Starting phenix.real_space_refine on Thu May 15 15:21:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5u_49039/05_2025/9n5u_49039.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5u_49039/05_2025/9n5u_49039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n5u_49039/05_2025/9n5u_49039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5u_49039/05_2025/9n5u_49039.map" model { file = "/net/cci-nas-00/data/ceres_data/9n5u_49039/05_2025/9n5u_49039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5u_49039/05_2025/9n5u_49039.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.033 sd= 0.603 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 Fe 36 7.16 5 Zn 2 6.06 5 P 3 5.49 5 S 126 5.16 5 C 8462 2.51 5 N 2244 2.21 5 O 2482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13355 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7466 Classifications: {'peptide': 953} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 904} Chain: "B" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4543 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 560} Chain breaks: 1 Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1188 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 97 Unusual residues: {'FAD': 1, 'FES': 1, 'SF4': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Unusual residues: {' ZN': 2, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4962 SG CYS A 640 40.787 64.187 77.144 1.00 21.44 S ATOM 4983 SG CYS A 643 46.610 67.430 77.828 1.00 24.67 S ATOM 5002 SG CYS A 646 41.025 70.273 78.552 1.00 14.20 S ATOM 5382 SG CYS A 693 43.491 68.205 72.749 1.00 17.59 S ATOM 788 SG CYS A 111 47.704 55.393 46.397 1.00 29.97 S ATOM 1091 SG CYS A 150 45.293 52.723 40.751 1.00 16.10 S ATOM 1120 SG CYS A 154 41.455 55.184 45.575 1.00 11.26 S ATOM 4560 SG CYS A 590 36.352 62.281 52.100 1.00 11.63 S ATOM 4580 SG CYS A 593 36.277 58.062 56.400 1.00 23.29 S ATOM 761 SG CYS A 107 41.162 58.015 51.911 1.00 17.30 S ATOM 1153 SG CYS A 158 35.547 55.697 50.556 1.00 37.22 S ATOM 4642 SG CYS A 601 48.111 63.144 67.931 1.00 18.20 S ATOM 736 SG CYS A 103 46.805 58.452 63.882 1.00 26.90 S ATOM 4590 SG CYS A 595 42.839 63.212 64.723 1.00 18.52 S ATOM 5840 SG CYS A 752 39.435 87.884 70.633 1.00 39.85 S ATOM 5626 SG CYS A 726 45.759 90.249 71.402 1.00 48.23 S ATOM 5598 SG CYS A 722 41.399 94.125 70.476 1.00 35.83 S ATOM 5580 SG CYS A 719 42.734 90.049 65.760 1.00 52.81 S ATOM 256 SG CYS A 41 51.788 66.239 81.993 1.00 23.74 S ATOM 343 SG CYS A 52 53.408 63.609 79.920 1.00 28.11 S ATOM 368 SG CYS A 55 58.117 64.641 82.387 1.00 34.20 S ATOM 455 SG CYS A 67 56.566 67.047 84.561 1.00 22.04 S ATOM 11317 SG CYS B 500 48.509 58.458 94.363 1.00 32.83 S ATOM 11005 SG CYS B 460 46.450 54.702 89.693 1.00 35.25 S ATOM 10981 SG CYS B 457 49.373 58.271 87.565 1.00 35.42 S ATOM 10962 SG CYS B 454 44.194 60.938 90.743 1.00 19.97 S ATOM 11920 SG CYS B 587 24.660 17.517 101.668 1.00 30.00 S ATOM 11685 SG CYS B 547 22.103 12.859 96.962 1.00121.84 S ATOM 11720 SG CYS B 553 22.081 19.251 98.333 1.00 30.00 S ATOM 11869 SG CYS B 580 23.950 29.173 95.584 1.00109.16 S ATOM 11886 SG CYS B 583 23.237 22.935 96.086 1.00 30.00 S ATOM 11846 SG CYS B 577 25.446 25.463 90.237 1.00114.52 S ATOM 11747 SG CYS B 557 19.530 25.778 93.388 1.00113.87 S ATOM 10825 SG CYS B 437 42.397 32.029 92.951 1.00 64.10 S ATOM 11544 SG CYS B 529 40.573 28.619 92.431 1.00 74.37 S ATOM 11578 SG CYS B 534 39.538 31.642 90.300 1.00 71.60 S ATOM 7549 SG CYS B 14 34.371 47.278 118.053 1.00 58.07 S ATOM 7787 SG CYS B 45 37.315 46.730 120.481 1.00 71.28 S ATOM 7812 SG CYS B 49 37.260 44.425 117.749 1.00 63.24 S ATOM 12612 SG CYS C 74 32.542 45.709 104.546 1.00 68.84 S ATOM 12644 SG CYS C 79 33.120 42.477 105.292 1.00 60.22 S ATOM 12910 SG CYS C 115 35.904 47.557 107.691 1.00 65.38 S ATOM 12934 SG CYS C 119 36.824 44.300 109.484 1.00 61.67 S Time building chain proxies: 8.15, per 1000 atoms: 0.61 Number of scatterers: 13355 At special positions: 0 Unit cell: (91.908, 130.824, 154.008, 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 