Starting phenix.real_space_refine on Tue Sep 15 05:55:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x26_21996/09_2026/6x26_21996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x26_21996/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6x26_21996/09_2026/6x26_21996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x26_21996/09_2026/6x26_21996.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6x26_21996/09_2026/6x26_21996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x26_21996/09_2026/6x26_21996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x26_21996/09_2026/6x26_21996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x26_21996/09_2026/6x26_21996.map" } 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): 0.28s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 7.97, per 1000 atoms: 0.22 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: 3.21 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: 4.55 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: 11.06 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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=" C3' DT P 115 " pdb=" O3' DT P 115 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" C3' DT P 106 " pdb=" C2' DT P 106 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+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 ... (remaining 36679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 49281 3.56 - 7.13: 746 7.13 - 10.69: 77 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=" O4' DC Q 211 " pdb=" C4' DC Q 211 " pdb=" C3' DC Q 211 " ideal model delta sigma weight residual 106.00 101.70 4.30 6.00e-01 2.78e+00 5.13e+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=" O4' DG P 112 " pdb=" C4' DG P 112 " pdb=" C3' DG P 112 " ideal model delta sigma weight residual 106.00 102.40 3.60 6.00e-01 2.78e+00 3.59e+01 ... (remaining 50109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 21262 35.40 - 70.79: 843 70.79 - 106.19: 39 106.19 - 141.59: 2 141.59 - 176.98: 1 Dihedral angle restraints: 22147 sinusoidal: 9727 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=" O5' A R 14 " pdb=" C5' A R 14 " pdb=" C4' A R 14 " pdb=" C3' A R 14 " ideal model delta sinusoidal sigma weight residual 180.00 147.85 32.15 3 6.40e+00 2.44e-02 2.90e+01 ... (remaining 22144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4992 0.091 - 0.181: 669 0.181 - 0.272: 57 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 44.840 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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= 0.416 Angle : 1.135 17.816 50120 Z= 0.671 Chirality : 0.062 0.453 5731 Planarity : 0.007 0.093 6171 Dihedral : 17.368 176.982 14139 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/Z covalent geometry : bond 0.00767 / 0.42 (36684) covalent geometry : angle 1.13258 / 0.67 (50114) hydrogen bonds : bond 0.15371 / 10.23 ( 1495) hydrogen bonds : angle 7.33347 / 5.25 ( 4094) metal coordination : bond 0.01900 / 1.48 ( 7) metal coordination : angle 7.15660 / 3.55 ( 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 : 1.739 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: 0.2073 time to fit residues: 135.8023 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 : 1.424 ------------------------------------------------------------------------------- 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: 50.0000 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... 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** ** A1107 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 = 0.3707 r_free = 0.3707 target = 0.086324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.069309 restraints weight = 178914.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070663 restraints weight = 107241.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.071338 restraints weight = 66511.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071931 restraints weight = 53209.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.071854 restraints weight = 49503.579| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 36691 Z= 0.189 Angle : 0.698 11.414 50120 Z= 0.372 Chirality : 0.046 0.289 5731 Planarity : 0.005 0.066 6171 Dihedral : 16.670 174.481 5930 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.75 % Rotamer: Outliers : 0.11 % Allowed : 5.76 % Favored : 94.13 % 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: -2.11 (0.12), residues: 4292 helix: -0.56 (0.12), residues: 1544 sheet: -1.18 (0.23), residues: 508 loop : -2.09 (0.12), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 193 TYR 0.016 0.002 TYR H 185 PHE 0.019 0.002 PHE A 184 TRP 0.010 0.001 TRP J 580 HIS 0.009 0.001 HIS A1110 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (36684) covalent geometry : angle 0.69762 / 0.37 (50114) hydrogen bonds : bond 0.05029 / 3.44 ( 1495) hydrogen bonds : angle 5.84438 / 4.17 ( 4094) metal coordination : bond 0.00598 / 0.46 ( 7) metal coordination : angle 2.92672 / 1.56 ( 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 374 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 370 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8306 (p0) cc_final: 0.8000 (p0) REVERT: A 511 LEU cc_start: 0.8717 (tp) cc_final: 0.8372 (tp) REVERT: A 854 MET cc_start: 0.6459 (ppp) cc_final: 0.6233 (ppp) REVERT: A 922 MET cc_start: 0.5638 (tpt) cc_final: 0.5136 (tpp) REVERT: A 1124 ASP cc_start: 0.7593 (p0) cc_final: 0.7382 (p0) REVERT: G 131 CYS cc_start: 0.8803 (p) cc_final: 0.8564 (p) REVERT: I 14 ASP cc_start: 0.8152 (t70) cc_final: 0.7791 (t0) REVERT: I 65 ASN cc_start: 0.8824 (m-40) cc_final: 0.8483 (t0) REVERT: I 160 ASP cc_start: 0.9061 (m-30) cc_final: 0.8039 (p0) REVERT: I 183 TRP