Starting phenix.real_space_refine on Sat Mar 7 01:18:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x26_21996/03_2026/6x26_21996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x26_21996/03_2026/6x26_21996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x26_21996/03_2026/6x26_21996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x26_21996/03_2026/6x26_21996.map" model { file = "/net/cci-nas-00/data/ceres_data/6x26_21996/03_2026/6x26_21996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x26_21996/03_2026/6x26_21996.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 1.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 112 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 22189 2.51 5 N 6361 2.21 5 O 7064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35870 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1142, 8791 Classifications: {'peptide': 1142} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 55, 'TRANS': 1086} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 17, 'TYR:plan': 1, 'GLU:plan': 14, 'GLN:plan1': 8, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 215 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1725 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10352 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "J" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10381 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 201 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna3p': 8} Chain: "P" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1112 Classifications: {'DNA': 55} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1011 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22998 SG CYS J 72 26.746 98.887 68.422 1.00194.84 S ATOM 23106 SG CYS J 85 24.928 95.941 67.223 1.00183.16 S ATOM 23130 SG CYS J 88 28.692 97.715 66.332 1.00192.34 S ATOM 28804 SG CYS J 814 53.086 34.405 76.404 1.00119.71 S ATOM 29369 SG CYS J 888 53.952 37.971 76.627 1.00107.46 S ATOM 29420 SG CYS J 895 53.267 36.405 79.807 1.00100.03 S ATOM 29441 SG CYS J 898 56.252 35.190 78.321 1.00104.70 S Time building chain proxies: 8.08, per 1000 atoms: 0.23 Number of scatterers: 35870 At special positions: 0 Unit cell: (139.1, 219.7, 166.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 141 16.00 P 112 15.00 Mg 1 11.99 O 7064 8.00 N 6361 7.00 C 22189 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " Number of angles added : 6 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8008 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 53 sheets defined 38.4% alpha, 15.6% beta 51 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 4.92 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 48 through 62 removed outlier: 3.850A pdb=" N ARG A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.661A pdb=" N ILE A 88 " --> pdb=" O HIS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 220 through 235 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.850A pdb=" N TYR A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.591A pdb=" N TYR A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.664A pdb=" N SER A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 371 through 381 Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.751A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.649A pdb=" N ARG A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 524 through 529 removed outlier: 4.623A pdb=" N HIS A 527 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 528 " --> pdb=" O SER A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 568 through 576 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.662A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 617 removed outlier: 3.524A pdb=" N GLN A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 648 removed outlier: 3.561A pdb=" N VAL A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 690 through 701 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 731 through 734 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 759 through 768 Processing helix chain 'A' and resid 794 through 809 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 821 through 833 removed outlier: 4.011A pdb=" N GLU A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 859 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 940 through 950 removed outlier: 4.126A pdb=" N ALA A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 986 removed outlier: 3.521A pdb=" N TYR A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 977 " --> pdb=" O SER A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1033 Processing helix chain 'A' and resid 1035 through 1051 Processing helix chain 'A' and resid 1054 through 1073 Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1127 through 1145 removed outlier: 3.517A pdb=" N ASN A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.677A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 removed outlier: 4.151A pdb=" N GLY G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.571A pdb=" N THR G 157 " --> pdb=" O PRO G 154 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 154 through 158' Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 48 removed outlier: 3.596A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 87 Processing helix chain 'H' and resid 212 through 226 removed outlier: 3.997A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 232 removed outlier: 4.518A pdb=" N ALA H 230 " --> pdb=" O GLN H 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.519A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 242 through 247 removed outlier: 4.007A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 289 through 293 Processing helix chain 'I' and resid 319 through 328 removed outlier: 3.544A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.720A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR I 350 " --> pdb=" O TYR I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 removed outlier: 3.723A pdb=" N ALA I 362 " --> pdb=" O ASP I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 390 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.986A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.450A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 528 Processing helix chain 'I' and resid 609 through 614 removed outlier: 4.166A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 656 through 661 removed outlier: 3.922A pdb=" N GLN I 659 " --> pdb=" O SER I 656 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL I 661 " --> pdb=" O GLN I 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 656 through 661' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.761A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 820 through 826 Processing helix chain 'I' and resid 942 through 978 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.788A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 997 removed outlier: 3.501A pdb=" N TRP I 997 " --> pdb=" O ARG I 994 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.725A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 Processing helix chain 'I' and resid 1137 through 1150 removed outlier: 3.628A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.682A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.551A pdb=" N ILE I1195 " --> pdb=" O LYS I1191 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1284 through 1291 Processing helix chain 'I' and resid 1297 through 1310 Processing helix chain 'I' and resid 1320 through 1333 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 removed outlier: 3.663A pdb=" N PHE J 62 " --> pdb=" O CYS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 128 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 207 Processing helix chain 'J' and resid 211 through 229 removed outlier: 3.726A pdb=" N VAL J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 removed outlier: 3.631A pdb=" N ARG J 250 " --> pdb=" O PRO J 