Starting phenix.real_space_refine on Thu Jan 15 14:15:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pat_71445/01_2026/9pat_71445.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pat_71445/01_2026/9pat_71445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pat_71445/01_2026/9pat_71445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pat_71445/01_2026/9pat_71445.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pat_71445/01_2026/9pat_71445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pat_71445/01_2026/9pat_71445.map" } resolution = 3.96 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 71 5.16 5 C 16065 2.51 5 N 4549 2.21 5 O 4967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25653 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 10796 Classifications: {'peptide': 1472} Link IDs: {'PTRANS': 85, 'TRANS': 1386} Chain breaks: 1 Chain: "B" Number of atoms: 8009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1090, 8009 Classifications: {'peptide': 1090} Link IDs: {'PTRANS': 59, 'TRANS': 1030} Chain breaks: 1 Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 578 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4HH:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "H" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 193} Chain breaks: 2 Chain: "I" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 2 Chain: "L" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1596 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 2 Time building chain proxies: 5.17, per 1000 atoms: 0.20 Number of scatterers: 25653 At special positions: 0 Unit cell: (113.3, 161.7, 203.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 1 15.00 O 4967 8.00 N 4549 7.00 C 16065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS I 39 " - pdb=" SG CYS I 109 " distance=2.03 Simple disulfide: pdb=" SG CYS I 156 " - pdb=" SG CYS I 216 " distance=2.03 Simple disulfide: pdb=" SG CYS L 39 " - pdb=" SG CYS L 109 " distance=2.03 Simple disulfide: pdb=" SG CYS L 156 " - pdb=" SG CYS L 216 " distance=2.04 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: 2.18 Conformation dependent library (CDL) restraints added in 1.0 seconds 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6252 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 45 sheets defined 34.9% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 4 through 33 removed outlier: 3.705A pdb=" N LYS A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.717A pdb=" N ARG A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 180 through 191 removed outlier: 3.806A pdb=" N GLY A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.540A pdb=" N VAL A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 310 through 326 removed outlier: 3.636A pdb=" N GLN A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.013A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 497 through 508 Processing helix chain 'A' and resid 522 through 533 Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.693A pdb=" N ALA A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 581 Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 600 through 622 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 633 through 644 removed outlier: 4.132A pdb=" N ILE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 638 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 666 Processing helix chain 'A' and resid 678 through 685 removed outlier: 3.812A pdb=" N ARG A 685 " --> pdb=" O ASP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 721 Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 777 through 787 Processing helix chain 'A' and resid 791 through 801 Processing helix chain 'A' and resid 815 through 823 removed outlier: 3.571A pdb=" N LEU A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 850 removed outlier: 3.692A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 850 " --> pdb=" O GLU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.523A pdb=" N ALA A 858 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'A' and resid 925 through 941 removed outlier: 3.965A pdb=" N LEU A 929 " --> pdb=" O PRO A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1024 through 1028 Processing helix chain 'A' and resid 1031 through 1043 removed outlier: 3.753A pdb=" N THR A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A1042 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.532A pdb=" N LEU A1135 " --> pdb=" O ALA A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1176 Processing helix chain 'A' and resid 1187 through 1189 No H-bonds generated for 'chain 'A' and resid 1187 through 1189' Processing helix chain 'A' and resid 1190 through 1197 Processing helix chain 'A' and resid 1239 through 1252 Processing helix chain 'A' and resid 1267 through 1277 removed outlier: 3.661A pdb=" N LEU A1277 " --> pdb=" O GLU A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1301 removed outlier: 3.524A pdb=" N GLU A1295 " --> pdb=" O ARG A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1335 Processing helix chain 'A' and resid 1337 through 1349 Processing helix chain 'A' and resid 1362 through 1367 Processing helix chain 'A' and resid 1371 through 1391 Processing helix chain 'A' and resid 1414 through 1424 removed outlier: 3.877A pdb=" N ILE A1424 " --> pdb=" O ARG A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1445 Processing helix chain 'A' and resid 1454 through 1465 Processing helix chain 'A' and resid 1469 through 1474 removed outlier: 3.754A pdb=" N GLY A1474 " --> pdb=" O PRO A1470 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 33 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 105 through 110 removed outlier: 4.127A pdb=" N PHE B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.557A pdb=" N ARG B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.668A pdb=" N LYS B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 180 through 191 removed outlier: 3.546A pdb=" N GLY B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 204 through 220 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.555A pdb=" N VAL B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.738A pdb=" N GLN B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.757A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 377 through 394 removed outlier: 3.781A pdb=" N GLY B 382 " --> pdb=" O GLN B 378 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 493 Processing helix chain 'B' and resid 497 through 508 Processing helix chain 'B' and resid 522 through 533 Processing helix chain 'B' and resid 558 through 566 removed outlier: 4.704A pdb=" N LEU B 562 " --> pdb=" O MET B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 581 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 600 through 622 Proline residue: B 606 - end of helix Processing helix chain 'B' and resid 633 through 644 removed outlier: 4.190A pdb=" N ILE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 638 " --> pdb=" O GLN B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 666 Processing helix chain 'B' and resid 678 through 685 removed outlier: 3.937A pdb=" N ARG B 685 