cc_start: 0.8949 (m-10) cc_final: 0.8729 (m-10) REVERT: I 239 MET cc_start: 0.7612 (tmm) cc_final: 0.7405 (tmm) REVERT: I 704 MET cc_start: 0.8748 (mmm) cc_final: 0.8148 (mmm) REVERT: I 1243 MET cc_start: 0.9088 (tmm) cc_final: 0.8430 (tmm) REVERT: I 1319 MET cc_start: 0.8951 (tmm) cc_final: 0.8433 (tmm) REVERT: I 1321 GLU cc_start: 0.7299 (mp0) cc_final: 0.7098 (mp0) REVERT: J 252 LEU cc_start: 0.8375 (tp) cc_final: 0.8097 (tp) REVERT: J 329 ASP cc_start: 0.8500 (m-30) cc_final: 0.8253 (m-30) REVERT: J 466 MET cc_start: 0.8346 (mtp) cc_final: 0.8134 (mtp) REVERT: J 724 MET cc_start: 0.9387 (mtm) cc_final: 0.8746 (mtp) REVERT: J 826 ILE cc_start: 0.7839 (mm) cc_final: 0.7573 (mm) REVERT: J 869 CYS cc_start: 0.9599 (m) cc_final: 0.9393 (m) REVERT: J 1334 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8488 (tm-30) REVERT: J 1344 LEU cc_start: 0.8961 (mt) cc_final: 0.8704 (mp) outliers start: 4 outliers final: 1 residues processed: 373 average time/residue: 0.1950 time to fit residues: 127.0636 Evaluate side-chains 278 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 397 optimal weight: 2.9990 chunk 412 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 48 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.085514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.068207 restraints weight = 176709.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069686 restraints weight = 99352.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.070464 restraints weight = 58519.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070625 restraints weight = 49527.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070755 restraints weight = 44708.498| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 36691 Z= 0.208 Angle : 0.692 11.506 50120 Z= 0.364 Chirality : 0.045 0.316 5731 Planarity : 0.005 0.068 6171 Dihedral : 16.465 173.380 5930 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.01 % Favored : 92.96 % Rotamer: Outliers : 0.08 % Allowed : 4.67 % Favored : 95.25 % 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: -1.89 (0.12), residues: 4292 helix: -0.30 (0.13), residues: 1548 sheet: -1.07 (0.23), residues: 493 loop : -2.03 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 69 TYR 0.015 0.002 TYR A 572 PHE 0.017 0.002 PHE A 265 TRP 0.010 0.001 TRP J 580 HIS 0.007 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (36684) covalent geometry : angle 0.69029 / 0.36 (50114) hydrogen bonds : bond 0.04833 / 3.29 ( 1495) hydrogen bonds : angle 5.62331 / 4.01 ( 4094) metal coordination : bond 0.01425 / 1.16 ( 7) metal coordination : angle 4.43017 / 2.34 ( 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 387 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 384 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8473 (tp) cc_final: 0.8266 (tp) REVERT: A 325 ASP cc_start: 0.8268 (p0) cc_final: 0.7910 (p0) REVERT: A 511 LEU cc_start: 0.8790 (tp) cc_final: 0.8351 (tp) REVERT: A 595 ASP cc_start: 0.8695 (m-30) cc_final: 0.8355 (m-30) REVERT: A 616 MET cc_start: 0.5903 (mtp) cc_final: 0.5698 (mtp) REVERT: A 854 MET cc_start: 0.6315 (ppp) cc_final: 0.6064 (ppp) REVERT: A 922 MET cc_start: 0.5460 (tpt) cc_final: 0.4842 (tpt) REVERT: A 1124 ASP cc_start: 0.7677 (p0) cc_final: 0.7440 (p0) REVERT: G 131 CYS cc_start: 0.8778 (p) cc_final: 0.8508 (p) REVERT: H 142 MET cc_start: 0.7361 (ppp) cc_final: 0.7087 (ppp) REVERT: I 14 ASP cc_start: 0.8217 (t70) cc_final: 0.7886 (t0) REVERT: I 65 ASN cc_start: 0.8919 (m-40) cc_final: 0.8510 (t0) REVERT: I 160 ASP cc_start: 0.9081 (m-30) cc_final: 0.8054 (p0) REVERT: I 183 TRP cc_start: 0.8953 (m-10) cc_final: 0.8687 (m-10) REVERT: I 239 MET cc_start: 0.7559 (tmm) cc_final: 0.7122 (tmm) REVERT: I 492 MET cc_start: 0.8637 (pmm) cc_final: 0.8431 (pmm) REVERT: I 653 MET cc_start: 0.7305 (tmm) cc_final: 0.6963 (tmm) REVERT: I 654 ASP cc_start: 0.8353 (m-30) cc_final: 0.8092 (m-30) REVERT: I 684 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8812 (m-40) REVERT: I 704 MET cc_start: 0.8724 (mmm) cc_final: 0.8266 (mmm) REVERT: I 785 ASP cc_start: 0.8682 (m-30) cc_final: 0.8470 (m-30) REVERT: I 1243 MET cc_start: 0.9018 (tmm) cc_final: 0.8426 (tmm) REVERT: I 1319 MET cc_start: 0.8945 (tmm) cc_final: 0.8583 (tmm) REVERT: J 252 LEU cc_start: 0.8346 (tp) cc_final: 0.8049 (tp) REVERT: J 329 ASP cc_start: 0.8419 (m-30) cc_final: 0.8089 (m-30) REVERT: J 697 MET cc_start: 0.8360 (tmm) cc_final: 0.8142 (ppp) REVERT: J 724 MET cc_start: 0.9376 (mtm) cc_final: 0.8731 (mtp) REVERT: J 743 MET cc_start: 0.7706 (tmm) cc_final: 0.7458 (tmm) REVERT: J 826 ILE cc_start: 0.7808 (mm) cc_final: 0.7583 (mm) REVERT: J 1203 ARG cc_start: 0.7464 (ttp80) cc_final: 0.6774 (mmt180) REVERT: J 1334 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8472 (tm-30) REVERT: K 26 ARG cc_start: 0.8766 (tpt170) cc_final: 0.8491 (tpt170) REVERT: K 69 ARG cc_start: 0.8720 (mpp-170) cc_final: 0.8376 (mtm-85) outliers start: 3 outliers final: 1 residues processed: 385 average time/residue: 0.2084 time to fit residues: 137.5449 Evaluate side-chains 286 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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: 0.9980 chunk 148 optimal weight: 5.9990 chunk 241 optimal weight: 9.9990 chunk 389 optimal weight: 0.0010 chunk 271 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 278 optimal weight: 0.5980 chunk 99 optimal weight: 30.0000 chunk 345 optimal weight: 0.5980 chunk 378 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 659 GLN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 HIS ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.088493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071421 restraints weight = 174824.