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 285 Processing helix chain 'J' and resid 288 through 309 Processing helix chain 'J' and resid 337 through 342 removed outlier: 3.599A pdb=" N LEU J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 394 through 404 Processing helix chain 'J' and resid 406 through 417 removed outlier: 4.182A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 452 through 458 removed outlier: 4.176A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 removed outlier: 3.519A pdb=" N ASN J 489 " --> pdb=" O SER J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 540 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.891A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 593 removed outlier: 3.671A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 613 removed outlier: 3.771A pdb=" N GLY J 613 " --> pdb=" O TYR J 609 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.597A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 Processing helix chain 'J' and resid 674 through 702 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 741 removed outlier: 3.616A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 803 removed outlier: 4.016A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP J 802 " --> pdb=" O ARG J 798 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 838 Processing helix chain 'J' and resid 865 through 874 Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.846A pdb=" N TYR J 899 " --> pdb=" O CYS J 895 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 895 through 900' Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1137 through 1146 removed outlier: 3.669A pdb=" N VAL J1141 " --> pdb=" O GLY J1137 " (cutoff:3.500A) Processing helix chain 'J' and resid 1216 through 1225 Processing helix chain 'J' and resid 1228 through 1244 removed outlier: 3.622A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.568A pdb=" N GLU J1254 " --> pdb=" O ASP J1250 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1281 through 1293 removed outlier: 3.634A pdb=" N VAL J1285 " --> pdb=" O GLU J1281 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG J1290 " --> pdb=" O LYS J1286 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1318 through 1325 removed outlier: 3.827A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 4.242A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.850A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1373 removed outlier: 4.281A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 55 Processing helix chain 'K' and resid 60 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 6.011A pdb=" N ARG A 17 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR A 285 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL A 42 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A 108 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 44 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N MET A 68 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 152 removed outlier: 6.327A pdb=" N ARG A 151 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR A 164 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A 161 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.471A pdb=" N VAL A 194 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 196 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 201 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 357 removed outlier: 5.639A pdb=" N VAL A 385 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N MET A 426 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N PHE A 387 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 531 removed outlier: 6.041A pdb=" N TYR A 493 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR A 512 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A 495 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE I 117 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU I 67 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 623 through 625 removed outlier: 5.815A pdb=" N ARG A 624 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 652 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLY A 709 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 654 " --> pdb=" O GLY A 709 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 787 through 792 removed outlier: 5.633A pdb=" N ILE A 883 " --> pdb=" O TRP A 913 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 915 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE A 885 " --> pdb=" O LEU A 915 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 812 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS A 867 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR A 814 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 839 " --> pdb=" O VAL A 864 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1077 through 1080 Processing sheet with id=AB1, first strand: chain 'G' and resid 12 through 18 removed outlier: 6.624A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLN G 18 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N HIS G 23 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 97 through 104 removed outlier: 3.571A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY G 151 " --> pdb=" O PRO G 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 97 through 104 removed outlier: 3.730A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AB5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.691A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 15 through 18 removed outlier: 5.542A pdb=" N HIS H 23 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR H 207 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 98 through 101 removed outlier: 7.001A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AC1, first strand: chain 'H' and resid 109 through 111 removed outlier: 7.023A pdb=" N VAL H 110 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.546A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 143 through 145 Processing sheet with id=AC4, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.560A pdb=" N GLN I 148 " --> pdb=" O ARG I 454 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AC6, first strand: chain 'I' and resid 284 through 286 removed outlier: 4.791A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.685A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.742A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 301 through 303 removed outlier: 6.472A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU I 308 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 580 through 581 removed outlier: 7.044A pdb=" N LEU I 587 " --> pdb=" O LEU I 606 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU I 606 " --> pdb=" O LEU I 587 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR I 589 " --> pdb=" O HIS I 604 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS I 604 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR I 591 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU I 602 " --> pdb=" O TYR I 591 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LYS I 593 " --> pdb=" O THR I 600 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AD3, first strand: chain 'I' and resid 616 through 617 Processing sheet with id=AD4, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.448A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.983A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.509A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AD8, first strand: chain 'I' and resid 1209 through 1213 removed outlier: 7.404A pdb=" N ILE I1210 " --> pdb=" O ARG I1223 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ARG I1223 " --> pdb=" O ILE I1210 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU I1212 " --> pdb=" O PHE I1221 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 830 through 838 removed outlier: 4.002A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 842 through 843 Processing