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 721 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 741 through 749 Processing helix chain 'B' and resid 777 through 787 Processing helix chain 'B' and resid 790 through 801 Processing helix chain 'B' and resid 815 through 824 Processing helix chain 'B' and resid 836 through 850 removed outlier: 3.629A pdb=" N LEU B 840 " --> pdb=" O GLY B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 921 No H-bonds generated for 'chain 'B' and resid 919 through 921' Processing helix chain 'B' and resid 925 through 940 removed outlier: 3.722A pdb=" N LEU B 929 " --> pdb=" O PRO B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 976 removed outlier: 3.665A pdb=" N ARG B 975 " --> pdb=" O GLY B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1028 Processing helix chain 'B' and resid 1031 through 1041 Processing helix chain 'C' and resid 1503 through 1518 Processing helix chain 'C' and resid 1537 through 1553 Processing helix chain 'C' and resid 1559 through 1564 removed outlier: 3.813A pdb=" N ASP C1563 " --> pdb=" O ALA C1559 " (cutoff:3.500A) Processing helix chain 'C' and resid 1566 through 1576 Processing helix chain 'G' and resid 66 through 69 Processing helix chain 'G' and resid 91 through 95 Processing helix chain 'H' and resid 30 through 34 removed outlier: 3.531A pdb=" N ASP H 33 " --> pdb=" O THR H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 91 through 95 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'I' and resid 100 through 104 removed outlier: 3.552A pdb=" N VAL I 104 " --> pdb=" O ALA I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 150 Processing helix chain 'I' and resid 205 through 211 removed outlier: 3.591A pdb=" N HIS I 211 " --> pdb=" O ASP I 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 149 removed outlier: 3.635A pdb=" N SER L 149 " --> pdb=" O GLU L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 211 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.581A pdb=" N VAL A 151 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N VAL A 199 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER A 153 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 226 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 228 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 230 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 270 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N CYS A 42 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 272 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET A 40 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 274 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 290 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 451 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER A 295 " --> pdb=" O HIS A 449 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N HIS A 449 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL A 297 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN A 447 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 334 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 439 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU A 365 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 475 Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 630 removed outlier: 6.618A pdb=" N VAL A 544 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 630 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TRP A 546 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 724 through 727 removed outlier: 4.286A pdb=" N MET A 672 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 671 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 705 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N SER A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA A 704 " --> pdb=" O VAL A 692 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 692 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 789 " --> pdb=" O ALA A 693 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 761 through 762 removed outlier: 4.793A pdb=" N PHE A 761 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 895 through 898 removed outlier: 5.963A pdb=" N ARG A 977 " --> pdb=" O THR A 997 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR A 997 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 979 " --> pdb=" O HIS A 995 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS A 995 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 981 " --> pdb=" O HIS A 993 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 991 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N HIS A 995 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU A 948 " --> pdb=" O HIS A 995 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR A 997 " --> pdb=" O GLY A 946 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 923 through 924 removed outlier: 4.097A pdb=" N VAL A 954 " --> pdb=" O VAL A 924 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1015 through 1017 Processing sheet with id=AB2, first strand: chain 'A' and resid 1056 through 1057 Processing sheet with id=AB3, first strand: chain 'A' and resid 1213 through 1216 removed outlier: 5.285A pdb=" N VAL A1108 " --> pdb=" O THR A1447 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N THR A1447 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A1397 " --> pdb=" O LEU A1448 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA A1450 " --> pdb=" O SER A1397 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA A1399 " --> pdb=" O ALA A1450 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE A1356 " --> pdb=" O VAL A1396 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE A1398 " --> pdb=" O PHE A1356 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A1358 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP A1400 " --> pdb=" O LEU A1358 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER A1360 " --> pdb=" O TRP A1400 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A1308 " --> pdb=" O ALA A1355 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL A1357 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL A1310 " --> pdb=" O VAL A1357 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE A1359 " --> pdb=" O VAL A1310 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N HIS A1312 " --> pdb=" O PHE A1359 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N SER A1361 " --> pdb=" O HIS A1312 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A1231 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A1310 " --> pdb=" O THR A1231 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A1233 " --> pdb=" O VAL A1310 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N HIS A1312 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR A1235 " --> pdb=" O HIS A1312 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A1232 " --> pdb=" O VAL A1259 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A1261 " --> pdb=" O VAL A1232 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE A1234 " --> pdb=" O VAL A1261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1213 through 1216 removed outlier: 5.285A pdb=" N VAL A1108 " --> pdb=" O THR A1447 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N THR A1447 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A1397 " --> pdb=" O LEU A1448 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA A1450 " --> pdb=" O SER A1397 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA A1399 " --> pdb=" O ALA A1450 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE A1356 " --> pdb=" O VAL A1396 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE A1398 " --> pdb=" O PHE A1356 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU A1358 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP A1400 " --> pdb=" O LEU A1358 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER A1360 " --> pdb=" O TRP A1400 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A1308 " --> pdb=" O ALA A1355 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL A1357 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL A1310 " --> pdb=" O VAL A1357 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE A1359 " --> pdb=" O VAL A1310 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N HIS A1312 " --> pdb=" O PHE A1359 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N SER A1361 " --> pdb=" O HIS A1312 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A1231 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A1310 " --> pdb=" O THR A1231 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU A1233 " --> pdb=" O VAL A1310 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N HIS A1312 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR A1235 " --> pdb=" O HIS A1312 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A1232 " --> pdb=" O VAL A1259 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A1261 " --> pdb=" O VAL A1232 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE A1234 " --> pdb=" O VAL A1261 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA A1284 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A1260 " --> pdb=" O ALA A1284 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1112 through 1113 removed outlier: 3.552A pdb=" N ALA A1209 " --> pdb=" O ILE A1113 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL A1204 " --> pdb=" O LEU A1182 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP A1184 " --> pdb=" O VAL A1204 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A1150 " --> pdb=" O VAL A1181 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A1183 " --> pdb=" O LEU A1150 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL A1152 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A1185 " --> pdb=" O VAL A1152 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A1124 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A1153 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR A1126 " --> pdb=" O VAL A1153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 196 through 199 removed outlier: 6.590A pdb=" N VAL B 151 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL B 199 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER B 153 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY B 150 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLY B 228 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE B 152 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL B 230 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY B 154 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 270 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N CYS B 42 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 272 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET B 40 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 274 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 38 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 290 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 292 " --> pdb=" O GLU B 453 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU B 453 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY B 294 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 334 " --> pdb=" O ARG B 435 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 439 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 368 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU B 365 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB8, first strand: chain 'B' and resid 103 through 104 Processing sheet with id=AB9, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AC1, first strand: chain 'B' and resid 469 through 475 Processing sheet with id=AC2, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.451A pdb=" N VAL B 544 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL B 630 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TRP B 546 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 806 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 690 through 691 removed outlier: 3.530A pdb=" N GLY B 705 " --> pdb=" O GLY B 671 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET B 672 " --> pdb=" O VAL B 727 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 761 through 763 removed outlier: 4.383A pdb=" N PHE B 761 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 895 through 898 removed outlier: 4.031A pdb=" N ALA B 994 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER B 983 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG B 992 " --> pdb=" O SER B 983 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA B 999 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 945 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 944 " --> pdb=" O SER B1056 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER B1056 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY B 946 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER B1050 " --> pdb=" O VAL B 950 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU B1076 " --> pdb=" O VAL B1084 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B1086 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B1074 " --> pdb=" O THR B1086 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 895 through 898 removed outlier: 4.031A pdb=" N ALA B 994 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER B 983 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG B 992 " --> pdb=" O SER B 983 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA B 999 " --> pdb=" O VAL B 945 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 945 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 944 " --> pdb=" O SER B1056 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER B1056 " --> pdb=" O VAL B 944 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY B 946 " --> pdb=" O GLY B1054 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER B1050 " --> pdb=" O VAL B 950 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG B1091 " --> pdb=" O SER B1050 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP B1052 " --> pdb=" O SER B1089 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER B1089 " --> pdb=" O TRP B1052 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 923 through 924 removed outlier: 4.218A pdb=" N VAL B 954 " --> pdb=" O VAL B 924 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 