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072970 restraints weight = 100274.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.073481 restraints weight = 60295.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073785 restraints weight = 50619.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073859 restraints weight = 45126.708| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 36691 Z= 0.125 Angle : 0.630 11.797 50120 Z= 0.330 Chirality : 0.045 0.280 5731 Planarity : 0.005 0.115 6171 Dihedral : 16.254 172.612 5930 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.89 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -1.63 (0.12), residues: 4292 helix: -0.00 (0.13), residues: 1556 sheet: -1.09 (0.23), residues: 518 loop : -1.90 (0.12), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG K 69 TYR 0.023 0.001 TYR I1229 PHE 0.032 0.001 PHE A 195 TRP 0.011 0.001 TRP A1134 HIS 0.009 0.001 HIS J 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (36684) covalent geometry : angle 0.62900 / 0.33 (50114) hydrogen bonds : bond 0.04151 / 2.82 ( 1495) hydrogen bonds : angle 5.21370 / 3.72 ( 4094) metal coordination : bond 0.01997 / 1.56 ( 7) metal coordination : angle 3.32207 / 1.58 ( 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 422 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.9168 (mmm) cc_final: 0.8897 (mmm) REVERT: A 325 ASP cc_start: 0.8218 (p0) cc_final: 0.7819 (p0) REVERT: A 426 MET cc_start: 0.4604 (mtt) cc_final: 0.4348 (mmm) REVERT: A 511 LEU cc_start: 0.8655 (tp) cc_final: 0.8271 (tp) REVERT: A 595 ASP cc_start: 0.8589 (m-30) cc_final: 0.8207 (m-30) REVERT: A 682 MET cc_start: 0.3922 (ttm) cc_final: 0.2328 (ttm) REVERT: A 854 MET cc_start: 0.6275 (ppp) cc_final: 0.6007 (ppp) REVERT: A 922 MET cc_start: 0.5281 (tpt) cc_final: 0.4931 (tpt) REVERT: A 976 MET cc_start: 0.9099 (mmp) cc_final: 0.8853 (mmm) REVERT: A 1124 ASP cc_start: 0.7597 (p0) cc_final: 0.7387 (p0) REVERT: G 131 CYS cc_start: 0.8832 (p) cc_final: 0.8447 (p) REVERT: G 145 LYS cc_start: 0.8105 (tttm) cc_final: 0.7652 (tttp) REVERT: H 147 GLN cc_start: 0.8288 (tt0) cc_final: 0.7059 (mp10) REVERT: H 200 LYS cc_start: 0.9001 (pptt) cc_final: 0.8674 (pptt) REVERT: I 14 ASP cc_start: 0.8200 (t70) cc_final: 0.7918 (t0) REVERT: I 65 ASN cc_start: 0.8890 (m-40) cc_final: 0.8497 (t0) REVERT: I 160 ASP cc_start: 0.9082 (m-30) cc_final: 0.8005 (p0) REVERT: I 239 MET cc_start: 0.7528 (tmm) cc_final: 0.7119 (tmm) REVERT: I 704 MET cc_start: 0.8609 (mmm) cc_final: 0.8144 (mmm) REVERT: I 785 ASP cc_start: 0.8684 (m-30) cc_final: 0.8478 (m-30) REVERT: I 849 GLU cc_start: 0.7626 (tp30) cc_final: 0.7021 (tp30) REVERT: I 1114 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8424 (tm-30) REVERT: I 1243 MET cc_start: 0.9026 (tmm) cc_final: 0.8546 (tmm) REVERT: I 1319 MET cc_start: 0.8682 (tmm) cc_final: 0.8473 (tmm) REVERT: J 252 LEU cc_start: 0.8436 (tp) cc_final: 0.8155 (tp) REVERT: J 298 MET cc_start: 0.8575 (mmp) cc_final: 0.7698 (mtt) REVERT: J 325 LYS cc_start: 0.9221 (mppt) cc_final: 0.8949 (mppt) REVERT: J 329 ASP cc_start: 0.8398 (m-30) cc_final: 0.8057 (m-30) REVERT: J 349 TYR cc_start: 0.9018 (m-10) cc_final: 0.8725 (m-10) REVERT: J 601 ILE cc_start: 0.9591 (mt) cc_final: 0.9285 (tt) REVERT: J 724 MET cc_start: 0.9340 (mtm) cc_final: 0.8835 (mtp) REVERT: J 785 ASP cc_start: 0.8284 (t70) cc_final: 0.8067 (t70) REVERT: J 826 ILE cc_start: 0.7794 (mm) cc_final: 0.7521 (mm) REVERT: J 1203 ARG cc_start: 0.7605 (ttp80) cc_final: 0.6943 (mmt180) REVERT: J 1275 LEU cc_start: 0.8929 (tp) cc_final: 0.8703 (tp) REVERT: J 1278 GLU cc_start: 0.7230 (tt0) cc_final: 0.7011 (tt0) REVERT: J 1305 ASP cc_start: 0.7880 (m-30) cc_final: 0.7645 (m-30) REVERT: J 1334 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8380 (tm-30) REVERT: K 46 THR cc_start: 0.8944 (p) cc_final: 0.8704 (p) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.2169 time to fit residues: 155.2261 Evaluate side-chains 309 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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: 9.9990 chunk 242 optimal weight: 0.0970 chunk 295 optimal weight: 0.0070 chunk 268 optimal weight: 10.0000 chunk 333 optimal weight: 2.9990 chunk 419 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 410 optimal weight: 7.9990 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 HIS ** 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 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 659 GLN I 761 GLN I 799 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 HIS J1108 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.086825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.069833 restraints weight = 176390.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.071100 restraints weight = 99211.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071864 restraints weight = 60722.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.072054 restraints weight = 51025.