sheet with id=AE2, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AE3, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.317A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 1335 through 1340 removed outlier: 3.782A pdb=" N ALA J 19 " --> pdb=" O GLU I1340 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 34 through 37 removed outlier: 4.256A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE7, first strand: chain 'J' and resid 547 through 556 Processing sheet with id=AE8, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE9, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AF1, first strand: chain 'J' and resid 825 through 826 removed outlier: 6.961A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 949 through 951 removed outlier: 4.058A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 991 through 996 removed outlier: 6.455A pdb=" N LEU J 984 " --> pdb=" O LYS J 992 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER J 994 " --> pdb=" O LEU J 982 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU J 982 " --> pdb=" O SER J 994 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE J 958 " --> pdb=" O GLU J1009 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU J1009 " --> pdb=" O ILE J 958 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 1024 through 1028 removed outlier: 4.426A pdb=" N ALA J1122 " --> pdb=" O VAL J1027 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1034 through 1035 Processing sheet with id=AF6, first strand: chain 'J' and resid 1046 through 1047 Processing sheet with id=AF7, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AF8, first strand: chain 'J' and resid 1264 through 1268 removed outlier: 6.726A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1376 hydrogen bonds defined for protein. 3828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 10.27 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9840 1.33 - 1.46: 7987 1.46 - 1.58: 18388 1.58 - 1.71: 221 1.71 - 1.83: 248 Bond restraints: 36684 Sorted by residual: bond pdb=" N PHE A 217 " pdb=" CA PHE A 217 " ideal model delta sigma weight residual 1.451 1.382 0.068 1.69e-02 3.50e+03 1.63e+01 bond pdb=" C ILE H 211 " pdb=" N ASP H 212 " ideal model delta sigma weight residual 1.330 1.272 0.058 1.47e-02 4.63e+03 1.56e+01 bond pdb=" N ILE A1075 " pdb=" CA ILE A1075 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" N THR J 853 " pdb=" CA THR J 853 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.18e+01 bond pdb=" C ARG A 336 " pdb=" N VAL A 337 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.48e-02 4.57e+03 1.01e+01 ... (remaining 36679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 49296 3.56 - 7.13: 732 7.13 - 10.69: 76 10.69 - 14.25: 9 14.25 - 17.82: 1 Bond angle restraints: 50114 Sorted by residual: angle pdb=" N ASP A 64 " pdb=" CA ASP A 64 " pdb=" C ASP A 64 " ideal model delta sigma weight residual 113.89 100.20 13.69 1.58e+00 4.01e-01 7.51e+01 angle pdb=" N VAL K 6 " pdb=" CA VAL K 6 " pdb=" C VAL K 6 " ideal model delta sigma weight residual 113.20 105.61 7.59 9.60e-01 1.09e+00 6.25e+01 angle pdb=" C PHE J1145 " pdb=" N GLU J1146 " pdb=" CA GLU J1146 " ideal model delta sigma weight residual 122.65 112.91 9.74 1.60e+00 3.91e-01 3.70e+01 angle pdb=" C PRO A 173 " pdb=" N MET A 174 " pdb=" CA MET A 174 " ideal model delta sigma weight residual 122.73 113.21 9.52 1.61e+00 3.86e-01 3.50e+01 angle pdb=" N ILE G 168 " pdb=" CA ILE G 168 " pdb=" C ILE G 168 " ideal model delta sigma weight residual 111.91 106.81 5.10 8.90e-01 1.26e+00 3.29e+01 ... (remaining 50109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 21281 35.40 - 70.79: 857 70.79 - 106.19: 40 106.19 - 141.59: 2 141.59 - 176.98: 1 Dihedral angle restraints: 22181 sinusoidal: 9761 harmonic: 12420 Sorted by residual: dihedral pdb=" CA ASN A 51 " pdb=" C ASN A 51 " pdb=" N ALA A 52 " pdb=" CA ALA A 52 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA SER J 210 " pdb=" C SER J 210 " pdb=" N GLU J 211 " pdb=" CA GLU J 211 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA THR J1169 " pdb=" C THR J1169 " pdb=" N LYS J1170 " pdb=" CA LYS J1170 " ideal model delta harmonic sigma weight residual 180.00 153.14 26.86 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 22178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 5025 0.091 - 0.181: 645 0.181 - 0.272: 48 0.272 - 0.362: 10 0.362 - 0.453: 3 Chirality restraints: 5731 Sorted by residual: chirality pdb=" CB ILE K 13 " pdb=" CA ILE K 13 " pdb=" CG1 ILE K 13 " pdb=" CG2 ILE K 13 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CB ILE I 117 " pdb=" CA ILE I 117 " pdb=" CG1 ILE I 117 " pdb=" CG2 ILE I 117 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB THR A 923 " pdb=" CA THR A 923 " pdb=" OG1 THR A 923 " pdb=" CG2 THR A 923 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 5728 not shown) Planarity restraints: 6171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 757 " -0.061 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO A 758 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 758 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 758 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR J 853 " -0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C THR J 853 " 0.058 2.00e-02 2.50e+03 pdb=" O THR J 853 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA J 854 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 108 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A 109 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " 0.045 5.00e-02 4.00e+02 ... (remaining 6168 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 413 2.57 - 3.15: 28888 3.15 - 3.73: 61057 3.73 - 4.32: 79640 4.32 - 4.90: 125193 Nonbonded interactions: 295191 Sorted by model distance: nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 1.983 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.013 2.170 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 2.046 2.170 nonbonded pdb=" NH2 ARG A 201 " pdb=" OD2 ASP A1048 " model vdw 2.080 3.120 nonbonded pdb=" CE MET A 130 " pdb=" CD1 LEU A 211 " model vdw 2.111 3.880 ... (remaining 295186 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' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 th \ rough 232)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } 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: 1.660 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 43.490 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 47.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 36691 Z= 0.357 Angle : 1.118 17.816 50120 Z= 0.621 Chirality : 0.061 0.453 5731 Planarity : 0.007 0.093 6171 Dihedral : 17.452 176.982 14173 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.71 % Favored : 92.19 % Rotamer: Outliers : 0.11 % Allowed : 0.67 % Favored : 99.22 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.17 % 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: -2.68 (0.11), residues: 4292 helix: -1.34 (0.12), residues: 1501 sheet: -1.09 (0.23), residues: 501 loop : -2.29 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 193 TYR 0.041 0.003 TYR I1229 PHE 0.045 0.003 PHE A 172 TRP 0.024 0.003 TRP A1134 HIS 0.015 0.002 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00757 (36684) covalent geometry : angle 1.11571 (50114) hydrogen bonds : bond 0.15371 ( 1495) hydrogen bonds : angle 7.33347 ( 4094) metal coordination : bond 0.01900 ( 7) metal coordination : angle 7.15660 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 378 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.8644 (mmm) cc_final: 0.8438 (mmm) REVERT: A 1024 LEU cc_start: 0.8999 (pp) cc_final: 0.8798 (pp) REVERT: A 1119 LEU cc_start: 0.8272 (tp) cc_final: 0.8042 (tp) REVERT: H 51 MET cc_start: 0.7982 (tpp) cc_final: 0.7337 (tpt) REVERT: H 142 MET cc_start: 0.7355 (ppp) cc_final: 0.7071 (ppp) REVERT: I 65 ASN cc_start: 0.8864 (m-40) cc_final: 0.8561 (t0) REVERT: I 160 ASP