.30), residues: 281 loop : -0.94 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.013 0.001 TYR A 325 PHE 0.016 0.002 PHE G 754 TRP 0.017 0.001 TRP G 693 HIS 0.007 0.001 HIS A 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (18504) covalent geometry : angle 0.61745 / 0.32 (25320) hydrogen bonds : bond 0.03909 / 2.60 ( 724) hydrogen bonds : angle 5.35538 / 3.71 ( 2019) metal coordination : bond 0.00205 / 0.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7676 (mmt) cc_final: 0.6760 (mmm) REVERT: A 338 LEU cc_start: 0.9031 (mt) cc_final: 0.8734 (tt) REVERT: A 372 MET cc_start: 0.7748 (mmt) cc_final: 0.7530 (mmt) REVERT: A 385 LYS cc_start: 0.9005 (mptt) cc_final: 0.8680 (mmtt) REVERT: A 610 ILE cc_start: 0.9613 (mt) cc_final: 0.9324 (mt) REVERT: A 614 CYS cc_start: 0.8072 (m) cc_final: 0.7819 (m) REVERT: A 692 GLN cc_start: 0.8834 (mp10) cc_final: 0.8617 (mm-40) REVERT: A 772 LYS cc_start: 0.8292 (mmmt) cc_final: 0.8041 (mmmm) REVERT: A 827 ILE cc_start: 0.8044 (mt) cc_final: 0.7735 (mt) REVERT: E 1 MET cc_start: 0.7353 (mpp) cc_final: 0.7017 (mpp) REVERT: E 13 MET cc_start: 0.7149 (mpp) cc_final: 0.6516 (mpp) REVERT: E 78 LEU cc_start: 0.8765 (mt) cc_final: 0.8332 (mt) REVERT: E 86 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7760 (mtm-85) REVERT: F 127 CYS cc_start: 0.7559 (p) cc_final: 0.6806 (p) REVERT: F 166 TYR cc_start: 0.8832 (m-80) cc_final: 0.8309 (m-80) REVERT: F 218 LEU cc_start: 0.8097 (pt) cc_final: 0.7493 (mm) REVERT: F 284 TYR cc_start: 0.7480 (m-10) cc_final: 0.6758 (m-10) REVERT: G 40 MET cc_start: 0.9273 (mmt) cc_final: 0.8995 (mmm) REVERT: G 49 MET cc_start: 0.5449 (mmm) cc_final: 0.4981 (mmm) REVERT: G 853 TYR cc_start: 0.8305 (m-10) cc_final: 0.8023 (m-10) REVERT: G 988 MET cc_start: 0.8892 (mmp) cc_final: 0.8514 (mmm) REVERT: G 1173 ASP cc_start: 0.7291 (t0) cc_final: 0.7067 (t0) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.1375 time to fit residues: 56.1264 Evaluate side-chains 198 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [44, 99, 64, 118, 196, 164, 50, 194, 137, 108, 18] chunk 44 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 196 optimal weight: 0.0770 chunk 164 optimal weight: 0.1980 chunk 50 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 18 optimal weight: 0.0020 overall best weight: 2.6550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 HIS A 673 HIS A 859 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN F 154 HIS ** G1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.084651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.073148 restraints weight = 108989.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.074838 restraints weight = 66454.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.076069 restraints weight = 46665.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.076927 restraints weight = 35660.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.077547 restraints weight = 29135.581| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18512 Z= 0.146 Angle : 0.607 10.814 25320 Z= 0.319 Chirality : 0.043 0.174 2883 Planarity : 0.005 0.053 3073 Dihedral : 11.945 87.216 3125 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: -0.75 (0.18), residues: 2097 helix: 0.22 (0.19), residues: 769 sheet: -0.70 (0.30), residues: 284 loop : -0.92 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 37 TYR 0.015 0.001 TYR G 781 PHE 0.038 0.002 PHE F 312 TRP 0.013 0.001 TRP G 693 HIS 0.029 0.002 HIS G1431 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (18504) covalent geometry : angle 0.60704 / 0.32 (25320) hydrogen bonds : bond 0.03825 / 2.55 ( 724) hydrogen bonds : angle 5.29789 / 3.67 ( 2019) metal coordination : bond 0.00196 / 0.12 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7720 (mmt) cc_final: 0.6959 (mmm) REVERT: A 338 LEU cc_start: 0.9021 (mt) cc_final: 0.8738 (tt) REVERT: A 372 MET cc_start: 0.7885 (mmt) cc_final: 0.7588 (mmt) REVERT: A 385 LYS cc_start: 0.9049 (mptt) cc_final: 0.8709 (mmtt) REVERT: A 610 ILE