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072098 restraints weight = 45999.827| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 36691 Z= 0.174 Angle : 0.644 11.168 50120 Z= 0.339 Chirality : 0.045 0.289 5731 Planarity : 0.005 0.066 6171 Dihedral : 16.177 172.045 5930 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.50 % Favored : 93.48 % Rotamer: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % 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: 1550 sheet: -0.88 (0.24), residues: 485 loop : -1.86 (0.12), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 69 TYR 0.021 0.001 TYR H 185 PHE 0.028 0.002 PHE I 828 TRP 0.010 0.001 TRP A1134 HIS 0.005 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (36684) covalent geometry : angle 0.64321 / 0.34 (50114) hydrogen bonds : bond 0.04204 / 2.89 ( 1495) hydrogen bonds : angle 5.17630 / 3.70 ( 4094) metal coordination : bond 0.00955 / 0.74 ( 7) metal coordination : angle 3.21830 / 1.42 ( 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 395 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 393 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8444 (tp) cc_final: 0.8224 (tp) REVERT: A 273 PHE cc_start: 0.7798 (m-10) cc_final: 0.7448 (m-80) REVERT: A 325 ASP cc_start: 0.8289 (p0) cc_final: 0.8011 (p0) REVERT: A 511 LEU cc_start: 0.8820 (tp) cc_final: 0.8338 (tp) REVERT: A 595 ASP cc_start: 0.8532 (m-30) cc_final: 0.8144 (m-30) REVERT: A 682 MET cc_start: 0.3544 (ttm) cc_final: 0.1143 (tmm) REVERT: A 854 MET cc_start: 0.6099 (ppp) cc_final: 0.5806 (ppp) REVERT: A 975 TYR cc_start: 0.8433 (t80) cc_final: 0.8208 (t80) REVERT: A 976 MET cc_start: 0.9177 (mmp) cc_final: 0.8886 (mmm) REVERT: A 1037 ASN cc_start: 0.9200 (m110) cc_final: 0.8997 (m110) REVERT: A 1124 ASP cc_start: 0.7721 (p0) cc_final: 0.7472 (p0) REVERT: H 142 MET cc_start: 0.7398 (ppp) cc_final: 0.7041 (ppp) REVERT: H 147 GLN cc_start: 0.7964 (tt0) cc_final: 0.6951 (mp10) REVERT: I 14 ASP cc_start: 0.8248 (t70) cc_final: 0.7995 (t0) REVERT: I 65 ASN cc_start: 0.8948 (m-40) cc_final: 0.8543 (t0) REVERT: I 158 ASP cc_start: 0.9143 (t0) cc_final: 0.8759 (t70) REVERT: I 160 ASP cc_start: 0.9121 (m-30) cc_final: 0.8118 (p0) REVERT: I 183 TRP cc_start: 0.8926 (m-10) cc_final: 0.8716 (m-10) REVERT: I 239 MET cc_start: 0.7591 (tmm) cc_final: 0.7179 (tmm) REVERT: I 427 ASP cc_start: 0.7474 (m-30) cc_final: 0.7271 (m-30) REVERT: I 654 ASP cc_start: 0.8363 (m-30) cc_final: 0.8122 (m-30) REVERT: I 704 MET cc_start: 0.8678 (mmm) cc_final: 0.8228 (mmm) REVERT: I 785 ASP cc_start: 0.8682 (m-30) cc_final: 0.8458 (m-30) REVERT: I 849 GLU cc_start: 0.7735 (tp30) cc_final: 0.7436 (tp30) REVERT: I 1243 MET cc_start: 0.9135 (tmm) cc_final: 0.8447 (tmm) REVERT: I 1319 MET cc_start: 0.8698 (tmm) cc_final: 0.8494 (tmm) REVERT: J 252 LEU cc_start: 0.8415 (tp) cc_final: 0.8124 (tp) REVERT: J 325 LYS cc_start: 0.9290 (mppt) cc_final: 0.8988 (mppt) REVERT: J 329 ASP cc_start: 0.8351 (m-30) cc_final: 0.8029 (m-30) REVERT: J 601 ILE cc_start: 0.9581 (mt) cc_final: 0.9283 (tt) REVERT: J 644 MET cc_start: 0.7468 (pmm) cc_final: 0.7238 (pmm) REVERT: J 724 MET cc_start: 0.9356 (mtm) cc_final: 0.8869 (mtp) REVERT: J 826 ILE cc_start: 0.7825 (mm) cc_final: 0.7594 (mm) REVERT: J 915 ILE cc_start: 0.9346 (pt) cc_final: 0.8842 (mp) REVERT: J 1275 LEU cc_start: 0.8934 (tp) cc_final: 0.8675 (tp) REVERT: J 1278 GLU cc_start: 0.7359 (tt0) cc_final: 0.7075 (tt0) REVERT: J 1305 ASP cc_start: 0.7830 (m-30) cc_final: 0.7612 (m-30) REVERT: J 1334 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8434 (tm-30) REVERT: K 30 MET cc_start: 0.7966 (mpp) cc_final: 0.6677 (mpp) REVERT: K 46 THR cc_start: 0.9029 (p) cc_final: 0.8817 (p) outliers start: 2 outliers final: 0 residues processed: 393 average time/residue: 0.1974 time to fit residues: 134.3231 Evaluate side-chains 299 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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: 2.9990 chunk 203 optimal weight: 8.9990 chunk 73 optimal weight: 0.0980 chunk 209 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 430 optimal weight: 30.0000 chunk 59 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 304 optimal weight: 5.9990 chunk 348 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** 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 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.087006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069163 restraints weight = 175501.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070757 restraints weight = 95614.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071764 restraints weight = 63327.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.072317 restraints weight = 48258.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.072728 restraints weight = 41144.800| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36691 Z= 0.160 Angle : 0.637 10.835 50120 Z= 0.333 Chirality : 0.045 0.286 5731 Planarity : 0.004 0.069 6171 Dihedral : 16.127 171.870 5930 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.34 % Favored : 93.64 % Rotamer: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.04 % 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: -1.40 (0.12), residues: 4292 helix: 0.24 (0.13), residues: 1551 sheet: -0.87 (0.24), residues: 483 loop : -1.83 (0.12), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 69 TYR 0.023 0.001 TYR H 185 PHE 0.037 0.001 PHE I 188 TRP 0.010 0.001 TRP A1134 HIS 0.006 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (36684) covalent geometry : angle 0.63582 / 0.33 (50114) hydrogen bonds : bond 0.04050 / 2.78 ( 1495) hydrogen bonds : angle 5.09009 / 3.64 ( 4094) metal coordination : bond 0.00689 / 0.54 ( 7) metal coordination : angle 2.99654 / 1.40 ( 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 394 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8498 (tp) cc_final: 0.8256 (tp) REVERT: A 157 MET cc_start: 0.9118 (mmm) cc_final: 0.8767 (mmm) REVERT: A 273 PHE cc_start: 0.7659 (m-10) cc_final: 0.7439 (m-80) REVERT: A 325 ASP cc_start: 0.8134 (p0) cc_final: 0.7769 (p0) REVERT: A 511 LEU cc_start: 0.8707 (tp) cc_final: 0.8274 (tp) REVERT: A 595 ASP cc_start: 0.8518 (m-30) cc_final: 0.8143 (m-30) REVERT: A 682 MET cc_start: 0.3321 (ttm) cc_final: 0.1063 (tmm) REVERT: A 854 MET cc_start: 0.6176 (ppp) cc_final: 0.5871 (ppp) REVERT: A 922 MET cc_start: 0.5278 (tpt) cc_final: 0.4788 (tpt) REVERT: A 976 MET cc_start: 0.9123 (mmp) cc_final: 0.8840 (mmm) REVERT: A 1037 ASN cc_start: 0.9165 (m110) cc_final: 