cc_start: 0.8818 (m-30) cc_final: 0.8122 (p0) REVERT: I 239 MET cc_start: 0.7912 (tmm) cc_final: 0.7653 (tmm) REVERT: I 515 MET cc_start: 0.8580 (ttt) cc_final: 0.8376 (ttt) REVERT: I 1017 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8899 (mt0) REVERT: I 1114 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8483 (tm-30) REVERT: I 1243 MET cc_start: 0.8950 (tmm) cc_final: 0.8439 (tmm) REVERT: I 1319 MET cc_start: 0.9226 (tmm) cc_final: 0.8753 (tmm) REVERT: J 56 LEU cc_start: 0.8204 (tp) cc_final: 0.7956 (tp) REVERT: J 245 LEU cc_start: 0.9399 (tp) cc_final: 0.9067 (tt) REVERT: J 325 LYS cc_start: 0.9391 (mppt) cc_final: 0.8972 (mppt) REVERT: J 724 MET cc_start: 0.9320 (mtm) cc_final: 0.9066 (mtp) REVERT: J 826 ILE cc_start: 0.7912 (mm) cc_final: 0.7563 (mm) REVERT: J 913 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6968 (mm-30) REVERT: J 1334 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8101 (tm-30) REVERT: K 19 LEU cc_start: 0.8734 (tt) cc_final: 0.8531 (tp) outliers start: 4 outliers final: 0 residues processed: 379 average time/residue: 0.2090 time to fit residues: 136.4842 Evaluate side-chains 280 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 230 GLN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1257 GLN J 320 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.086313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068937 restraints weight = 179005.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.070798 restraints weight = 107942.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.071233 restraints weight = 65281.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.071581 restraints weight = 53318.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071766 restraints weight = 49942.780| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 36691 Z= 0.184 Angle : 0.662 11.955 50120 Z= 0.353 Chirality : 0.043 0.175 5731 Planarity : 0.005 0.064 6171 Dihedral : 16.755 177.540 5964 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.99 % Favored : 92.99 % Rotamer: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.01 (0.12), residues: 4292 helix: -0.44 (0.13), residues: 1540 sheet: -1.11 (0.23), residues: 501 loop : -2.06 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1131 TYR 0.020 0.002 TYR A1111 PHE 0.017 0.001 PHE A 265 TRP 0.010 0.001 TRP J 580 HIS 0.010 0.001 HIS A1110 Details of bonding type rmsd covalent geometry : bond 0.00391 (36684) covalent geometry : angle 0.66182 (50114) hydrogen bonds : bond 0.04724 ( 1495) hydrogen bonds : angle 5.71782 ( 4094) metal coordination : bond 0.00723 ( 7) metal coordination : angle 2.70017 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 377 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8305 (p0) cc_final: 0.7996 (p0) REVERT: A 511 LEU cc_start: 0.8755 (tp) cc_final: 0.8407 (tp) REVERT: A 595 ASP cc_start: 0.8718 (m-30) cc_final: 0.8369 (m-30) REVERT: A 854 MET cc_start: 0.6450 (ppp) cc_final: 0.6222 (ppp) REVERT: A 922 MET cc_start: 0.5543 (tpt) cc_final: 0.5092 (tpp) REVERT: A 1124 ASP cc_start: 0.7521 (p0) cc_final: 0.7287 (p0) REVERT: G 131 CYS cc_start: 0.8938 (p) cc_final: 0.8574 (p) REVERT: H 145 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8667 (mtpt) REVERT: H 188 GLU cc_start: 0.8838 (pt0) cc_final: 0.8623 (pt0) REVERT: I 14 ASP cc_start: 0.8189 (t70) cc_final: 0.7889 (t0) REVERT: I 65 ASN cc_start: 0.8825 (m-40) cc_final: 0.8508 (t0) REVERT: I 160 ASP cc_start: 0.9062 (m-30) cc_final: 0.8036 (p0) REVERT: I 704 MET cc_start: 0.8686 (mmm) cc_final: 0.8117 (mmm) REVERT: I 1243 MET cc_start: 0.9105 (tmm) cc_final: 0.8452 (tmm) REVERT: I 1319 MET cc_start: 0.8887 (tmm) cc_final: 0.8413 (tmm) REVERT: J 252 LEU cc_start: 0.8311 (tp) cc_final: 0.8009 (tp) REVERT: J 325 LYS cc_start: 0.9276 (mppt) cc_final: 0.8891 (mppt) REVERT: J 329 ASP cc_start: 0.8481 (m-30) cc_final: 0.8231 (m-30) REVERT: J 724 MET cc_start: 0.9369 (mtm) cc_final: 0.8775 (mtp) REVERT: J 826 ILE cc_start: 0.7741 (mm) cc_final: 0.7482 (mm) REVERT: J 869 CYS cc_start: 0.9601 (m) cc_final: 0.9384 (m) REVERT: J 1278 GLU cc_start: 0.7420 (tt0) cc_final: 0.7162 (tt0) REVERT: J 1334 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8488 (tm-30) REVERT: J 1344 LEU cc_start: 0.8981 (mt) cc_final: 0.8695 (mp) REVERT: K 46 THR cc_start: 0.9051 (p) cc_final: 0.8842 (p) REVERT: K 54 ILE cc_start: 0.9009 (mm) cc_final: 0.8801 (mm) outliers start: 3 outliers final: 1 residues processed: 379 average time/residue: 0.1967 time to fit residues: 129.6679 Evaluate side-chains 286 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 174 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 369 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 chunk 397 optimal weight: 20.0000 chunk 412 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A 764 ASN A 908 HIS ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN G 132 HIS ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 GLN I 684 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 665 GLN ** J 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.083431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.065639 restraints weight = 179392.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.067136 restraints weight = 100721.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068077 restraints weight = 67644.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068586 restraints weight = 52356.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.069005 restraints weight = 44904.301| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 36691 Z= 0.321 Angle : 0.779 12.291 50120 Z= 0.408 Chirality : 0.046 0.192 5731 Planarity : 0.006 0.072 6171 Dihedral : 16.772 179.244 5964 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.60 % Favored : 91.38 % Rotamer: Outliers : 0.22 % Allowed : 6.32 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.05 (0.12), residues: 4292 helix: -0.48 (0.12), residues: 1553 sheet: -1.28 (0.22), residues: 531 loop : -2.05 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 336 TYR 0.016 0.002 TYR J 723 PHE 0.020 0.002 PHE A 184 TRP 0.028 0.002 TRP I 183 HIS 0.011 0.002 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00679 (36684) covalent geometry : angle 0.77625 (50114) hydrogen bonds : bond 0.05326 ( 1495) hydrogen bonds : angle 5.83432 ( 4094) metal coordination : bond 0.02021 ( 7) metal coordination : angle 6.45738 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 361 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8567 (tp) cc_final: 0.8251 (tp) REVERT: A 325 ASP cc_start: 0.8143 (p0) cc_final: 0.7753 (p0) REVERT: A 511 LEU cc_start: 0.8768 (tp) cc_final: 0.8508 (tp) REVERT: A 595 ASP cc_start: 0.8743 (m-30) cc_final: 0.8427 (m-30) REVERT: A 616 MET cc_start: 0.5930 (mtp) cc_final: 0.5718 (mtp) REVERT: A 682 MET cc_start: 0.4324 (ttm) cc_final: 0.3674 (mtt) REVERT: A 854 MET cc_start: 0.6261 (ppp) cc_final: 0.5988 (ppp) REVERT: A 922 MET cc_start: 0.5378 (tpt) cc_final: 0.5006 (tpt) REVERT: A 1124 ASP cc_start: 0.7520 (p0) cc_final: 0.7316 (p0) REVERT: G 131 CYS cc_start: 0.8766 (p) cc_final: 0.8547 (p) REVERT: H 25 LYS cc_start: 0.9265 (mtmt) cc_final: 0.8737 (mtpp) REVERT: H 142 MET cc_start: 0.7204 (ppp) cc_final: 0.6858 (ppp) REVERT: I 14 ASP cc_start: 0.8384 (t70) cc_final: 0.8106 (t0) REVERT: I 65 ASN cc_start: 0.8821 (m-40) cc_final: 0.8455 (t0) REVERT: I 81 ASP cc_start: 0.7418 (p0) cc_final: 0.6980 (p0) REVERT: I 160 ASP cc_start: 0.9081 (m-30) cc_final: 0.8078 (p0) REVERT: I 492 MET cc_start: 0.8604 (pmm) cc_final: 0.8266 (pmm) REVERT: I 653 MET cc_start: 0.7219 (tmm) cc_final: 0.6975 (tmm) REVERT: I 684 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.9019 (m-40) REVERT: I 704 MET cc_start: 0.8823 (mmm) cc_final: 0.8362 (mmm) REVERT: I 741 MET cc_start: 0.7686 (mtp) cc_final: 0.7308 (mtp) REVERT: I 785 ASP cc_start: 0.8724 (m-30) cc_final: 0.8483 (m-30) REVERT: I 1243 MET cc_start: 0.9245 (tmm) cc_final: 0.8963 (tmm) REVERT: I 1319 MET cc_start: 0.8927 (tmm) cc_final: 0.8566 (tmm) REVERT: J 252 LEU cc_start: 0.8392 (tp) cc_final: 0.8117 (tp) REVERT: J 329 ASP cc_start: 0.8406 (m-30) cc_final: 0.8122 (m-30) REVERT: J 500 ILE cc_start: 0.8670 (mt) cc_final: 0.8361 (tp) REVERT: J 697 MET cc_start: 0.8462 (tmm) cc_final: 0.8065 (tmm) REVERT: J 724 MET cc_start: 0.9413 (mtm) cc_final: 0.8817 (mtp) REVERT: J 826 ILE cc_start: 0.7859 (mm) cc_final: 0.7579 (mm) REVERT: J 1203 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7054 (ttt90) REVERT: J 1334 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8501 (tm-30) REVERT: K 65 ASP cc_start: 0.8784 (m-30) cc_final: 0.8564 (m-30) REVERT: K 69 ARG cc_start: 0.8782 (mpp-170) cc_final: 0.8409 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 367 average time/residue: 0.2073 time to fit residues: 130.9758 Evaluate side-chains 274 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 270 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 352 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 389 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 345 optimal weight: 0.2980 chunk 378 optimal weight: 7.