Fe 36 26.01 S 126 16.00 P 3 15.00 O 2482 8.00 N 2244 7.00 C 8462 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1007 " pdb="FE1 FES A1007 " - pdb=" SG CYS A 52 " pdb="FE2 FES A1007 " - pdb=" SG CYS A 55 " pdb="FE1 FES A1007 " - pdb=" SG CYS A 41 " pdb="FE2 FES A1007 " - pdb=" SG CYS A 67 " pdb=" FES C 201 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 79 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 74 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 119 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 115 " pdb=" SF4 A1001 " pdb="FE2 SF4 A1001 " - pdb=" SG CYS A 643 " pdb="FE4 SF4 A1001 " - pdb=" SG CYS A 693 " pdb="FE1 SF4 A1001 " - pdb=" SG CYS A 640 " pdb="FE3 SF4 A1001 " - pdb=" SG CYS A 646 " pdb=" SF4 A1002 " pdb="FE4 SF4 A1002 " - pdb=" SG CYS A 154 " pdb="FE1 SF4 A1002 " - pdb=" SG CYS A 111 " pdb="FE2 SF4 A1002 " - pdb=" SG CYS A 150 " pdb=" SF4 A1003 " pdb="FE4 SF4 A1003 " - pdb=" SG CYS A 158 " pdb="FE3 SF4 A1003 " - pdb=" SG CYS A 107 " pdb="FE1 SF4 A1003 " - pdb=" SG CYS A 590 " pdb="FE2 SF4 A1003 " - pdb=" SG CYS A 593 " pdb=" SF4 A1004 " pdb="FE4 SF4 A1004 " - pdb=" NE2 HIS A 99 " pdb="FE2 SF4 A1004 " - pdb=" SG CYS A 103 " pdb="FE1 SF4 A1004 " - pdb=" SG CYS A 601 " pdb="FE3 SF4 A1004 " - pdb=" SG CYS A 595 " pdb=" SF4 A1006 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 726 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 752 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 722 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 719 " pdb=" SF4 B 701 " pdb="FE3 SF4 B 701 " - pdb=" SG CYS B 457 " pdb="FE4 SF4 B 701 " - pdb=" SG CYS B 454 " pdb="FE1 SF4 B 701 " - pdb=" SG CYS B 500 " pdb="FE2 SF4 B 701 " - pdb=" SG CYS B 460 " pdb=" SF4 B 703 " pdb="FE3 SF4 B 703 " - pdb=" SG CYS B 553 " pdb="FE1 SF4 B 703 " - pdb=" SG CYS B 587 " pdb="FE2 SF4 B 703 " - pdb=" SG CYS B 547 " pdb=" SF4 B 704 " pdb="FE2 SF4 B 704 " - pdb=" SG CYS B 583 " pdb="FE4 SF4 B 704 " - pdb=" SG CYS B 557 " pdb="FE3 SF4 B 704 " - pdb=" SG CYS B 577 " pdb="FE1 SF4 B 704 " - pdb=" SG CYS B 580 " Number of angles added : 99 Zn2+ tetrahedral coordination pdb=" ZN B 705 " pdb="ZN ZN B 705 " - pdb=" NE2 HIS B 524 " pdb="ZN ZN B 705 " - pdb=" SG CYS B 529 " pdb="ZN ZN B 705 " - pdb=" SG CYS B 534 " pdb="ZN ZN B 705 " - pdb=" SG CYS B 437 " pdb=" ZN B 706 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 45 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 14 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 49 " Number of angles added : 3 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 19 sheets defined 44.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.804A pdb=" N PHE A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.584A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 128 through 137 Processing helix chain 'A' and resid 142 through 150 Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.501A pdb=" N GLU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 244 through 257 Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 481 through 500 Processing helix chain 'A' and resid 503 through 513 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 517 through 524 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.506A pdb=" N TYR A 548 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 579 through 588 removed outlier: 4.223A pdb=" N LEU A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.554A pdb=" N THR A 668 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 681 Processing helix chain 'A' and resid 687 through 693 removed outlier: 4.100A pdb=" N ASP A 691 " --> pdb=" O GLY A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 760 through 763 removed outlier: 3.638A pdb=" N GLN A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 776 through 787 Processing helix chain 'A' and resid 798 through 813 Processing helix chain 'A' and resid 828 through 835 Processing helix chain 'A' and resid 848 through 854 removed outlier: 4.057A pdb=" N LEU A 852 " --> pdb=" O PRO