0.8958 (m110) REVERT: G 131 CYS cc_start: 0.8838 (p) cc_final: 0.8452 (p) REVERT: H 147 GLN cc_start: 0.7944 (tt0) cc_final: 0.6953 (mp10) REVERT: I 14 ASP cc_start: 0.8322 (t70) cc_final: 0.8073 (t0) REVERT: I 65 ASN cc_start: 0.8821 (m-40) cc_final: 0.8474 (t0) REVERT: I 158 ASP cc_start: 0.9107 (t0) cc_final: 0.8720 (t70) REVERT: I 160 ASP cc_start: 0.9045 (m-30) cc_final: 0.8138 (p0) REVERT: I 239 MET cc_start: 0.7573 (tmm) cc_final: 0.7161 (tmm) REVERT: I 427 ASP cc_start: 0.7474 (m-30) cc_final: 0.7269 (m-30) REVERT: I 704 MET cc_start: 0.8669 (mmm) cc_final: 0.8157 (mmm) REVERT: I 785 ASP cc_start: 0.8714 (m-30) cc_final: 0.8475 (m-30) REVERT: I 849 GLU cc_start: 0.7680 (tp30) cc_final: 0.7367 (tp30) REVERT: I 1243 MET cc_start: 0.9167 (tmm) cc_final: 0.8438 (tmm) REVERT: J 252 LEU cc_start: 0.8400 (tp) cc_final: 0.8113 (tp) REVERT: J 325 LYS cc_start: 0.9297 (mppt) cc_final: 0.8978 (mppt) REVERT: J 329 ASP cc_start: 0.8355 (m-30) cc_final: 0.8026 (m-30) REVERT: J 517 CYS cc_start: 0.8554 (t) cc_final: 0.8328 (t) REVERT: J 544 LEU cc_start: 0.9488 (tp) cc_final: 0.9252 (tp) REVERT: J 601 ILE cc_start: 0.9589 (mt) cc_final: 0.9274 (tt) REVERT: J 724 MET cc_start: 0.9357 (mtm) cc_final: 0.8853 (mtp) REVERT: J 785 ASP cc_start: 0.8017 (t0) cc_final: 0.7770 (t70) REVERT: J 826 ILE cc_start: 0.7832 (mm) cc_final: 0.7551 (mm) REVERT: J 915 ILE cc_start: 0.9264 (pt) cc_final: 0.8713 (mp) REVERT: J 1235 ASN cc_start: 0.9203 (t0) cc_final: 0.8844 (t0) REVERT: J 1275 LEU cc_start: 0.9001 (tp) cc_final: 0.8734 (tp) REVERT: J 1278 GLU cc_start: 0.7309 (tt0) cc_final: 0.7073 (tt0) REVERT: J 1305 ASP cc_start: 0.8052 (m-30) cc_final: 0.7756 (m-30) REVERT: J 1334 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8443 (tm-30) REVERT: K 55 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7348 (mm-30) REVERT: K 69 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8440 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.2013 time to fit residues: 136.4249 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 : 1.703 ------------------------------------------------------------------------------- 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: 5.9990 chunk 135 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 30.0000 chunk 346 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 297 optimal weight: 8.9990 chunk 247 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** 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 659 GLN I 799 ASN ** 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 477 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.085729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.068080 restraints weight = 176377.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069620 restraints weight = 98196.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070605 restraints weight = 65554.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071133 restraints weight = 50308.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.071571 restraints weight = 43089.384| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 36691 Z= 0.228 Angle : 0.684 10.747 50120 Z= 0.358 Chirality : 0.045 0.302 5731 Planarity : 0.005 0.073 6171 Dihedral : 16.154 172.109 5930 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.75 % Rotamer: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.79 % 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: 0.18 (0.13), residues: 1553 sheet: -1.01 (0.23), residues: 506 loop : -1.83 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 3 TYR 0.029 0.002 TYR G 177 PHE 0.021 0.002 PHE I 188 TRP 0.010 0.001 TRP A 334 HIS 0.007 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.23 (36684) covalent geometry : angle 0.68298 / 0.36 (50114) hydrogen bonds : bond 0.04335 / 2.98 ( 1495) hydrogen bonds : angle 5.22052 / 3.72 ( 4094) metal coordination : bond 0.01032 / 0.79 ( 7) metal coordination : angle 3.57407 / 1.83 ( 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 386 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 1.421 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: 0.8459 (tp) cc_final: 0.8227 (tp) REVERT: A 325 ASP cc_start: 0.8144 (p0) cc_final: 0.7794 (p0) REVERT: A 511 LEU cc_start: 0.8692 (tp) cc_final: 0.8290 (tp) REVERT: A 595 ASP cc_start: 0.8508 (m-30) cc_final: 0.8141 (m-30) REVERT: A 682 MET cc_start: 0.3350 (ttm) cc_final: 0.1102 (tmm) REVERT: A 854 MET cc_start: 0.6200 (ppp) cc_final: 0.5865 (ppp) REVERT: A 922 MET cc_start: 0.5144 (tpt) cc_final: 0.4893 (tpt) REVERT: A 976 MET cc_start: 0.9205 (mmp) cc_final: 0.8831 (mmm) REVERT: A 1037 ASN cc_start: 0.9093 (m110) cc_final: 0.8879 (m110) REVERT: G 131 CYS cc_start: 0.8684 (p) cc_final: 0.8404 (p) REVERT: H 142 MET cc_start: 0.7032 (ppp) cc_final: 0.6753 (ppp) REVERT: H 147 GLN cc_start: 0.8054 (tt0) cc_final: 0.6950 (mp10) REVERT: I 14 ASP cc_start: 0.8315 (t70) cc_final: 0.8103 (t0) REVERT: I 65 ASN cc_start: 0.8754 (m-40) cc_final: 0.8409 (t0) REVERT: I 160 ASP cc_start: 0.9032 (m-30) cc_final: 0.8234 (p0) REVERT: I 183 TRP cc_start: 0.8935 (m-10) cc_final: 0.8680 (m-10) REVERT: I 239 MET cc_start: 0.7601 (tmm) cc_final: 0.7180 (tmm) REVERT: I 704 MET cc_start: 0.8667 (mmm) cc_final: 0.8111 (mmm) REVERT: I 785 ASP cc_start: 0.8737 (m-30) cc_final: 0.8516 (m-30) REVERT: I 849 GLU cc_start: 0.7738 (tp30) cc_final: 0.7441 (tp30) REVERT: I 1243 MET cc_start: 0.9055 (tmm) cc_final: 0.8524 (tmm) REVERT: I 1319 MET cc_start: 0.8859 (tmm) cc_final: 0.8251 (tmm) REVERT: J 252 LEU cc_start: 0.8327 (tp) cc_final: 0.8001 (tp) REVERT: J 298 MET cc_start: 0.8500 (mmp) cc_final: 0.7844 (mtt) REVERT: J 325 LYS cc_start: 0.9345 (mppt) cc_final: 0.8998 (mppt) REVERT: J 329 ASP cc_start: 0.8375 (m-30) cc_final: 0.7971 (m-30) REVERT: J 517 CYS cc_start: 0.8581 (t) cc_final: 0.8363 (t) REVERT: J 544 LEU cc_start: 0.9504 (tp) cc_final: 0.9263 (tp) REVERT: J 697 MET cc_start: 0.8522 (ppp) cc_final: 0.8213 (ppp) REVERT: J 698 MET cc_start: 0.8632 (tpp) cc_final: 0.8410 (tpp) REVERT: J 724 MET cc_start: 0.9373 (mtm) cc_final: 0.8826 (mtt) REVERT: J 826 ILE cc_start: 0.7920 (mm) cc_final: 0.7666 (mm) REVERT: J 915 ILE cc_start: 0.9330 (pt) cc_final: 0.8883 (mp) REVERT: J 1305 ASP cc_start: 0.7868 (m-30) cc_final: 0.7634 (m-30) REVERT: J 1334 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8445 (tm-30) REVERT: K 69 ARG cc_start: 0.8718 (mtm-85) cc_final: 0.8198 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 385 average time/residue: 0.2031 time to fit residues: 134.4015 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 : 1.451 ------------------------------------------------------------------------------- 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: 3.9990 chunk 249 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 412 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 chunk 329 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 420 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 436 optimal weight: 40.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** 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 462 ASN ** 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** I1244 HIS J 489 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.068692 restraints weight = 175543.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070223 restraints weight = 97948.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.071220 restraints weight = 65706.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071750 restraints weight = 50530.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.072193 restraints weight = 43191.467| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36691 Z= 0.190 Angle : 0.665 11.115 50120 Z= 0.347 Chirality : 0.045 0.296 5731 Planarity : 0.005 0.083 6171 Dihedral : 16.138 172.470 5930 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.78 % Favored : 93.20 % Rotamer: Outliers : 0.08 % Allowed : 1.45 % Favored : 98.46 % 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: -1.42 (0.12), residues: 4292 helix: 0.23 (0.13), residues: 1559 sheet: -1.08 (0.23), residues: 512 loop : -1.79 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 3 TYR 0.015 0.001 TYR A 513 PHE 0.020 0.002 PHE I 188 TRP 0.010 0.001 TRP A1134 HIS 0.004 0.001 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (36684) covalent geometry : angle 0.66062 / 0.35 (50114) hydrogen bonds : bond 0.04150 / 2.85 ( 1495) hydrogen bonds : angle 5.16297 / 3.69 ( 4094) metal coordination : bond 0.01423 / 1.17 ( 7) metal coordination : angle 6.70225 / 3.48 ( 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 387 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 384 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8606 (tp) cc_final: 0.8371 (tp) REVERT: A 273 PHE cc_start: 0.7605 (m-10) cc_final: 0.7349 (m-80) REVERT: A 325 ASP cc_start: 0.7982 (p0) cc_final: 0.7555 (p0) REVERT: A 511 LEU cc_start: 0.8557 (tp) cc_final: 0.8169 (tp) REVERT: A 595 ASP cc_start: 0.8491 (m-30) cc_final: 0.8129 (m-30) REVERT: A 682 MET cc_start: 0.3337 (ttm) cc_final: 0.1077 (tmm) REVERT: A 854 MET cc_start: 0.6401 (ppp) cc_final: 0.6030 (ppp) REVERT: A 922 MET cc_start: 0.5213 (tpt) cc_final: 0.4965 (tpt) REVERT: A 975 TYR cc_start: 0.8297 (t80) cc_final: 0.8088 (t80) REVERT: A 976 MET cc_start: 0.9185 (mmp) cc_final: 0.8768 (mmt) REVERT: A 1037 ASN cc_start: 0.9065 (m110) cc_final: 0.8843 (m110) REVERT: G 131 CYS cc_start: 0.8842 (p) cc_final: 0.8453 (p) REVERT: H 142 MET cc_start: 0.6961 (ppp) cc_final: 0.6703 (ppp) REVERT: H 147 GLN cc_start: 0.8074 (tt0) cc_final: 0.6983 (mp10) REVERT: I 65 ASN cc_start: 0.8757 (m-40) cc_final: 0.8395 (t0) REVERT: I 160 ASP cc_start: 0.9039 (m-30) cc_final: 0.8210 (p0) REVERT: I 239 MET cc_start: 0.7570 (tmm) cc_final: 0.7158 (tmm) REVERT: I 427 ASP cc_start: 0.7457 (m-30) cc_final: 0.7253 (m-30) REVERT: I 704 MET cc_start: 0.8623 (mmm) cc_final: 0.8071 (mmm) REVERT: I 785 ASP cc_start: 0.8751 (m-30) cc_final: 0.8530 (m-30) REVERT: I 849 GLU cc_start: 0.7784 (tp30) cc_final: 0.7472 (tp30) REVERT: I 1114 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8663 (tm-30) REVERT: I 1319 MET cc_start: 0.8794 (tmm) cc_final: 0.8431 (tmm) REVERT: J 252 LEU cc_start: 0.8323 (tp) cc_final: 0.8007 (tp) REVERT: J 325 LYS cc_start: 0.9308 (mppt) cc_final: 0.8987 (mppt) REVERT: J 329 ASP cc_start: 0.8337 (m-30) cc_final: 0.7967 (m-30) REVERT: J 517 CYS cc_start: 0.8556 (t) cc_final: 0.8330 (t) REVERT: J 544 LEU cc_start: 0.9480 (tp) cc_final: 0.9165 (tp) REVERT: J 697 MET cc_start: 0.8511 (ppp) cc_final: 0.8187 (ppp) REVERT: J 698 MET cc_start: 0.8555 (tpp) cc_final: 0.8355 (tpp) REVERT: J 724 MET cc_start: 0.9370 (mtm) cc_final: 0.8845 (mtt) REVERT: J 785 ASP cc_start: 0.8116 (t70) cc_final: 0.7903 (t70) REVERT: J 826 ILE cc_start: 0.7891 (mm) cc_final: 0.7636 (mm) REVERT: J 915 ILE cc_start: 0.9255 (pt) cc_final: 0.8823 (mp) REVERT: J 1305 ASP cc_start: 0.7816 (m-30) cc_final: 0.7609 (m-30) REVERT: J 1334 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8437 (tm-30) REVERT: K 69 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8249 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 385 average time/residue: 0.2043 time to fit residues: 136.8113 Evaluate side-chains 289 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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: 10.0000 chunk 332 optimal weight: 4.9990 chunk 345 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 319 optimal weight: 6.9990 chunk 303 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** 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 462 ASN ** I 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS I 659 GLN I 799 ASN ** I1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN K 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.085678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067984 restraints weight = 176563.