cc_start: 0.9629 (mt) cc_final: 0.9351 (mt) REVERT: A 614 CYS cc_start: 0.8019 (m) cc_final: 0.7746 (m) REVERT: A 665 MET cc_start: 0.7906 (tmm) cc_final: 0.7679 (tmm) REVERT: A 772 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8053 (mmmt) REVERT: A 819 SER cc_start: 0.6462 (t) cc_final: 0.6166 (t) REVERT: A 827 ILE cc_start: 0.8092 (mt) cc_final: 0.7751 (mt) REVERT: E 13 MET cc_start: 0.7137 (mpp) cc_final: 0.6492 (mpp) REVERT: E 78 LEU cc_start: 0.8778 (mt) cc_final: 0.8323 (mt) REVERT: E 86 ARG cc_start: 0.8080 (ttp-110) cc_final: 0.7734 (mtm-85) REVERT: F 127 CYS cc_start: 0.7709 (p) cc_final: 0.7038 (p) REVERT: F 166 TYR cc_start: 0.8754 (m-80) cc_final: 0.8231 (m-80) REVERT: F 284 TYR cc_start: 0.7471 (m-10) cc_final: 0.6793 (m-10) REVERT: G 40 MET cc_start: 0.9250 (mmt) cc_final: 0.8934 (mmm) REVERT: G 49 MET cc_start: 0.5458 (mmm) cc_final: 0.4970 (mmm) REVERT: G 763 ARG cc_start: 0.8535 (ttm170) cc_final: 0.8011 (mmt-90) REVERT: G 853 TYR cc_start: 0.8476 (m-10) cc_final: 0.8150 (m-10) REVERT: G 870 LEU cc_start: 0.8623 (mm) cc_final: 0.8423 (mm) REVERT: G 988 MET cc_start: 0.8911 (mmp) cc_final: 0.8529 (mmm) REVERT: G 1173 ASP cc_start: 0.7364 (t0) cc_final: 0.7118 (t0) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.1337 time to fit residues: 54.4631 Evaluate side-chains 203 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [54, 85, 179, 7, 211, 98, 133, 202, 180, 4, 150] chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN A 573 HIS A 673 HIS ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 HIS F 142 GLN ** G1425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.081471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.070458 restraints weight = 112721.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.072043 restraints weight = 68648.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.073173 restraints weight = 48308.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.073979 restraints weight = 37101.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.074500 restraints weight = 30499.608| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18512 Z= 0.249 Angle : 0.727 10.230 25320 Z= 0.385 Chirality : 0.047 0.200 2883 Planarity : 0.006 0.074 3073 Dihedral : 12.190 89.141 3125 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: -1.13 (0.18), residues: 2097 helix: -0.06 (0.18), residues: 764 sheet: -0.97 (0.29), residues: 301 loop : -1.15 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 231 TYR 0.019 0.002 TYR A 298 PHE 0.034 0.003 PHE F 312 TRP 0.022 0.002 TRP G 657 HIS 0.009 0.002 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (18504) covalent geometry : angle 0.72705 / 0.39 (25320) hydrogen bonds : bond 0.04874 / 3.13 ( 724) hydrogen bonds : angle 5.65058 / 3.91 ( 2019) metal coordination : bond 0.00480 / 0.24 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7823 (mmt) cc_final: 0.6986 (mmm) REVERT: A 334 LYS cc_start: 0.9207 (mppt) cc_final: 0.8575 (mmtm) REVERT: A 372 MET cc_start: 0.8072 (mmt) cc_final: 0.7765 (mmt) REVERT: A 385 LYS cc_start: 0.9202 (mptt) cc_final: 0.8836 (mmtt) REVERT: A 610 ILE cc_start: 0.9684 (mt) cc_final: 0.9458 (mt) REVERT: A 665 MET cc_start: 0.7846 (tmm) cc_final: 0.7553 (tmm) REVERT: A 819 SER cc_start: 0.6626 (t) cc_final: 0.5990 (t) REVERT: A 827 ILE cc_start: 0.8336 (mt) cc_final: 0.8052 (mt) REVERT: E 73 MET cc_start: 0.8938 (mtm) cc_final: 0.8689 (mtp) REVERT: E 78 LEU cc_start: 0.8821 (mt) cc_final: 0.8354 (mt) REVERT: E 86 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7762 (mtm-85) REVERT: F 127 CYS cc_start: 0.7767 (p) cc_final: 0.7059 (p) REVERT: F 166 TYR cc_start: 0.8914 (m-80) cc_final: 0.8396 (m-80) REVERT: F 284 TYR cc_start: 0.7586 (m-10) cc_final: 0.6935 (m-80) REVERT: G 40 MET cc_start: 0.9263 (mmt) cc_final: 0.8936 (mmm) REVERT: G 49 MET cc_start: 0.5538 (mmm) cc_final: 0.5223 (mmm) REVERT: G 763 ARG cc_start: 0.8572 (ttm170) cc_final: 0.8076 (mmt-90) REVERT: G 765 ARG cc_start: 0.7779 (tmm160) cc_final: 0.7568 (ttp80) REVERT: G 870 LEU cc_start: 0.8592 (mm) cc_final: 0.8329 (mm) REVERT: G 988 MET cc_start: 0.8958 (mmp) cc_final: 0.8564 (mmm) REVERT: G 1190 TYR cc_start: 0.6099 (m-80) cc_final: 0.5864 (m-80) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1309 time to fit residues: 51.0640 Evaluate side-chains 189 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [46, 150, 132, 9, 177, 124, 158, 155, 197, 27, 43] chunk 46 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 132 optimal weight: 0.0670 chunk 9 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 HIS A 673 HIS ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 HIS F 142 GLN G 756 GLN ** G1425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.082450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.071261 restraints weight = 109879.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.072896 restraints weight = 66855.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.074070 restraints weight = 46905.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.074893 restraints weight = 35941.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.075407 restraints weight = 29441.898| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18512 Z= 0.168 Angle : 0.654 11.647 25320 Z= 0.344 Chirality : 0.045 0.164 2883 Planarity : 0.005 0.052 3073 Dihedral : 12.164 88.109 3125 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.96 (0.18), residues: 2097 helix: 0.06 (0.18), residues: 758 sheet: -0.79 (0.30), residues: 295 loop : -1.05 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 231 TYR 0.019 0.002 TYR A 271 PHE 0.019 0.002 PHE G 754 TRP 0.036 0.003 TRP A 362 HIS 0.007 0.001 HIS G1431 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (18504) covalent geometry : angle 0.65426 / 0.34 (25320) hydrogen bonds : bond 0.03979 / 2.62 ( 724) hydrogen bonds : angle 5.49464 / 3.79 ( 2019) metal coordination : bond 0.00281 / 0.15 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.7960 (tt) cc_final: 0.7726 (pt) REVERT: A 267 MET cc_start: 0.7604 (mmt) cc_final: 0.6184 (mmm) REVERT: A 315 MET cc_start: 0.7550 (ppp) cc_final: 0.7235 (tmm) REVERT: A 334 LYS cc_start: 0.9356 (mppt) cc_final: 0.9055 (mptt) REVERT: A 360 VAL cc_start: 0.8979 (m) cc_final: 0.8750 (p) REVERT: A 372 MET cc_start: 0.8184 (mmt) cc_final: 0.7887 (mmt) REVERT: A 385 LYS cc_start: 0.9155 (mptt) cc_final: 0.8798 (mmtt) REVERT: A 610 ILE cc_start: 0.9630 (mt) cc_final: 0.9409 (mt) REVERT: A 665 MET cc_start: 0.7857 (tmm) cc_final: 0.7576 (tmm) REVERT: A 772 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8118 (mmmt) REVERT: A 819 SER cc_start: 0.6428 (t) cc_final: 0.5636 (t) REVERT: A 827 ILE cc_start: 0.8225 (mt) cc_final: 0.7888 (mt) REVERT: E 73 MET cc_start: 0.8881 (mtm) cc_final: 0.8611 (mtp) REVERT: E 78 LEU cc_start: 0.8833 (mt) cc_final: 0.8412 (mt) REVERT: E 86 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7716 (mtm-85) REVERT: E 101 GLU cc_start: 0.7396 (pp20) cc_final: 0.7148 (pm20) REVERT: F 127 CYS cc_start: 0.7771 (p) cc_final: 0.7053 (p) REVERT: F 166 TYR cc_start: 0.8918 (m-80) cc_final: 0.8383 (m-80) REVERT: F 284 TYR cc_start: 0.7459 (m-10) cc_final: 0.6744 (m-80) REVERT: G 40 MET cc_start: 0.9228 (mmt) cc_final: 0.8887 (mmm) REVERT: G 49 MET cc_start: 0.5519 (mmm) cc_final: 0.5230 (mmm) REVERT: G 763 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8104 (mmt-90) REVERT: G 765 ARG cc_start: 0.7662 (tmm160) cc_final: 0.7251 (tmm160) REVERT: G 884 ILE cc_start: 0.8123 (mp) cc_final: 0.7886 (tp) REVERT: G 988 MET cc_start: 0.8910 (mmp) cc_final: 0.8507 (mmm) REVERT: G 1190 TYR cc_start: 0.6095 (m-80) cc_final: 0.5822 (m-80) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1330 time to fit residues: 51.6943 Evaluate side-chains 200 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [201, 165, 52, 23, 26, 72, 46, 11, 82, 91, 166] chunk 201 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 11 optimal weight: 0.0670 chunk 82 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 overall best weight: 2.