5 through 9 Processing sheet with id=AC9, first strand: chain 'G' and resid 12 through 14 removed outlier: 5.980A pdb=" N GLY G 12 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG G 40 " --> pdb=" O TRP G 49 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TRP G 49 " --> pdb=" O ARG G 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 12 through 14 removed outlier: 5.980A pdb=" N GLY G 12 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG G 102 " --> pdb=" O TYR G 109 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR G 109 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 127 through 131 removed outlier: 4.745A pdb=" N GLY G 146 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL G 189 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU G 148 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER G 187 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS G 150 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU G 185 " --> pdb=" O LYS G 150 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 127 through 131 removed outlier: 4.745A pdb=" N GLY G 146 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL G 189 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU G 148 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER G 187 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS G 150 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU G 185 " --> pdb=" O LYS G 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 158 through 161 Processing sheet with id=AD5, first strand: chain 'H' and resid 5 through 9 Processing sheet with id=AD6, first strand: chain 'H' and resid 12 through 14 removed outlier: 6.302A pdb=" N GLY H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 12 through 14 removed outlier: 6.302A pdb=" N GLY H 12 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR H 109 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.063A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 127 through 131 removed outlier: 6.063A pdb=" N TYR H 183 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.473A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 21 through 22 Processing sheet with id=AE3, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.699A pdb=" N LEU I 27 " --> pdb=" O LYS I 125 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP I 127 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY I 105 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU I 54 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR I 70 " --> pdb=" O LEU I 54 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP I 56 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 136 through 140 removed outlier: 3.522A pdb=" N VAL I 155 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR I 195 " --> pdb=" O ASN I 160 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 167 through 170 Processing sheet with id=AE6, first strand: chain 'L' and resid 21 through 22 Processing sheet with id=AE7, first strand: chain 'L' and resid 74 through 75 removed outlier: 5.719A pdb=" N LEU L 67 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU L 58 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE L 69 " --> pdb=" O TRP L 56 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 136 through 140 removed outlier: 3.634A pdb=" N VAL L 155 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER L 199 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR L 195 " --> pdb=" O ASN L 160 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 167 through 169 1233 hydrogen bonds defined for protein. 3330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8787 1.34 - 1.46: 5504 1.46 - 1.58: 11755 1.58 - 1.70: 2 1.70 - 1.82: 109 Bond restraints: 26157 Sorted by residual: bond pdb=" N VAL A1096 " pdb=" CA VAL A1096 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N GLU A1098 " pdb=" CA GLU A1098 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.28e-02 6.10e+03 8.81e+00 bond pdb=" N ASP I 192 " pdb=" CA ASP I 192 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.33e-02 5.65e+03 6.99e+00 bond pdb=" N PHE A1095 " pdb=" CA PHE A1095 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.40e-02 5.10e+03 6.78e+00 bond pdb=" N THR A 829 " pdb=" CA THR A 829 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.18e+00 ... (remaining 26152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 35208 2.11 - 4.23: 420 4.23 - 6.34: 43 6.34 - 8.46: 8 8.46 - 10.57: 6 Bond angle restraints: 35685 Sorted by residual: angle pdb=" C ALA A 202 " pdb=" CA ALA A 202 " pdb=" CB ALA A 202 " ideal model delta sigma weight residual 116.54 110.07 6.47 1.15e+00 7.56e-01 3.16e+01 angle pdb=" CA MET G 87 " pdb=" CB MET G 87 " pdb=" CG MET G 87 " ideal model delta sigma weight residual 114.10 122.51 -8.41 2.00e+00 2.50e-01 1.77e+01 angle pdb=" CA ARG B 975 " pdb=" CB ARG B 975 " pdb=" CG ARG B 975 " ideal model delta sigma weight residual 114.10 122.02 -7.92 2.00e+00 2.50e-01 1.57e+01 angle pdb=" CA ALA A 202 " pdb=" C ALA A 202 " pdb=" N CYS A 203 " ideal model delta sigma weight residual 119.52 116.73 2.79 7.90e-01 1.60e+00 1.25e+01 angle pdb=" CA ALA A1097 " pdb=" C ALA A1097 " pdb=" O ALA A1097 " ideal model delta sigma weight residual 121.40 117.55 3.85 1.11e+00 8.12e-01 1.20e+01 ... (remaining 35680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.52: 14696 25.52 - 51.04: 795 51.04 - 76.56: 87 76.56 - 102.08: 20 102.08 - 127.60: 1 Dihedral angle restraints: 15599 sinusoidal: 5833 harmonic: 9766 Sorted by residual: dihedral pdb=" CA LEU A 13 " pdb=" C LEU A 13 " pdb=" N ARG A 14 " pdb=" CA ARG A 14 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CQ 4HH C1538 " pdb=" CO 4HH C1538 " pdb=" CP 4HH C1538 " pdb=" NN 4HH C1538 " ideal model delta sinusoidal sigma weight residual 156.22 -76.18 -127.60 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CA ASP L 192 " pdb=" CB ASP L 192 " pdb=" CG ASP L 192 " pdb=" OD1 ASP L 192 " ideal model delta sinusoidal sigma weight residual -30.00 -89.51 59.51 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 15596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2992 0.037 - 0.074: 742 0.074 - 0.112: 368 0.112 - 0.149: 43 0.149 - 0.186: 4 Chirality restraints: 4149 Sorted by residual: chirality pdb=" CB VAL A1096 " pdb=" CA VAL A1096 " pdb=" CG1 VAL A1096 " pdb=" CG2 VAL A1096 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CG LEU A 421 " pdb=" CB LEU A 421 " pdb=" CD1 LEU A 421 " pdb=" CD2 LEU A 421 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA LEU A 13 " pdb=" N LEU A 13 " pdb=" C LEU A 13 " pdb=" CB LEU A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 4146 not shown) Planarity restraints: 4685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 975 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ARG B 975 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG B 975 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 976 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 13 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C LEU A 13 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU A 13 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG A 14 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1078 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A1079 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1079 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1079 " -0.023 5.00e-02 4.00e+02 ... (remaining 4682 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 662 2.67 - 3.23: 25842 3.23 - 3.79: 43134 3.79 - 4.34: 54399 4.34 - 4.90: 87770 Nonbonded interactions: 211807 Sorted by model distance: nonbonded pdb=" OG SER B 633 " pdb=" OE1 GLN B 634 " model vdw 2.118 3.040 nonbonded pdb=" O ARG B 975 " pdb=" NH1 ARG B 975 " model vdw 2.144 3.120 nonbonded pdb=" O THR A1235 " pdb=" OG1 THR A1313 " model vdw 2.202 3.040 nonbonded pdb=" O LEU B 126 " pdb=" OG SER B 130 " model vdw 2.208 3.040 nonbonded pdb=" OG SER L 41 " pdb=" O GLN L 43 " model vdw 2.210 3.040 ... (remaining 211802 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } 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: 6.