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069498 restraints weight = 98033.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.070469 restraints weight = 65750.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.070950 restraints weight = 50456.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.071432 restraints weight = 43573.426| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2137 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= 0.221 Angle : 0.694 10.869 50120 Z= 0.361 Chirality : 0.045 0.303 5731 Planarity : 0.005 0.077 6171 Dihedral : 16.144 172.620 5930 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.46 % Favored : 92.52 % Rotamer: Outliers : 0.08 % Allowed : 1.01 % Favored : 98.91 % 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: -1.43 (0.12), residues: 4292 helix: 0.20 (0.13), residues: 1552 sheet: -1.08 (0.23), residues: 518 loop : -1.78 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 3 TYR 0.024 0.002 TYR H 185 PHE 0.021 0.002 PHE A 184 TRP 0.010 0.001 TRP A 321 HIS 0.006 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (36684) covalent geometry : angle 0.69048 / 0.36 (50114) hydrogen bonds : bond 0.04317 / 2.96 ( 1495) hydrogen bonds : angle 5.23206 / 3.73 ( 4094) metal coordination : bond 0.01577 / 1.24 ( 7) metal coordination : angle 6.34059 / 2.98 ( 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 374 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 371 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8560 (tp) cc_final: 0.8274 (tp) REVERT: A 325 ASP cc_start: 0.7996 (p0) cc_final: 0.7548 (p0) REVERT: A 511 LEU cc_start: 0.8685 (tp) cc_final: 0.8149 (tp) REVERT: A 595 ASP cc_start: 0.8488 (m-30) cc_final: 0.8140 (m-30) REVERT: A 682 MET cc_start: 0.3406 (ttm) cc_final: 0.1308 (tmm) REVERT: A 922 MET cc_start: 0.5250 (tpt) cc_final: 0.4993 (tpt) REVERT: A 976 MET cc_start: 0.9122 (mmp) cc_final: 0.8866 (mmm) REVERT: A 1037 ASN cc_start: 0.9051 (m110) cc_final: 0.8819 (m110) REVERT: G 131 CYS cc_start: 0.8849 (p) cc_final: 0.8467 (p) REVERT: H 142 MET cc_start: 0.7058 (ppp) cc_final: 0.6832 (ppp) REVERT: H 147 GLN cc_start: 0.8070 (tt0) cc_final: 0.6971 (mp10) REVERT: I 65 ASN cc_start: 0.8771 (m-40) cc_final: 0.8346 (t0) REVERT: I 158 ASP cc_start: 0.8911 (t0) cc_final: 0.8572 (t70) REVERT: I 160 ASP cc_start: 0.9067 (m-30) cc_final: 0.8244 (p0) REVERT: I 183 TRP cc_start: 0.8924 (m-10) cc_final: 0.8630 (m-10) REVERT: I 239 MET cc_start: 0.7574 (tmm) cc_final: 0.7181 (tmm) REVERT: I 414 ILE cc_start: 0.9108 (pt) cc_final: 0.8803 (mm) REVERT: I 704 MET cc_start: 0.8649 (mmm) cc_final: 0.8077 (mmm) REVERT: I 785 ASP cc_start: 0.8782 (m-30) cc_final: 0.8559 (m-30) REVERT: I 849 GLU cc_start: 0.7842 (tp30) cc_final: 0.7528 (tp30) REVERT: I 1114 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8635 (tm-30) REVERT: I 1243 MET cc_start: 0.9148 (tmm) cc_final: 0.8675 (tmm) REVERT: I 1319 MET cc_start: 0.8837 (tmm) cc_final: 0.8394 (tmm) REVERT: J 252 LEU cc_start: 0.8359 (tp) cc_final: 0.8028 (tp) REVERT: J 325 LYS cc_start: 0.9318 (mppt) cc_final: 0.8965 (mppt) REVERT: J 329 ASP cc_start: 0.8343 (m-30) cc_final: 0.7957 (m-30) REVERT: J 517 CYS cc_start: 0.8554 (t) cc_final: 0.8329 (t) REVERT: J 544 LEU cc_start: 0.9490 (tp) cc_final: 0.9174 (tp) REVERT: J 697 MET cc_start: 0.8547 (ppp) cc_final: 0.8219 (ppp) REVERT: J 724 MET cc_start: 0.9394 (mtm) cc_final: 0.8840 (mtt) REVERT: J 743 MET cc_start: 0.8060 (tmm) cc_final: 0.7826 (tmm) REVERT: J 826 ILE cc_start: 0.7902 (mm) cc_final: 0.7652 (mm) REVERT: J 915 ILE cc_start: 0.9293 (pt) cc_final: 0.8903 (mp) REVERT: J 1203 ARG cc_start: 0.7884 (ttp80) cc_final: 0.6973 (ttt90) REVERT: J 1334 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8461 (tm-30) REVERT: K 69 ARG cc_start: 0.8760 (mtm-85) cc_final: 0.8272 (mtm-85) outliers start: 3 outliers final: 0 residues processed: 372 average time/residue: 0.2072 time to fit residues: 132.6835 Evaluate side-chains 289 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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: 9.9990 chunk 302 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 365 optimal weight: 0.9990 chunk 331 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 421 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A1069 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN H 103 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 GLN I 462 ASN ** 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** J 157 GLN K 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.088170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071043 restraints weight = 174491.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.072702 restraints weight = 95997.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.073559 restraints weight = 55256.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.073767 restraints weight = 45711.