A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 896 Processing helix chain 'A' and resid 956 through 962 removed outlier: 3.531A pdb=" N LEU A 960 " --> pdb=" O ASP A 956 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 961 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 19 through 34 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.809A pdb=" N GLU B 52 " --> pdb=" O CYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 130 through 137 removed outlier: 3.568A pdb=" N TYR B 134 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.502A pdb=" N LYS B 144 " --> pdb=" O TYR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 211 through 227 removed outlier: 4.124A pdb=" N VAL B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 256 Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.738A pdb=" N GLY B 265 " --> pdb=" O ASN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.581A pdb=" N GLY B 284 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 311 through 315 Processing helix chain 'B' and resid 322 through 335 Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 413 through 421 removed outlier: 3.974A pdb=" N THR B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 453 Processing helix chain 'B' and resid 457 through 476 removed outlier: 3.998A pdb=" N LYS B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 498 removed outlier: 3.576A pdb=" N ILE B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 507 through 517 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.653A pdb=" N TYR B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 removed outlier: 4.131A pdb=" N ILE B 555 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'C' and resid 3 through 11 removed outlier: 4.001A pdb=" N GLU C 6 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR C 7 " --> pdb=" O GLN C 4 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 8 " --> pdb=" O LEU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 16 No H-bonds generated for 'chain 'C' and resid 14 through 16' Processing helix chain 'C' and resid 17 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 47 through 58 removed outlier: 3.688A pdb=" N TYR C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 83 through 96 Processing helix chain 'C' and resid 136 through 149 removed outlier: 3.561A pdb=" N GLU C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 8.989A pdb=" N ILE A 77 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR A 13 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 264 removed outlier: 6.241A pdb=" N ILE A 198 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N PHE A 224 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 200 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 283 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.890A pdb=" N ARG A 327 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE A 431 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 329 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 383 through 389 removed outlier: 5.695A pdb=" N THR A 383 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET A 402 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 400 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 383 through 389 removed outlier: 5.695A pdb=" N THR A 383 " --> pdb=" O MET A 402 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET A 402 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 400 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 633 through 635 Processing sheet with id=AB1, first strand: chain 'A' and resid 660 through 662 Processing sheet with id=AB2, first strand: chain 'A' and resid 713 through 718 removed outlier: 3.631A pdb=" N ARG A 739 " --> pdb=" O GLU A 731 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 773 through 774 removed outlier: 6.733A pdb=" N TYR A 906 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU A 925 " --> pdb=" O TYR A 906 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 908 " --> pdb=" O LEU A 925 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 