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 HIS ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1108 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.067561 restraints weight = 176017.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.069044 restraints weight = 98200.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070060 restraints weight = 65767.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070588 restraints weight = 50702.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071029 restraints weight = 43397.558| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 36691 Z= 0.205 Angle : 0.668 10.796 50120 Z= 0.352 Chirality : 0.044 0.197 5731 Planarity : 0.005 0.071 6171 Dihedral : 16.654 178.590 5964 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.12), residues: 4292 helix: -0.22 (0.13), residues: 1553 sheet: -1.15 (0.23), residues: 504 loop : -1.97 (0.12), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 3 TYR 0.023 0.002 TYR I1229 PHE 0.021 0.002 PHE A 227 TRP 0.030 0.002 TRP I 183 HIS 0.008 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00443 (36684) covalent geometry : angle 0.66689 (50114) hydrogen bonds : bond 0.04498 ( 1495) hydrogen bonds : angle 5.49661 ( 4094) metal coordination : bond 0.00877 ( 7) metal coordination : angle 4.24398 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8554 (tp) cc_final: 0.8309 (tp) REVERT: A 325 ASP cc_start: 0.8076 (p0) cc_final: 0.7615 (p0) REVERT: A 511 LEU cc_start: 0.8632 (tp) cc_final: 0.8148 (tp) REVERT: A 595 ASP cc_start: 0.8624 (m-30) cc_final: 0.8291 (m-30) REVERT: A 682 MET cc_start: 0.3332 (ttm) cc_final: 0.1424 (tmm) REVERT: A 854 MET cc_start: 0.6209 (ppp) cc_final: 0.5899 (ppp) REVERT: A 976 MET cc_start: 0.9123 (mmp) cc_final: 0.8913 (mmm) REVERT: A 1037 ASN cc_start: 0.9173 (m110) cc_final: 0.8959 (m110) REVERT: G 131 CYS cc_start: 0.8907 (p) cc_final: 0.8503 (p) REVERT: G 145 LYS cc_start: 0.8371 (tttm) cc_final: 0.7958 (tttp) REVERT: H 142 MET cc_start: 0.7053 (ppp) cc_final: 0.6776 (ppp) REVERT: I 14 ASP cc_start: 0.8401 (t70) cc_final: 0.8158 (t0) REVERT: I 160 ASP cc_start: 0.9077 (m-30) cc_final: 0.8061 (p0) REVERT: I 492 MET cc_start: 0.8607 (pmm) cc_final: 0.8401 (pmm) REVERT: I 704 MET cc_start: 0.8707 (mmm) cc_final: 0.8214 (mmm) REVERT: I 785 ASP cc_start: 0.8868 (m-30) cc_final: 0.8621 (m-30) REVERT: I 1180 MET cc_start: 0.9038 (tmm) cc_final: 0.8789 (tmm) REVERT: I 1319 MET cc_start: 0.8802 (tmm) cc_final: 0.8461 (tmm) REVERT: J 56 LEU cc_start: 0.8466 (tp) cc_final: 0.8261 (tp) REVERT: J 69 GLU cc_start: 0.7966 (tt0) cc_final: 0.7304 (tm-30) REVERT: J 252 LEU cc_start: 0.8327 (tp) cc_final: 0.8045 (tp) REVERT: J 325 LYS cc_start: 0.9315 (mppt) cc_final: 0.9027 (mppt) REVERT: J 329 ASP cc_start: 0.8372 (m-30) cc_final: 0.8056 (m-30) REVERT: J 544 LEU cc_start: 0.9508 (tp) cc_final: 0.9304 (tp) REVERT: J 724 MET cc_start: 0.9400 (mtm) cc_final: 0.8947 (mtp) REVERT: J 785 ASP cc_start: 0.8317 (t70) cc_final: 0.8089 (t70) REVERT: J 869 CYS cc_start: 0.9573 (m) cc_final: 0.9350 (m) REVERT: J 915 ILE cc_start: 0.9279 (pt) cc_final: 0.8748 (mp) REVERT: J 932 MET cc_start: 0.6474 (mtp) cc_final: 0.6235 (mtt) REVERT: J 1203 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7063 (ttt90) REVERT: J 1305 ASP cc_start: 0.7847 (m-30) cc_final: 0.7638 (m-30) REVERT: J 1334 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8463 (tm-30) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2035 time to fit residues: 134.0672 Evaluate side-chains 283 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 400 optimal weight: 10.0000 chunk 242 optimal weight: 0.6980 chunk 295 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 333 optimal weight: 1.9990 chunk 419 optimal weight: 6.9990 chunk 307 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 410 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 908 HIS ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 761 GLN I 799 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1114 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.087392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069696 restraints weight = 174917.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071244 restraints weight = 96689.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072263 restraints weight = 64682.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.072867 restraints weight = 49426.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073194 restraints weight = 41765.869| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36691 Z= 0.135 Angle : 0.611 10.842 50120 Z= 0.320 Chirality : 0.043 0.174 5731 Planarity : 0.004 0.066 6171 Dihedral : 16.443 177.498 5964 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.55 % Favored : 93.43 % Rotamer: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4292 helix: 0.15 (0.13), residues: 1547 sheet: -0.99 (0.24), residues: 491 loop : -1.82 (0.13), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 69 TYR 0.018 0.001 TYR I1229 PHE 0.014 0.001 PHE A 265 TRP 0.019 0.001 TRP I 183 HIS 0.004 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00298 (36684) covalent geometry : angle 0.60977 (50114) hydrogen bonds : bond 0.03937 ( 1495) hydrogen bonds : angle 5.11371 ( 4094) metal coordination : bond 0.00500 ( 7) metal coordination : angle 3.51124 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 404 time to evaluate : 1.353 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 44 LEU cc_start: 0.8546 (tp) cc_final: 0.8344 (tp) REVERT: A 70 LEU cc_start: 0.7453 (tp) cc_final: 0.7232 (tp) REVERT: A 325 ASP cc_start: 0.8076 (p0) cc_final: 0.7661 (p0) REVERT: A 511 LEU cc_start: 0.8474 (tp) cc_final: 0.8020 (tp) REVERT: A 595 ASP cc_start: 0.8537 (m-30) cc_final: 0.8167 (m-30) REVERT: A 682 MET cc_start: 0.3285 (ttm) cc_final: 0.1103 (tmm) REVERT: A 854 MET cc_start: 0.6232 (ppp) cc_final: 0.5892 (ppp) REVERT: A 922 MET cc_start: 0.5143 (tpt) cc_final: 0.4769 (tpt) REVERT: A 976 MET cc_start: 0.9162 (mmp) cc_final: 0.8837 (mmm) REVERT: A 1037 ASN cc_start: 0.9113 (m110) cc_final: 0.8898 (m110) REVERT: G 131 CYS cc_start: 0.8596 (p) cc_final: 0.8326 (p) REVERT: H 142 MET cc_start: 0.7015 (ppp) cc_final: 0.6722 (ppp) REVERT: H 188 GLU cc_start: 0.8885 (pt0) cc_final: 0.8432 (pm20) REVERT: I 14 ASP cc_start: 0.8327 (t70) cc_final: 0.8105 (t0) REVERT: I 65 ASN cc_start: 0.8739 (m-40) cc_final: 0.8362 (t0) REVERT: I 158 ASP cc_start: 0.8830 (t0) cc_final: 0.8514 (t70) REVERT: I 160 ASP cc_start: 0.9026 (m-30) cc_final: 0.8107 (p0) REVERT: I 239 MET cc_start: 0.7365 (tmm) cc_final: 0.6989 (tmm) REVERT: I 704 MET cc_start: 0.8610 (mmm) cc_final: 0.8129 (mmm) REVERT: I 785 ASP cc_start: 0.8836 (m-30) cc_final: 0.8622 (m-30) REVERT: I 1114 