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN A 673 HIS ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 855 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN ** G1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.083002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.071797 restraints weight = 108423.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.073428 restraints weight = 65522.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.074609 restraints weight = 45926.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.075432 restraints weight = 34995.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.076017 restraints weight = 28603.597| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18512 Z= 0.144 Angle : 0.641 11.528 25320 Z= 0.334 Chirality : 0.044 0.169 2883 Planarity : 0.005 0.051 3073 Dihedral : 12.117 88.338 3125 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -0.84 (0.18), residues: 2097 helix: 0.16 (0.19), residues: 754 sheet: -0.67 (0.30), residues: 287 loop : -1.01 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 231 TYR 0.014 0.001 TYR A 245 PHE 0.023 0.002 PHE F 312 TRP 0.027 0.002 TRP A 362 HIS 0.005 0.001 HIS G1425 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (18504) covalent geometry : angle 0.64052 / 0.33 (25320) hydrogen bonds : bond 0.03785 / 2.51 ( 724) hydrogen bonds : angle 5.32903 / 3.68 ( 2019) metal coordination : bond 0.00236 / 0.14 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7483 (mmt) cc_final: 0.6700 (mmm) REVERT: A 315 MET cc_start: 0.7530 (ppp) cc_final: 0.7177 (tmm) REVERT: A 372 MET cc_start: 0.8207 (mmt) cc_final: 0.7913 (mmt) REVERT: A 385 LYS cc_start: 0.9142 (mptt) cc_final: 0.8788 (mmtt) REVERT: A 610 ILE cc_start: 0.9613 (mt) cc_final: 0.9387 (mt) REVERT: A 665 MET cc_start: 0.7705 (tmm) cc_final: 0.7435 (tmm) REVERT: A 772 LYS cc_start: 0.8386 (mmmt) cc_final: 0.7986 (mmmm) REVERT: A 827 ILE cc_start: 0.8096 (mt) cc_final: 0.7765 (mt) REVERT: E 73 MET cc_start: 0.8868 (mtm) cc_final: 0.8564 (mtp) REVERT: E 78 LEU cc_start: 0.8808 (mt) cc_final: 0.8398 (mt) REVERT: E 86 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7657 (mtm-85) REVERT: E 101 GLU cc_start: 0.7388 (pp20) cc_final: 0.7157 (pm20) REVERT: F 127 CYS cc_start: 0.7814 (p) cc_final: 0.7108 (p) REVERT: F 166 TYR cc_start: 0.8828 (m-80) cc_final: 0.8283 (m-80) REVERT: F 203 LYS cc_start: 0.6646 (mmtt) cc_final: 0.6345 (tptt) REVERT: F 284 TYR cc_start: 0.7545 (m-10) cc_final: 0.6746 (m-80) REVERT: G 40 MET cc_start: 0.9220 (mmt) cc_final: 0.8921 (mmm) REVERT: G 49 MET cc_start: 0.5599 (mmm) cc_final: 0.4945 (mmm) REVERT: G 763 ARG cc_start: 0.8562 (ttm170) cc_final: 0.8152 (mmt-90) REVERT: G 765 ARG cc_start: 0.7651 (tmm160) cc_final: 0.7230 (tmm160) REVERT: G 884 ILE cc_start: 0.8165 (mp) cc_final: 0.7935 (tp) REVERT: G 988 MET cc_start: 0.8945 (mmp) cc_final: 0.8539 (mmm) REVERT: G 1161 LEU cc_start: 0.9352 (mp) cc_final: 0.9148 (mp) REVERT: G 1190 TYR cc_start: 0.6071 (m-80) cc_final: 0.5815 (m-80) REVERT: G 1341 TRP cc_start: 0.7194 (m100) cc_final: 0.6164 (m100) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1379 time to fit residues: 52.5670 Evaluate side-chains 202 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [190, 70, 206, 99, 122, 168, 100, 23, 49, 169, 90] chunk 190 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 206 optimal weight: 30.0000 chunk 99 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 HIS A 673 HIS ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN ** G1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.082288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.071272 restraints weight = 109369.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.072872 restraints weight = 66296.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.074040 restraints weight = 46402.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.074861 restraints weight = 35359.