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.330 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.003 0.041 26163 Z= 0.138 Angle : 0.570 10.573 35697 Z= 0.299 Chirality : 0.041 0.186 4149 Planarity : 0.004 0.040 4685 Dihedral : 15.223 127.603 9329 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.19 % Allowed : 19.65 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.28 (0.15), residues: 3428 helix: 1.22 (0.17), residues: 994 sheet: 0.10 (0.20), residues: 712 loop : -0.31 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 975 TYR 0.015 0.001 TYR B 12 PHE 0.011 0.001 PHE H 52 TRP 0.011 0.001 TRP A 583 HIS 0.003 0.001 HIS B 803 Details of bonding type rmsd covalent geometry : bond 0.00269 (26157) covalent geometry : angle 0.57040 (35685) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.53181 ( 12) hydrogen bonds : bond 0.16076 ( 1167) hydrogen bonds : angle 6.95670 ( 3330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4396 (tpt) cc_final: 0.3466 (tpt) REVERT: B 672 MET cc_start: 0.8865 (mmp) cc_final: 0.8603 (mmp) REVERT: G 87 MET cc_start: 0.9127 (mmp) cc_final: 0.8678 (mmp) outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.1852 time to fit residues: 20.0590 Evaluate side-chains 53 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain H residue 87 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 ASN A1082 GLN ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.044694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.028777 restraints weight = 285697.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.029450 restraints weight = 163285.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.029845 restraints weight = 113636.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.030105 restraints weight = 89371.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.030269 restraints weight = 75960.248| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26163 Z= 0.246 Angle : 0.627 6.500 35697 Z= 0.324 Chirality : 0.042 0.185 4149 Planarity : 0.005 0.064 4685 Dihedral : 5.173 122.309 3751 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.11 % Allowed : 18.26 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.12 (0.15), residues: 3428 helix: 1.11 (0.16), residues: 1032 sheet: -0.04 (0.19), residues: 750 loop : -0.44 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 975 TYR 0.018 0.002 TYR B 12 PHE 0.017 0.002 PHE C1531 TRP 0.022 0.001 TRP A 583 HIS 0.006 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00513 (26157) covalent geometry : angle 0.62687 (35685) SS BOND : bond 0.00382 ( 6) SS BOND : angle 0.68809 ( 12) hydrogen bonds : bond 0.04221 ( 1167) hydrogen bonds : angle 5.68886 ( 3330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 51 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8872 (mmp80) REVERT: A 319 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8806 (mtm-85) REVERT: A 672 MET cc_start: 0.8963 (mmm) cc_final: 0.8678 (mmt) REVERT: A 844 MET cc_start: 0.9733 (ptp) cc_final: 0.9528 (ptp) REVERT: A 1027 ARG cc_start: 0.9515 (OUTLIER) cc_final: 0.9250 (tpm170) REVERT: A 1091 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8105 (mmp-170) REVERT: A 1409 MET cc_start: -0.0419 (mmt) cc_final: -0.0785 (mmt) REVERT: B 672 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8158 (mmm) REVERT: I 20 MET cc_start: 0.8766 (ppp) cc_final: 0.8496 (ppp) REVERT: I 70 TYR cc_start: 0.9540 (OUTLIER) cc_final: 0.8294 (p90) REVERT: I 74 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8207 (p0) REVERT: L 140 PHE cc_start: 0.2791 (OUTLIER) cc_final: 0.2392 (t80) outliers start: 83 outliers final: 34 residues processed: 129 average time/residue: 0.1963 time to fit residues: 39.3446 Evaluate side-chains 89 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 47 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 342 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 117 optimal weight: 40.0000 chunk 322 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 285 optimal weight: 1.9990 chunk 160 optimal weight: 0.0370 chunk 189 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.045580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.029567 restraints weight = 277575.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.030064 restraints weight = 152428.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.030489 restraints weight = 103834.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.030771 restraints weight = 81162.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.030939 restraints weight = 70551.804| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26163 Z= 0.109 Angle : 0.512 6.663 35697 Z= 0.260 Chirality : 0.041 0.160 4149 Planarity : 0.004 0.049 4685 Dihedral : 4.826 121.273 3748 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.69 % Allowed : 18.49 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.47 (0.15), residues: 3428 helix: 1.62 (0.16), residues: 1036 sheet: 0.09 (0.20), residues: 731 loop : -0.36 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 790 TYR 0.013 0.001 TYR B 12 PHE 0.009 0.001 PHE L 161 TRP 0.010 0.001 TRP A 555 HIS 0.003 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00235 (26157) covalent geometry : angle 0.51215 (35685) SS BOND : bond 0.00300 ( 6) SS BOND : angle 0.51997 ( 12) hydrogen bonds : bond 0.03524 ( 1167) hydrogen bonds : angle 5.15633 ( 3330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 54 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 MET cc_start: 0.9166 (mmm) cc_final: 0.8827 (mmt) REVERT: A 1027 ARG cc_start: 0.9549 (OUTLIER) cc_final: 0.9241 (tpm170) REVERT: A 1435 MET cc_start: 0.4561 (mmp) cc_final: 0.4237 (mmp) REVERT: B 672 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7748 (mmm) REVERT: L 140 PHE cc_start: 0.2336 (OUTLIER) cc_final: 0.2001 (t80) outliers start: 72 outliers final: 41 residues processed: 120 average time/residue: 0.1626 time to fit residues: 32.7036 Evaluate side-chains 94 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 50 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1312 HIS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 69 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 216 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 334 optimal weight: 7.9990 chunk 261 optimal weight: 40.0000 chunk 25 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 120 optimal weight: 40.