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8469 (tm-30) REVERT: J 252 LEU cc_start: 0.8317 (tp) cc_final: 0.8005 (tp) REVERT: J 298 MET cc_start: 0.8435 (mmp) cc_final: 0.7544 (mtt) REVERT: J 325 LYS cc_start: 0.9328 (mppt) cc_final: 0.8954 (mtpp) REVERT: J 329 ASP cc_start: 0.8365 (m-30) cc_final: 0.8082 (m-30) REVERT: J 517 CYS cc_start: 0.8573 (t) cc_final: 0.8343 (t) REVERT: J 544 LEU cc_start: 0.9458 (tp) cc_final: 0.9142 (tp) REVERT: J 724 MET cc_start: 0.9400 (mtm) cc_final: 0.8875 (mtp) REVERT: J 785 ASP cc_start: 0.8195 (t70) cc_final: 0.7993 (t70) REVERT: J 826 ILE cc_start: 0.7911 (mm) cc_final: 0.7650 (mm) REVERT: J 869 CYS cc_start: 0.9529 (m) cc_final: 0.9292 (m) REVERT: J 915 ILE cc_start: 0.9280 (pt) cc_final: 0.8757 (mp) REVERT: J 932 MET cc_start: 0.6165 (mtp) cc_final: 0.5691 (mtt) REVERT: J 1278 GLU cc_start: 0.7271 (tt0) cc_final: 0.6989 (tt0) REVERT: J 1305 ASP cc_start: 0.7974 (m-30) cc_final: 0.7727 (m-30) REVERT: J 1334 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8388 (tm-30) REVERT: K 26 ARG cc_start: 0.8530 (tpt170) cc_final: 0.7601 (tpt170) REVERT: K 30 MET cc_start: 0.7859 (mpp) cc_final: 0.6630 (mpp) outliers start: 1 outliers final: 0 residues processed: 404 average time/residue: 0.2154 time to fit residues: 148.1512 Evaluate side-chains 295 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 392 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 209 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 430 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 304 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.085943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068285 restraints weight = 176601.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069833 restraints weight = 117085.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.070728 restraints weight = 69355.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071806 restraints weight = 52453.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071785 restraints weight = 43978.104| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36691 Z= 0.204 Angle : 0.653 11.141 50120 Z= 0.343 Chirality : 0.043 0.195 5731 Planarity : 0.005 0.072 6171 Dihedral : 16.365 176.531 5964 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.25 % Favored : 92.73 % Rotamer: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.12), residues: 4292 helix: 0.13 (0.13), residues: 1555 sheet: -0.97 (0.23), residues: 504 loop : -1.81 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 69 TYR 0.022 0.002 TYR H 185 PHE 0.022 0.002 PHE I 188 TRP 0.017 0.002 TRP I 183 HIS 0.006 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00443 (36684) covalent geometry : angle 0.65219 (50114) hydrogen bonds : bond 0.04140 ( 1495) hydrogen bonds : angle 5.18370 ( 4094) metal coordination : bond 0.00835 ( 7) metal coordination : angle 3.80757 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8606 (tp) cc_final: 0.8334 (tp) REVERT: A 325 ASP cc_start: 0.8083 (p0) cc_final: 0.7604 (p0) REVERT: A 511 LEU cc_start: 0.8732 (tp) cc_final: 0.8336 (tp) REVERT: A 595 ASP cc_start: 0.8537 (m-30) cc_final: 0.8183 (m-30) REVERT: A 682 MET cc_start: 0.3382 (ttm) cc_final: 0.1341 (tmm) REVERT: A 854 MET cc_start: 0.6426 (ppp) cc_final: 0.6039 (ppp) REVERT: A 922 MET cc_start: 0.5295 (tpt) cc_final: 0.4988 (tpt) REVERT: A 976 MET cc_start: 0.9131 (mmp) cc_final: 0.8761 (mmt) REVERT: A 1037 ASN cc_start: 0.9087 (m110) cc_final: 0.8865 (m110) REVERT: G 131 CYS cc_start: 0.8635 (p) cc_final: 0.8367 (p) REVERT: H 142 MET cc_start: 0.7158 (ppp) cc_final: 0.6946 (ppp) REVERT: I 14 ASP cc_start: 0.8320 (t70) cc_final: 0.8115 (t0) REVERT: I 65 ASN cc_start: 0.8872 (m-40) cc_final: 0.8400 (t0) REVERT: I 158 ASP cc_start: 0.9019 (t0) cc_final: 0.8686 (t70) REVERT: I 160 ASP cc_start: 0.9065 (m-30) cc_final: 0.8221 (p0) REVERT: I 239 MET cc_start: 0.7563 (tmm) cc_final: 0.7199 (tmm) REVERT: I 465 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7854 (tmt170) REVERT: I 618 GLN cc_start: 0.7614 (tt0) cc_final: 0.6964 (tt0) REVERT: I 704 MET cc_start: 0.8609 (mmm) cc_final: 0.8143 (mmm) REVERT: I 741 MET cc_start: 0.7378 (mtp) cc_final: 0.7119 (mpp) REVERT: I 785 ASP cc_start: 0.8865 (m-30) cc_final: 0.8638 (m-30) REVERT: I 817 LEU cc_start: 0.9277 (tp) cc_final: 0.9068 (tp) REVERT: I 1319 MET cc_start: 0.8661 (tmm) cc_final: 0.8216 (tmm) REVERT: J 115 TRP cc_start: 0.8779 (m-10) cc_final: 0.8572 (m-10) REVERT: J 252 LEU cc_start: 0.8369 (tp) cc_final: 0.8033 (tp) REVERT: J 325 LYS cc_start: 0.9372 (mppt) cc_final: 0.9033 (mtpp) REVERT: J 329 ASP cc_start: 0.8286 (m-30) cc_final: 0.7935 (m-30) REVERT: J 517 CYS cc_start: 0.8501 (t) cc_final: 0.8247 (t) REVERT: J 544 LEU cc_start: 0.9465 (tp) cc_final: 0.9152 (tp) REVERT: J 644 MET cc_start: 0.7603 (pmm) cc_final: 0.7281 (pmm) REVERT: J 724 MET cc_start: 0.9394 (mtm) cc_final: 0.8859 (mtt) REVERT: J 785 ASP cc_start: 0.8178 (t70) cc_final: 0.7931 (t70) REVERT: J 826 ILE cc_start: 0.7985 (mm) cc_final: 0.7749 (mm) REVERT: J 869 CYS cc_start: 0.9539 (m) cc_final: 0.9297 (m) REVERT: J 915 ILE cc_start: 0.9291 (pt) cc_final: 0.8853 (mp) REVERT: J 932 MET cc_start: 0.6121 (mtp) cc_final: 0.5698 (mtt) REVERT: J 1305 ASP cc_start: 0.7762 (m-30) cc_final: 0.7544 (m-30) REVERT: J 1334 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8448 (tm-30) REVERT: K 69 ARG cc_start: 0.8741 (mpp-170) cc_final: 0.8417 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.2104 time to fit residues: 136.6015 Evaluate side-chains 291 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 270 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 80 optimal weight: 50.0000 chunk 346 optimal weight: 4.9990 chunk 198 optimal weight: 0.0980 chunk 200 optimal weight: 8.9990 chunk 297 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.084944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.067181 restraints weight = 179125.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.068667 restraints weight = 101222.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.069509 restraints weight = 68622.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070148 restraints weight = 53813.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.070541 restraints weight = 45676.715| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 36691 Z= 0.233 Angle : 0.689 12.229 50120 Z= 0.359 Chirality : 0.044 0.201 5731 Planarity : 0.005 0.079 6171 Dihedral : 16.375 176.362 5964 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.67 % Favored : 92.31 % Rotamer: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.12), residues: 4292 helix: 0.06 (0.13), residues: 1558 sheet: -1.15 (0.23), residues: 530 loop : -1.80 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 69 TYR 0.018 0.002 TYR I1229 PHE 0.028 0.002 PHE A 184 TRP 0.016 0.002 TRP I 183 HIS 0.006 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00501 (36684) covalent geometry : angle 0.68552 (50114) hydrogen bonds : bond 0.04329 ( 1495) hydrogen bonds : angle 5.28698 ( 4094) metal coordination : bond 0.02424 ( 7) metal coordination : angle 6.40187 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8542 (tp) cc_final: 0.8262 (tp) REVERT: A 70 LEU cc_start: 0.7486 (tp) cc_final: 0.7246 (tp) REVERT: A 325 ASP cc_start: 0.7899 (p0) cc_final: 0.7354 (p0) REVERT: A 511 LEU cc_start: 0.8547 (tp) cc_final: 0.8059 (tp) REVERT: A 595 ASP cc_start: 0.8512 (m-30) cc_final: 0.8162 (m-30) REVERT: A 682 MET cc_start: 0.3303 (ttm) cc_final: 0.1565 (tmm) REVERT: A 854 MET cc_start: 0.5528 (ppp) cc_final: 0.5168 (ppp) REVERT: A 976 MET cc_start: 0.9140 (mmp) cc_final: 0.8878 (mmm) REVERT: A 1037 ASN cc_start: 0.8970 (m110) cc_final: 0.8732 (m110) REVERT: G 131 CYS cc_start: 0.8639 (p) cc_final: 0.8391 (p) REVERT: I 158 ASP cc_start: 0.8844 (t0) cc_final: 0.8499 (t70) REVERT: I 160 ASP cc_start: 0.8999 (m-30) cc_final: 0.8267 (p0) REVERT: I 239 MET cc_start: 0.7540 (tmm) cc_final: 0.7194 (tmm) REVERT: I 