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.073754 restraints weight = 40785.468| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2293 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= 0.124 Angle : 0.645 11.520 50120 Z= 0.333 Chirality : 0.045 0.273 5731 Planarity : 0.004 0.073 6171 Dihedral : 16.021 172.232 5930 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.66 % 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: -1.23 (0.13), residues: 4292 helix: 0.41 (0.13), residues: 1553 sheet: -1.00 (0.23), residues: 503 loop : -1.69 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 3 TYR 0.017 0.001 TYR J 679 PHE 0.018 0.001 PHE I 405 TRP 0.017 0.001 TRP A1134 HIS 0.004 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (36684) covalent geometry : angle 0.64250 / 0.33 (50114) hydrogen bonds : bond 0.03802 / 2.60 ( 1495) hydrogen bonds : angle 4.93797 / 3.53 ( 4094) metal coordination : bond 0.00907 / 0.74 ( 7) metal coordination : angle 5.21780 / 2.32 ( 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 419 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 416 time to evaluate : 1.352 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: 0.8652 (tp) cc_final: 0.8445 (tp) REVERT: A 157 MET cc_start: 0.8879 (mmm) cc_final: 0.8561 (mmm) REVERT: A 325 ASP cc_start: 0.7934 (p0) cc_final: 0.7415 (p0) REVERT: A 511 LEU cc_start: 0.8511 (tp) cc_final: 0.8034 (tp) REVERT: A 595 ASP cc_start: 0.8527 (m-30) cc_final: 0.8174 (m-30) REVERT: A 682 MET cc_start: 0.3224 (ttm) cc_final: 0.0993 (tmm) REVERT: A 922 MET cc_start: 0.4967 (tpt) cc_final: 0.4736 (tpt) REVERT: A 976 MET cc_start: 0.9234 (mmp) cc_final: 0.8879 (mmm) REVERT: A 1037 ASN cc_start: 0.9043 (m110) cc_final: 0.8813 (m110) REVERT: G 131 CYS cc_start: 0.8776 (p) cc_final: 0.8387 (p) REVERT: H 41 ASN cc_start: 0.9009 (t0) cc_final: 0.8718 (t0) REVERT: H 142 MET cc_start: 0.7085 (ppp) cc_final: 0.6829 (ppp) REVERT: H 147 GLN cc_start: 0.7916 (tt0) cc_final: 0.6899 (mp10) REVERT: I 65 ASN cc_start: 0.8876 (m-40) cc_final: 0.8392 (t0) REVERT: I 158 ASP cc_start: 0.8875 (t0) cc_final: 0.8539 (t70) REVERT: I 160 ASP cc_start: 0.9063 (m-30) cc_final: 0.8211 (p0) REVERT: I 239 MET cc_start: 0.7537 (tmm) cc_final: 0.7120 (tmm) REVERT: I 414 ILE cc_start: 0.9096 (pt) cc_final: 0.8796 (mm) REVERT: I 704 MET cc_start: 0.8580 (mmm) cc_final: 0.8006 (mmm) REVERT: I 785 ASP cc_start: 0.8770 (m-30) cc_final: 0.8490 (m-30) REVERT: I 849 GLU cc_start: 0.7856 (tp30) cc_final: 0.7546 (tp30) REVERT: I 1073 LYS cc_start: 0.9015 (ptpt) cc_final: 0.8739 (ptmt) REVERT: I 1095 ASP cc_start: 0.8724 (m-30) cc_final: 0.8472 (m-30) REVERT: I 1114 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8695 (tm-30) REVERT: I 1243 MET cc_start: 0.9039 (tmm) cc_final: 0.8665 (tmm) REVERT: I 1290 MET cc_start: 0.8587 (tpp) cc_final: 0.8277 (tpp) REVERT: I 1319 MET cc_start: 0.8724 (tmm) cc_final: 0.8398 (tmm) REVERT: J 252 LEU cc_start: 0.8374 (tp) cc_final: 0.8082 (tp) REVERT: J 298 MET cc_start: 0.8478 (mmp) cc_final: 0.7721 (mtt) REVERT: J 325 LYS cc_start: 0.9247 (mppt) cc_final: 0.8889 (mtpp) REVERT: J 329 ASP cc_start: 0.8339 (m-30) cc_final: 0.8003 (m-30) REVERT: J 349 TYR cc_start: 0.9044 (m-10) cc_final: 0.8836 (m-10) REVERT: J 517 CYS cc_start: 0.8416 (t) cc_final: 0.8173 (t) REVERT: J 544 LEU cc_start: 0.9457 (tp) cc_final: 0.9153 (tp) REVERT: J 571 ASP cc_start: 0.8389 (p0) cc_final: 0.7993 (p0) REVERT: J 724 MET cc_start: 0.9358 (mtm) cc_final: 0.8795 (mtp) REVERT: J 785 ASP cc_start: 0.8225 (t70) cc_final: 0.7969 (t70) REVERT: J 826 ILE cc_start: 0.7915 (mm) cc_final: 0.7632 (mm) REVERT: J 915 ILE cc_start: 0.9277 (pt) cc_final: 0.8823 (mp) REVERT: J 1040 MET cc_start: -0.0797 (tpp) cc_final: -0.1000 (tpp) REVERT: J 1235 ASN cc_start: 0.9209 (t0) cc_final: 0.8882 (t0) REVERT: J 1278 GLU cc_start: 0.7164 (tt0) cc_final: 0.6946 (tt0) REVERT: J 1305 ASP cc_start: 0.7852 (m-30) cc_final: 0.7509 (m-30) REVERT: J 1334 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8400 (tm-30) outliers start: 3 outliers final: 1 residues processed: 417 average time/residue: 0.2072 time to fit residues: 147.6548 Evaluate side-chains 300 residues out of total 3669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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: 6.9990 chunk 326 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 321 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 435 optimal weight: 50.0000 chunk 244 optimal weight: 9.9990 chunk 409 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 374 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.085790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.068203 restraints weight = 176079.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069721 restraints weight = 98740.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.070668 restraints weight = 66336.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071219 restraints weight = 51243.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071445 restraints weight = 43880.742| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 36691 Z= 0.233 Angle : 0.703 10.893 50120 Z= 0.365 Chirality : 0.045 0.300 5731 Planarity : 0.005 0.073 6171 Dihedral : 16.069 171.860 5930 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.08 % Favored : 92.89 % 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 : 0.54 % 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: -1.30 (0.13), residues: 4292 helix: 0.29 (0.13), residues: 1553 sheet: -0.96 (0.23), residues: 523 loop : -1.71 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A1128 TYR 0.024 0.002 TYR J 512 PHE 0.024 0.002 PHE A 184 TRP 0.013 0.002 TRP A 321 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.23 (36684) covalent geometry : angle 0.70032 / 0.36 (50114) hydrogen bonds : bond 0.04255 / 2.92 ( 1495) hydrogen bonds : angle 5.12603 / 3.66 ( 4094) metal coordination : bond 0.01498 / 1.18 ( 7) metal coordination : angle 5.21629 / 2.47 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5755.21 seconds wall clock time: 100 minutes 47.87 seconds (6047.87 seconds total)