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 788 GLN ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN L 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.044731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.028769 restraints weight = 280710.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.029378 restraints weight = 160173.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.029928 restraints weight = 108282.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.030177 restraints weight = 84810.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.030286 restraints weight = 72753.172| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26163 Z= 0.192 Angle : 0.561 8.737 35697 Z= 0.285 Chirality : 0.041 0.187 4149 Planarity : 0.004 0.048 4685 Dihedral : 4.944 116.844 3748 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.12 % Allowed : 18.49 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.38 (0.15), residues: 3428 helix: 1.55 (0.16), residues: 1042 sheet: -0.02 (0.19), residues: 743 loop : -0.41 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1529 TYR 0.021 0.001 TYR A 782 PHE 0.015 0.001 PHE H 107 TRP 0.018 0.001 TRP A 583 HIS 0.006 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00402 (26157) covalent geometry : angle 0.56060 (35685) SS BOND : bond 0.00359 ( 6) SS BOND : angle 0.55007 ( 12) hydrogen bonds : bond 0.03670 ( 1167) hydrogen bonds : angle 5.19350 ( 3330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 48 time to evaluate : 1.150 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 114 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8752 (mmp80) REVERT: A 319 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8799 (mtm-85) REVERT: A 672 MET cc_start: 0.9161 (mmm) cc_final: 0.8764 (mmt) REVERT: A 1027 ARG cc_start: 0.9540 (OUTLIER) cc_final: 0.9248 (tpm170) REVERT: A 1435 MET cc_start: 0.4257 (mmp) cc_final: 0.3966 (mmp) REVERT: B 672 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7955 (mmm) REVERT: B 747 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.9016 (pt0) REVERT: G 215 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8067 (m-30) REVERT: I 70 TYR cc_start: 0.9458 (OUTLIER) cc_final: 0.8492 (p90) REVERT: L 140 PHE cc_start: 0.2390 (OUTLIER) cc_final: 0.2125 (t80) outliers start: 110 outliers final: 70 residues processed: 154 average time/residue: 0.1683 time to fit residues: 42.9395 Evaluate side-chains 127 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 49 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1312 HIS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 140 PHE Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 141 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 309 optimal weight: 0.3980 chunk 260 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 334 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 159 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 HIS ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.044894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.028842 restraints weight = 278504.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.029548 restraints weight = 154754.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.029947 restraints weight = 105383.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.030188 restraints weight = 83085.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.030363 restraints weight = 71068.323| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26163 Z= 0.148 Angle : 0.536 9.278 35697 Z= 0.269 Chirality : 0.041 0.220 4149 Planarity : 0.004 0.049 4685 Dihedral : 4.755 115.012 3745 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.89 % Allowed : 19.31 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.48 (0.15), residues: 3428 helix: 1.71 (0.16), residues: 1044 sheet: 0.04 (0.20), residues: 729 loop : -0.41 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1511 TYR 0.017 0.001 TYR A 782 PHE 0.011 0.001 PHE H 107 TRP 0.013 0.001 TRP A 583 HIS 0.004 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00315 (26157) covalent geometry : angle 0.53642 (35685) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.52610 ( 12) hydrogen bonds : bond 0.03439 ( 1167) hydrogen bonds : angle 5.03208 ( 3330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 51 time to evaluate : 0.971 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 114 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8713 (mmp80) REVERT: A 319 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8758 (mtm-85) REVERT: A 672 MET cc_start: 0.8967 (mmm) cc_final: 0.8682 (mmm) REVERT: A 1027 ARG cc_start: 0.9522 (OUTLIER) cc_final: 0.9236 (tpm170) REVERT: A 1435 MET cc_start: 0.4335 (mmp) cc_final: 0.4096 (mmp) REVERT: B 612 MET cc_start: 0.9474 (mtp) cc_final: 0.9062 (mtp) REVERT: B 672 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7858 (mmm) REVERT: G 87 MET cc_start: 0.9040 (mmp) cc_final: 0.8468 (mmp) REVERT: H 36 MET cc_start: 0.9603 (mmm) cc_final: 0.9382 (mmp) REVERT: I 20 MET cc_start: 0.8578 (ppp) cc_final: 0.8182 (ppp) REVERT: I 70 TYR cc_start: 0.9446 (OUTLIER) cc_final: 0.8478 (p90) outliers start: 104 outliers final: 75 residues processed: 149 average time/residue: 0.1651 time to fit residues: 41.0089 Evaluate side-chains 129 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 49 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1312 HIS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 215 ASP Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 115 optimal weight: 1.9990 chunk 301 optimal weight: 30.0000 chunk 203 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 223 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.044890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.028750 restraints weight = 278975.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.029488 restraints weight = 155895.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.029998 restraints weight = 106024.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.030154 restraints weight = 82464.