504 GLU cc_start: 0.8492 (pp20) cc_final: 0.8273 (pp20) REVERT: I 618 GLN cc_start: 0.7742 (tt0) cc_final: 0.7340 (tt0) REVERT: I 704 MET cc_start: 0.8569 (mmm) cc_final: 0.8069 (mmm) REVERT: I 1319 MET cc_start: 0.8668 (tmm) cc_final: 0.8391 (tmm) REVERT: J 115 TRP cc_start: 0.8859 (m-10) cc_final: 0.8652 (m-10) REVERT: J 252 LEU cc_start: 0.8214 (tp) cc_final: 0.7871 (tp) REVERT: J 325 LYS cc_start: 0.9427 (mppt) cc_final: 0.9082 (mtpp) REVERT: J 329 ASP cc_start: 0.8291 (m-30) cc_final: 0.7959 (m-30) REVERT: J 644 MET cc_start: 0.7602 (pmm) cc_final: 0.7386 (pmm) REVERT: J 724 MET cc_start: 0.9372 (mtm) cc_final: 0.8944 (mtp) REVERT: J 826 ILE cc_start: 0.7943 (mm) cc_final: 0.7706 (mm) REVERT: J 869 CYS cc_start: 0.9507 (m) cc_final: 0.9284 (m) REVERT: J 1334 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8383 (tm-30) outliers start: 1 outliers final: 0 residues processed: 370 average time/residue: 0.2093 time to fit residues: 132.1181 Evaluate side-chains 274 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 40 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 412 optimal weight: 5.9990 chunk 53 optimal weight: 40.0000 chunk 329 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 350 optimal weight: 5.9990 chunk 420 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 436 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN ** I 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 761 GLN I 799 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.085319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.068681 restraints weight = 178464.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069725 restraints weight = 101784.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070557 restraints weight = 64753.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.070671 restraints weight = 54758.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.070911 restraints weight = 49489.619| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 36691 Z= 0.211 Angle : 0.669 11.084 50120 Z= 0.349 Chirality : 0.044 0.211 5731 Planarity : 0.005 0.075 6171 Dihedral : 16.365 176.283 5964 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.69 % Favored : 92.29 % Rotamer: Outliers : 0.06 % Allowed : 1.87 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.12), residues: 4292 helix: 0.13 (0.13), residues: 1548 sheet: -1.23 (0.22), residues: 545 loop : -1.76 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 3 TYR 0.024 0.002 TYR J 512 PHE 0.024 0.002 PHE A 184 TRP 0.012 0.001 TRP I 183 HIS 0.006 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00457 (36684) covalent geometry : angle 0.66605 (50114) hydrogen bonds : bond 0.04196 ( 1495) hydrogen bonds : angle 5.22977 ( 4094) metal coordination : bond 0.01275 ( 7) metal coordination : angle 5.76890 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8546 (tp) cc_final: 0.8249 (tp) REVERT: A 325 ASP cc_start: 0.7853 (p0) cc_final: 0.7330 (p0) REVERT: A 426 MET cc_start: 0.6546 (mmt) cc_final: 0.6085 (mmt) REVERT: A 511 LEU cc_start: 0.8394 (tp) cc_final: 0.7757 (tp) REVERT: A 595 ASP cc_start: 0.8493 (m-30) cc_final: 0.8152 (m-30) REVERT: A 682 MET cc_start: 0.3237 (ttm) cc_final: 0.1566 (tmm) REVERT: A 976 MET cc_start: 0.9072 (mmp) cc_final: 0.8859 (mmm) REVERT: A 1037 ASN cc_start: 0.8950 (m110) cc_final: 0.8714 (m110) REVERT: G 131 CYS cc_start: 0.8585 (p) cc_final: 0.8344 (p) REVERT: H 25 LYS cc_start: 0.9313 (mtpt) cc_final: 0.8786 (mtpp) REVERT: H 41 ASN cc_start: 0.8829 (t0) cc_final: 0.8537 (t0) REVERT: I 14 ASP cc_start: 0.8209 (t0) cc_final: 0.8004 (t0) REVERT: I 158 ASP cc_start: 0.9075 (t0) cc_final: 0.8691 (t70) REVERT: I 160 ASP cc_start: 0.9000 (m-30) cc_final: 0.8277 (p0) REVERT: I 239 MET cc_start: 0.7544 (tmm) cc_final: 0.7201 (tmm) REVERT: I 504 GLU cc_start: 0.8616 (pp20) cc_final: 0.8403 (pp20) REVERT: I 618 GLN cc_start: 0.7674 (tt0) cc_final: 0.7188 (tt0) REVERT: I 704 MET cc_start: 0.8550 (mmm) cc_final: 0.8056 (mmm) REVERT: I 1319 MET cc_start: 0.8659 (tmm) cc_final: 0.8456 (tmm) REVERT: J 115 TRP cc_start: 0.8902 (m-10) cc_final: 0.8699 (m-10) REVERT: J 252 LEU cc_start: 0.8225 (tp) cc_final: 0.7874 (tp) REVERT: J 325 LYS cc_start: 0.9412 (mppt) cc_final: 0.9051 (mtpp) REVERT: J 329 ASP cc_start: 0.8319 (m-30) cc_final: 0.7973 (m-30) REVERT: J 544 LEU cc_start: 0.9435 (tp) cc_final: 0.9164 (tp) REVERT: J 724 MET cc_start: 0.9360 (mtm) cc_final: 0.8902 (mtp) REVERT: J 826 ILE cc_start: 0.7988 (mm) cc_final: 0.7766 (mm) REVERT: J 869 CYS cc_start: 0.9509 (m) cc_final: 0.9285 (m) REVERT: J 1049 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7947 (pp30) REVERT: J 1334 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8370 (tm-30) REVERT: K 65 ASP cc_start: 0.8797 (m-30) cc_final: 0.8539 (m-30) REVERT: K 69 ARG cc_start: 0.8717 (mpp-170) cc_final: 0.8317 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 357 average time/residue: 0.2086 time to fit residues: 127.5480 Evaluate side-chains 282 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 312 optimal weight: 10.0000 chunk 399 optimal weight: 6.9990 chunk 332 optimal weight: 1.9990 chunk 345 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 83 optimal weight: 50.0000 chunk 67 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 319 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068570 restraints weight = 178650.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070025 restraints weight = 121909.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070808 restraints weight = 72592.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071705 restraints weight = 56308.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071637 restraints weight = 50602.819| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36691 Z= 0.176 Angle : 0.657 11.313 50120 Z= 0.342 Chirality : 0.044 0.197 5731 Planarity : 0.005 0.073 6171 Dihedral : 16.310 175.659 5964 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.15 % Favored : 92.82 % Rotamer: Outliers : 0.06 % Allowed : 0.98 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 4292 helix: 0.23 (0.13), residues: 1546 sheet: -1.13 (0.22), residues: 541 loop : -1.69 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 3 TYR 0.030 0.001 TYR I1229 PHE 0.025 0.002 PHE I 514 TRP 0.018 0.001 TRP A 676 HIS 0.005 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00385 (36684) covalent geometry : angle 0.65433 (50114) hydrogen bonds : bond 0.03999 ( 1495) hydrogen bonds : angle 5.13014 ( 4094) metal coordination : bond 0.01398 ( 7) metal coordination : angle 5.17889 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 369 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8497 (tp) cc_final: 0.8211 (tp) REVERT: A 70 LEU cc_start: 0.7420 (tp) cc_final: 0.7150 (tp) REVERT: A 325 ASP cc_start: 0.7692 (p0) cc_final: 0.7253 (p0) REVERT: A 426 MET cc_start: 0.6311 (mmt) cc_final: 0.5835 (mmt) REVERT: A 511 LEU cc_start: 0.8339 (tp) cc_final: 0.7755 (tp) REVERT: A 595 ASP cc_start: 0.8480 (m-30) cc_final: 0.8144 (m-30) REVERT: A 682 MET cc_start: 0.3210 (ttm) cc_final: 0.1236 (tmm) REVERT: A 765 MET cc_start: 0.7730 (ptt) cc_final: 0.7371 (ptp) REVERT: A 922 MET cc_start: 0.4849 (tpt) cc_final: 0.4331 (tpp) REVERT: A 976 MET cc_start: 0.9125 (mmp) cc_final: 0.8915 (mmm) REVERT: A 1037 ASN cc_start: 0.8934 (m110) cc_final: 0.8687 (m110) REVERT: G 131 CYS cc_start: 0.8701 (p) cc_final: 0.8329 (p) REVERT: H 25 LYS cc_start: 0.9318 (mtpt) cc_final: 0.8827 (mtpp) REVERT: H 41 ASN cc_start: 0.8877 (t0) cc_final: 0.8552 (t0) REVERT: H 200 LYS cc_start: 0.9023 (tmmt) cc_final: 0.8538 (tmmt) REVERT: I 14 ASP cc_start: 0.8294 (t0) cc_final: 0.8069 (t0) REVERT: I 158 ASP cc_start: 0.9043 (t0) cc_final: 0.8667 (t70) REVERT: I 160 ASP cc_start: 0.9016 (m-30) cc_final: 0.8255 (p0) REVERT: I 239 MET cc_start: 0.7542 (tmm) cc_final: 0.7169 (tmm) REVERT: I 414 ILE cc_start: 0.9096 (pt) cc_final: 0.8795 (mm) REVERT: I 504 GLU cc_start: 