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.075470 restraints weight = 28777.439| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18512 Z= 0.175 Angle : 0.662 11.725 25320 Z= 0.347 Chirality : 0.045 0.166 2883 Planarity : 0.005 0.049 3073 Dihedral : 12.166 91.094 3125 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.18), residues: 2097 helix: 0.06 (0.18), residues: 766 sheet: -0.73 (0.29), residues: 295 loop : -1.06 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 231 TYR 0.014 0.002 TYR A 298 PHE 0.019 0.002 PHE A 283 TRP 0.019 0.002 TRP A 362 HIS 0.008 0.001 HIS A 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (18504) covalent geometry : angle 0.66218 / 0.35 (25320) hydrogen bonds : bond 0.03993 / 2.62 ( 724) hydrogen bonds : angle 5.39589 / 3.73 ( 2019) metal coordination : bond 0.00384 / 0.21 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: 0.7795 (mmt) cc_final: 0.6941 (mmm) REVERT: A 372 MET cc_start: 0.8233 (mmt) cc_final: 0.7922 (mmt) REVERT: A 385 LYS cc_start: 0.9208 (mptt) cc_final: 0.8836 (mmtt) REVERT: A 610 ILE cc_start: 0.9627 (mt) cc_final: 0.9412 (mt) REVERT: A 665 MET cc_start: 0.7784 (tmm) cc_final: 0.7515 (tmm) REVERT: A 827 ILE cc_start: 0.8136 (mt) cc_final: 0.7842 (mt) REVERT: E 73 MET cc_start: 0.8848 (mtm) cc_final: 0.8568 (mtp) REVERT: E 78 LEU cc_start: 0.8793 (mt) cc_final: 0.8382 (mt) REVERT: E 86 ARG cc_start: 0.8044 (ttp-110) cc_final: 0.7686 (mtm-85) REVERT: F 127 CYS cc_start: 0.7812 (p) cc_final: 0.7158 (p) REVERT: F 166 TYR cc_start: 0.8874 (m-80) cc_final: 0.8354 (m-80) REVERT: F 203 LYS cc_start: 0.6661 (mmtt) cc_final: 0.6400 (tptt) REVERT: F 284 TYR cc_start: 0.7491 (m-10) cc_final: 0.6713 (m-80) REVERT: G 40 MET cc_start: 0.9194 (mmt) cc_final: 0.8874 (mmm) REVERT: G 49 MET cc_start: 0.5756 (mmm) cc_final: 0.5113 (mmm) REVERT: G 763 ARG cc_start: 0.8585 (ttm170) cc_final: 0.8178 (mmt-90) REVERT: G 765 ARG cc_start: 0.7711 (tmm160) cc_final: 0.7222 (tmm160) REVERT: G 884 ILE cc_start: 0.8222 (mp) cc_final: 0.8011 (tp) REVERT: G 988 MET cc_start: 0.8944 (mmp) cc_final: 0.8543 (mmm) REVERT: G 1190 TYR cc_start: 0.5975 (m-80) cc_final: 0.5688 (m-80) REVERT: G 1341 TRP cc_start: 0.7207 (m100) cc_final: 0.6107 (m100) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1370 time to fit residues: 51.9201 Evaluate side-chains 192 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [122, 154, 66, 185, 42, 21, 2, 67, 167, 28, 99] chunk 122 optimal weight: 5.9990 chunk 154 optimal weight: 30.0000 chunk 66 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 673 HIS ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 ASN ** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 GLN ** G1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.082306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.071294 restraints weight = 109993.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.072926 restraints weight = 66618.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.074084 restraints weight = 46503.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.074890 restraints weight = 35399.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.075426 restraints weight = 28931.339| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18512 Z= 0.169 Angle : 0.658 11.275 25320 Z= 0.344 Chirality : 0.045 0.231 2883 Planarity : 0.005 0.050 3073 Dihedral : 12.207 90.502 3125 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2097 helix: 0.06 (0.18), residues: 768 sheet: -0.83 (0.29), residues: 303 loop : -1.09 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 231 TYR 0.015 0.002 TYR A 245 PHE 0.024 0.002 PHE F 344 TRP 0.018 0.002 TRP A 362 HIS 0.004 0.001 HIS G1425 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (18504) covalent geometry : angle 0.65820 / 0.34 (25320) hydrogen bonds : bond 0.03911 / 2.56 ( 724) hydrogen bonds : angle 5.38595 / 3.71 ( 2019) metal coordination : bond 0.00312 / 0.16 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.19 seconds wall clock time: 52 minutes 16.21 seconds (3136.21 seconds total)