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.030339 restraints weight = 73406.286| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26163 Z= 0.137 Angle : 0.531 15.662 35697 Z= 0.264 Chirality : 0.041 0.186 4149 Planarity : 0.004 0.049 4685 Dihedral : 4.688 113.560 3745 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.44 % Allowed : 20.10 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.52 (0.15), residues: 3428 helix: 1.82 (0.16), residues: 1044 sheet: 0.05 (0.20), residues: 707 loop : -0.42 (0.16), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1511 TYR 0.014 0.001 TYR A 782 PHE 0.012 0.001 PHE G 107 TRP 0.014 0.001 TRP A 583 HIS 0.004 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00294 (26157) covalent geometry : angle 0.53087 (35685) SS BOND : bond 0.00273 ( 6) SS BOND : angle 0.50830 ( 12) hydrogen bonds : bond 0.03310 ( 1167) hydrogen bonds : angle 4.93888 ( 3330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 48 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8722 (mmp80) REVERT: A 245 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8978 (mm-40) REVERT: A 319 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8751 (mtm-85) REVERT: A 672 MET cc_start: 0.8953 (mmm) cc_final: 0.8611 (mmm) REVERT: A 1027 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.9295 (tpm170) REVERT: A 1435 MET cc_start: 0.4451 (mmp) cc_final: 0.4239 (mmp) REVERT: B 672 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7855 (mmm) REVERT: I 20 MET cc_start: 0.8625 (ppp) cc_final: 0.8265 (ppp) REVERT: I 70 TYR cc_start: 0.9447 (OUTLIER) cc_final: 0.8448 (p90) REVERT: I 96 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.8673 (tp) outliers start: 92 outliers final: 76 residues processed: 136 average time/residue: 0.1623 time to fit residues: 37.2525 Evaluate side-chains 130 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 47 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1312 HIS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 184 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 245 optimal weight: 20.0000 chunk 267 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 340 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.045251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.029108 restraints weight = 277074.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.029649 restraints weight = 154199.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.030131 restraints weight = 106295.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.030361 restraints weight = 82901.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.030569 restraints weight = 71460.743| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26163 Z= 0.104 Angle : 0.514 12.228 35697 Z= 0.253 Chirality : 0.041 0.177 4149 Planarity : 0.004 0.049 4685 Dihedral : 4.541 112.611 3745 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.41 % Allowed : 19.87 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.66 (0.15), residues: 3428 helix: 1.93 (0.17), residues: 1045 sheet: 0.13 (0.20), residues: 733 loop : -0.33 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1547 TYR 0.011 0.001 TYR A 782 PHE 0.009 0.001 PHE L 161 TRP 0.012 0.001 TRP A 583 HIS 0.005 0.001 HIS A1176 Details of bonding type rmsd covalent geometry : bond 0.00228 (26157) covalent geometry : angle 0.51401 (35685) SS BOND : bond 0.00287 ( 6) SS BOND : angle 0.46289 ( 12) hydrogen bonds : bond 0.03090 ( 1167) hydrogen bonds : angle 4.76503 ( 3330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 50 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8752 (mmp80) REVERT: A 245 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.9004 (mm-40) REVERT: A 319 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8765 (mtm-85) REVERT: A 672 MET cc_start: 0.8952 (mmm) cc_final: 0.8598 (mmm) REVERT: A 1027 ARG cc_start: 0.9555 (OUTLIER) cc_final: 0.9319 (tpm170) REVERT: B 612 MET cc_start: 0.9461 (mtp) cc_final: 0.9005 (mtp) REVERT: B 672 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7749 (mmm) REVERT: I 70 TYR cc_start: 0.9441 (OUTLIER) cc_final: 0.8423 (p90) outliers start: 91 outliers final: 71 residues processed: 137 average time/residue: 0.1639 time to fit residues: 37.2952 Evaluate side-chains 126 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 49 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1312 HIS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain C residue 1525 VAL Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 194 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 295 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 292 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 chunk 258 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 HIS ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.044270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.029010 restraints weight = 283173.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.030062 restraints weight = 173171.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.029917 restraints weight = 95751.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030054 restraints weight = 86152.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.030115 restraints weight = 82100.296| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26163 Z= 0.205 Angle : 0.582 11.823 35697 Z= 0.293 Chirality : 0.041 0.199 4149 Planarity : 0.004 0.048 4685 Dihedral : 4.763 108.526 3745 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.78 % Allowed : 19.57 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.47 (0.15), residues: 3428 helix: 1.76 (0.16), residues: 1044 sheet: 0.07 (0.20), residues: 702 loop : -0.47 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 658 TYR 0.014 0.002 TYR L 70 PHE 0.018 0.001 PHE H 107 TRP 0.057 0.002 TRP A 583 HIS 0.006 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00428 (26157) covalent geometry : angle 0.58223 (35685) SS BOND : bond 0.00334 ( 6) SS BOND : angle 0.59328 ( 12) hydrogen bonds : bond 0.03562 ( 1167) hydrogen bonds : angle 5.00683 ( 3330) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 48 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8749 (mmp80) REVERT: A 245 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8982 (mm-40) REVERT: A 319 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8812 (mtm-85) REVERT: A 672 MET cc_start: 0.8915 (mmm) cc_final: 0.8557 (mmm) REVERT: A 1027 ARG cc_start: 0.9528 (OUTLIER) cc_final: 0.9305 (tpm170) REVERT: B 672 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7998 (mmm) REVERT: B 859 MET cc_start: 0.9010 (mpp) cc_final: 0.8751 (mpp) REVERT: G 87 MET cc_start: 0.9106 (mmp) cc_final: 0.8514 (mmp) REVERT: I 70 TYR cc_start: 0.9512 (OUTLIER) cc_final: 0.8541 (p90) REVERT: I 96 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.8672 (tp) outliers start: 101 outliers final: 81 residues processed: 145 average time/residue: 0.1506 time to fit residues: 36.9185 Evaluate side-chains 135 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 47 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1312 HIS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 3 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 293 optimal weight: 0.0470 chunk 204 optimal weight: 9.9990 chunk 268 optimal weight: 0.1980 chunk 319 optimal weight: 10.0000 chunk 285 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 HIS ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.044653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.028887 restraints weight = 280977.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.029220 restraints weight = 154893.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.029622 restraints weight = 107015.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.029938 restraints weight = 84751.