0.8637 (pp20) cc_final: 0.8410 (pp20) REVERT: I 618 GLN cc_start: 0.7768 (tt0) cc_final: 0.7296 (tt0) REVERT: I 704 MET cc_start: 0.8550 (mmm) cc_final: 0.8059 (mmm) REVERT: J 252 LEU cc_start: 0.8225 (tp) cc_final: 0.7888 (tp) REVERT: J 298 MET cc_start: 0.8482 (mmp) cc_final: 0.7596 (mtt) REVERT: J 325 LYS cc_start: 0.9380 (mppt) cc_final: 0.9077 (mtpp) REVERT: J 329 ASP cc_start: 0.8315 (m-30) cc_final: 0.7969 (m-30) REVERT: J 330 MET cc_start: 0.7985 (mmm) cc_final: 0.7406 (mmp) REVERT: J 375 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8569 (tm-30) REVERT: J 544 LEU cc_start: 0.9419 (tp) cc_final: 0.9179 (tp) REVERT: J 724 MET cc_start: 0.9326 (mtm) cc_final: 0.8798 (mtp) REVERT: J 826 ILE cc_start: 0.8014 (mm) cc_final: 0.7769 (mm) REVERT: J 869 CYS cc_start: 0.9518 (m) cc_final: 0.9269 (m) REVERT: J 915 ILE cc_start: 0.9342 (pt) cc_final: 0.8946 (mp) REVERT: J 1040 MET cc_start: -0.0371 (tpp) cc_final: -0.0621 (tpp) REVERT: J 1049 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7907 (pp30) REVERT: J 1278 GLU cc_start: 0.7386 (tt0) cc_final: 0.7084 (tt0) REVERT: J 1334 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8344 (tm-30) outliers start: 2 outliers final: 0 residues processed: 369 average time/residue: 0.2188 time to fit residues: 137.2022 Evaluate side-chains 286 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 187 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 365 optimal weight: 5.9990 chunk 331 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 421 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 GLN I 799 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 HIS K 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.088282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070685 restraints weight = 176467.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072210 restraints weight = 97800.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.073280 restraints weight = 65790.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073844 restraints weight = 49973.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.074287 restraints weight = 42594.062| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36691 Z= 0.127 Angle : 0.626 11.787 50120 Z= 0.323 Chirality : 0.043 0.193 5731 Planarity : 0.004 0.070 6171 Dihedral : 16.189 174.316 5964 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.10 % Favored : 93.87 % Rotamer: Outliers : 0.06 % Allowed : 0.36 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4292 helix: 0.44 (0.13), residues: 1551 sheet: -0.98 (0.23), residues: 506 loop : -1.64 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 69 TYR 0.026 0.001 TYR H 185 PHE 0.025 0.001 PHE I 514 TRP 0.016 0.001 TRP J 580 HIS 0.004 0.001 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00280 (36684) covalent geometry : angle 0.62441 (50114) hydrogen bonds : bond 0.03635 ( 1495) hydrogen bonds : angle 4.89230 ( 4094) metal coordination : bond 0.00838 ( 7) metal coordination : angle 4.53059 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8584 Ramachandran restraints generated. 4292 Oldfield, 0 Emsley, 4292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 391 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8654 (tp) cc_final: 0.8391 (tp) REVERT: A 325 ASP cc_start: 0.7791 (p0) cc_final: 0.7396 (p0) REVERT: A 426 MET cc_start: 0.5748 (mmt) cc_final: 0.5401 (mmt) REVERT: A 511 LEU cc_start: 0.8358 (tp) cc_final: 0.7887 (tp) REVERT: A 595 ASP cc_start: 0.8551 (m-30) cc_final: 0.8232 (m-30) REVERT: A 682 MET cc_start: 0.3194 (ttm) cc_final: 0.1184 (tmm) REVERT: A 922 MET cc_start: 0.5521 (tpt) cc_final: 0.4997 (tpp) REVERT: A 975 TYR cc_start: 0.8249 (t80) cc_final: 0.7794 (t80) REVERT: A 976 MET cc_start: 0.9227 (mmp) cc_final: 0.8616 (mmm) REVERT: A 1037 ASN cc_start: 0.9086 (m110) cc_final: 0.8842 (m110) REVERT: H 25 LYS cc_start: 0.9304 (mtpt) cc_final: 0.8803 (mtpp) REVERT: H 41 ASN cc_start: 0.8957 (t0) cc_final: 0.8729 (t0) REVERT: H 200 LYS cc_start: 0.8902 (tmmt) cc_final: 0.8258 (tmmt) REVERT: I 14 ASP cc_start: 0.8380 (t0) cc_final: 0.8139 (t0) REVERT: I 65 ASN cc_start: 0.8721 (m-40) cc_final: 0.8237 (t0) REVERT: I 160 ASP cc_start: 0.9033 (m-30) cc_final: 0.8199 (p0) REVERT: I 239 MET cc_start: 0.7494 (tmm) cc_final: 0.7130 (tmm) REVERT: I 414 ILE cc_start: 0.9103 (pt) cc_final: 0.8795 (mm) REVERT: I 504 GLU cc_start: 0.8674 (pp20) cc_final: 0.8426 (pp20) REVERT: I 618 GLN cc_start: 0.7660 (tt0) cc_final: 0.7197 (tt0) REVERT: I 704 MET cc_start: 0.8493 (mmm) cc_final: 0.8021 (mmm) REVERT: I 785 ASP cc_start: 0.8744 (m-30) cc_final: 0.8532 (m-30) REVERT: I 824 GLN cc_start: 0.9117 (tt0) cc_final: 0.8788 (tt0) REVERT: I 1243 MET cc_start: 0.9107 (tmm) cc_final: 0.8722 (tmm) REVERT: I 1319 MET cc_start: 0.8447 (tmm) cc_final: 0.8104 (tmm) REVERT: I 1321 GLU cc_start: 0.7562 (mp0) cc_final: 0.7270 (mp0) REVERT: J 252 LEU cc_start: 0.8322 (tp) cc_final: 0.8041 (tp) REVERT: J 298 MET cc_start: 0.8502 (mmp) cc_final: 0.7542 (mtt) REVERT: J 325 LYS cc_start: 0.9321 (mppt) cc_final: 0.9075 (mtpp) REVERT: J 329 ASP cc_start: 0.8315 (m-30) cc_final: 0.7996 (m-30) REVERT: J 330 MET cc_start: 0.8082 (mmm) cc_final: 0.7696 (mmp) REVERT: J 517 CYS cc_start: 0.8509 (t) cc_final: 0.8272 (t) REVERT: J 544 LEU cc_start: 0.9461 (tp) cc_final: 0.9200 (tp) REVERT: J 571 ASP cc_start: 0.8324 (p0) cc_final: 0.8041 (p0) REVERT: J 724 MET cc_start: 0.9386 (mtm) cc_final: 0.8675 (mtp) REVERT: J 826 ILE cc_start: 0.7880 (mm) cc_final: 0.7614 (mm) REVERT: J 869 CYS cc_start: 0.9512 (m) cc_final: 0.9115 (m) REVERT: J 870 ASP cc_start: 0.8963 (m-30) cc_final: 0.8478 (t0) REVERT: J 915 ILE cc_start: 0.9263 (pt) cc_final: 0.8856 (mp) REVERT: J 1040 MET cc_start: -0.0124 (tpp) cc_final: -0.0352 (tpp) REVERT: J 1049 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7918 (pp30) REVERT: J 1235 ASN cc_start: 0.9205 (t0) cc_final: 0.8900 (t0) REVERT: J 1278 GLU cc_start: 0.7164 (tt0) cc_final: 0.6963 (tt0) REVERT: J 1334 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8357 (tm-30) outliers start: 2 outliers final: 0 residues processed: 391 average time/residue: 0.2099 time to fit residues: 140.6983 Evaluate side-chains 298 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 317 optimal weight: 10.0000 chunk 326 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 435 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 409 optimal weight: 0.0870 chunk 232 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 overall best weight: 4.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.085794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068487 restraints weight = 176383.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069922 restraints weight = 121299.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070783 restraints weight = 70662.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071786 restraints weight = 53463.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071787 restraints weight = 46386.178| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 36691 Z= 0.210 Angle : 0.676 10.943 50120 Z= 0.351 Chirality : 0.044 0.207 5731 Planarity : 0.005 0.069 6171 Dihedral : 16.229 174.948 5964 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.43 % Favored : 92.54 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 4292 helix: 0.38 (0.13), residues: 1546 sheet: -1.01 (0.23), residues: 542 loop : -1.64 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 69 TYR 0.027 0.002 TYR I1229 PHE 0.039 0.002 PHE A 172 TRP 0.012 0.002 TRP I 183 HIS 0.009 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00456 (36684) covalent geometry : angle 0.67324 (50114) hydrogen bonds : bond 0.04041 ( 1495) hydrogen bonds : angle 5.07844 ( 4094) metal coordination : bond 0.01324 ( 7) metal coordination : angle 5.13699 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5657.33 seconds wall clock time: 99 minutes 7.27 seconds (5947.27 seconds total)