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.030094 restraints weight = 72795.183| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26163 Z= 0.139 Angle : 0.537 11.433 35697 Z= 0.267 Chirality : 0.041 0.195 4149 Planarity : 0.004 0.049 4685 Dihedral : 4.637 108.009 3745 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.48 % Allowed : 20.06 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.57 (0.15), residues: 3428 helix: 1.85 (0.16), residues: 1047 sheet: 0.12 (0.20), residues: 703 loop : -0.42 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1511 TYR 0.013 0.001 TYR A 782 PHE 0.012 0.001 PHE G 107 TRP 0.033 0.001 TRP A 583 HIS 0.005 0.001 HIS A1176 Details of bonding type rmsd covalent geometry : bond 0.00299 (26157) covalent geometry : angle 0.53653 (35685) SS BOND : bond 0.00291 ( 6) SS BOND : angle 0.53914 ( 12) hydrogen bonds : bond 0.03298 ( 1167) hydrogen bonds : angle 4.87123 ( 3330) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 49 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8687 (mmp80) REVERT: A 245 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8952 (mm-40) REVERT: A 319 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8751 (mtm-85) REVERT: A 672 MET cc_start: 0.8915 (mmm) cc_final: 0.8524 (mmm) REVERT: A 1027 ARG cc_start: 0.9525 (OUTLIER) cc_final: 0.9306 (tpm170) REVERT: B 612 MET cc_start: 0.9482 (mtp) cc_final: 0.9017 (mtp) REVERT: B 672 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7803 (mmm) REVERT: B 859 MET cc_start: 0.8968 (mpp) cc_final: 0.8712 (mpp) REVERT: G 87 MET cc_start: 0.9025 (mmp) cc_final: 0.8423 (mmp) REVERT: I 70 TYR cc_start: 0.9466 (OUTLIER) cc_final: 0.8427 (p90) REVERT: I 96 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.8665 (tp) outliers start: 93 outliers final: 81 residues processed: 138 average time/residue: 0.1613 time to fit residues: 37.3233 Evaluate side-chains 136 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 48 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1312 HIS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 942 THR Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 226 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 110 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.044277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.028376 restraints weight = 282134.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.029035 restraints weight = 157279.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.029337 restraints weight = 107675.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.029674 restraints weight = 87194.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.029841 restraints weight = 72698.533| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26163 Z= 0.175 Angle : 0.570 12.462 35697 Z= 0.284 Chirality : 0.042 0.341 4149 Planarity : 0.004 0.048 4685 Dihedral : 4.716 104.401 3745 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.33 % Allowed : 20.28 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.46 (0.15), residues: 3428 helix: 1.76 (0.16), residues: 1047 sheet: 0.08 (0.20), residues: 706 loop : -0.50 (0.16), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1511 TYR 0.015 0.001 TYR A 782 PHE 0.017 0.001 PHE G 107 TRP 0.037 0.001 TRP A 583 HIS 0.005 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00371 (26157) covalent geometry : angle 0.57017 (35685) SS BOND : bond 0.00321 ( 6) SS BOND : angle 0.55027 ( 12) hydrogen bonds : bond 0.03447 ( 1167) hydrogen bonds : angle 4.96317 ( 3330) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6856 Ramachandran restraints generated. 3428 Oldfield, 0 Emsley, 3428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 49 time to evaluate : 1.080 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 114 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8666 (mmp80) REVERT: A 245 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8988 (mm-40) REVERT: A 319 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8761 (mtm-85) REVERT: A 672 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8553 (mmm) REVERT: A 844 MET cc_start: 0.9628 (ptp) cc_final: 0.9413 (ptp) REVERT: A 1027 ARG cc_start: 0.9506 (OUTLIER) cc_final: 0.9297 (tpm170) REVERT: B 156 MET cc_start: 0.8443 (mmt) cc_final: 0.8154 (mmt) REVERT: B 612 MET cc_start: 0.9520 (mtp) cc_final: 0.9072 (mtp) REVERT: B 672 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7855 (mmm) REVERT: B 859 MET cc_start: 0.8963 (mpp) cc_final: 0.8671 (mpp) REVERT: G 87 MET cc_start: 0.8966 (mmp) cc_final: 0.8391 (mmp) REVERT: I 70 TYR cc_start: 0.9487 (OUTLIER) cc_final: 0.8455 (p90) REVERT: I 96 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.8679 (tp) outliers start: 89 outliers final: 78 residues processed: 133 average time/residue: 0.1655 time to fit residues: 36.7350 Evaluate side-chains 134 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 48 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1027 ARG Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1068 THR Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1312 HIS Chi-restraints excluded: chain A residue 1398 ILE Chi-restraints excluded: chain A residue 1418 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 233 MET Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 866 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 997 THR Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain I residue 70 TYR Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 149 SER Chi-restraints excluded: chain L residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 167 optimal weight: 0.2980 chunk 135 optimal weight: 30.0000 chunk 7 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 8 optimal weight: 0.0770 chunk 334 optimal weight: 20.0000 chunk 199 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 overall best weight: 2.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.044526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.028549 restraints weight = 278252.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029156 restraints weight = 155408.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.029563 restraints weight = 106101.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.029836 restraints weight = 83160.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.029911 restraints weight = 70912.812| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26163 Z= 0.140 Angle : 0.542 11.174 35697 Z= 0.268 Chirality : 0.042 0.351 4149 Planarity : 0.004 0.049 4685 Dihedral : 4.582 102.663 3745 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.33 % Allowed : 20.40 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.56 (0.15), residues: 3428 helix: 1.86 (0.16), residues: 1049 sheet: 0.14 (0.20), residues: 707 loop : -0.44 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1511 TYR 0.014 0.001 TYR A 782 PHE 0.011 0.001 PHE H 107 TRP 0.028 0.001 TRP A 583 HIS 0.010 0.001 HIS C1512 Details of bonding type rmsd covalent geometry : bond 0.00301 (26157) covalent geometry : angle 0.54216 (35685) SS BOND : bond 0.00311 ( 6) SS BOND : angle 0.52919 ( 12) hydrogen bonds : bond 0.03234 ( 1167) hydrogen bonds : angle 4.84056 ( 3330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5708.03 seconds wall clock time: 98 minutes 50.66 seconds (5930.66 seconds total)