858 through 859 removed outlier: 6.818A pdb=" N ARG A 837 " --> pdb=" O VAL A 866 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 868 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A 839 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU A 870 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LYS A 841 " --> pdb=" O GLU A 870 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA A 867 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N LEU A 883 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 869 " --> pdb=" O LEU A 883 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 935 through 938 Processing sheet with id=AB6, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.642A pdb=" N LYS B 39 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU B 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 271 through 277 removed outlier: 6.254A pdb=" N GLY B 231 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS B 275 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE B 233 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY B 277 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 235 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG B 236 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 363 through 368 Processing sheet with id=AB9, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=AC1, first strand: chain 'C' and resid 108 through 113 removed outlier: 3.544A pdb=" N CYS C 74 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL C 124 " --> pdb=" O CYS C 74 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 5415 1.43 - 1.64: 7999 1.64 - 1.86: 128 1.86 - 2.07: 0 2.07 - 2.28: 104 Bond restraints: 13646 Sorted by residual: bond pdb=" C4 FMN B 702 " pdb=" C4A FMN B 702 " ideal model delta sigma weight residual 1.485 1.379 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O3P FAD A1005 " pdb=" P FAD A1005 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C4A FMN B 702 " pdb=" N5 FMN B 702 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O5' FMN B 702 " pdb=" P FMN B 702 " ideal model delta sigma weight residual 1.676 1.605 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" O5B FAD A1005 " pdb=" PA FAD A1005 " ideal model delta sigma weight residual 1.634 1.564 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 13641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 18206 1.92 - 3.83: 261 3.83 - 5.75: 25 5.75 - 7.67: 9 7.67 - 9.58: 2 Bond angle restraints: 18503 Sorted by residual: angle pdb=" N ARG B 303 " pdb=" CA ARG B 303 " pdb=" C ARG B 303 " ideal model delta sigma weight residual 109.81 119.39 -9.58 2.21e+00 2.05e-01 1.88e+01 angle pdb=" CA TYR A 120 " pdb=" CB TYR A 120 " pdb=" CG TYR A 120 " ideal model delta sigma weight residual 113.90 120.05 -6.15 1.80e+00 3.09e-01 1.17e+01 angle pdb=" O1P FAD A1005 " pdb=" P FAD A1005 " pdb=" O2P FAD A1005 " ideal model delta sigma weight residual 122.50 114.03 8.47 3.00e+00 1.11e-01 7.96e+00 angle pdb=" N GLY A 920 " pdb=" CA GLY A 920 " pdb=" C GLY A 920 " ideal model delta sigma weight residual 111.56 114.24 -2.68 1.01e+00 9.80e-01 7.06e+00 angle pdb=" C4A FMN B 702 " pdb=" C4 FMN B 702 " pdb=" N3 FMN B 702 " ideal model delta sigma weight residual 113.24 120.82 -7.58 3.00e+00 1.11e-01 6.38e+00 ... (remaining 18498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.46: 8049 27.46 - 54.92: 184 54.92 - 82.38: 13 82.38 - 109.84: 1 109.84 - 137.30: 1 Dihedral angle restraints: 8248 sinusoidal: 3428 harmonic: 4820 Sorted by residual: dihedral pdb=" CA LEU C 121 " pdb=" C LEU C 121 " pdb=" N ALA C 122 " pdb=" CA ALA C 122 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PRO B 304 " pdb=" C PRO B 304 " pdb=" N PRO B 305 " pdb=" CA PRO B 305 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PHE A 40 " pdb=" C PHE A 40 " pdb=" N CYS A 41 " pdb=" CA CYS A 41 " ideal model delta harmonic sigma weight residual 180.00 -157.11 -22.89 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 8245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1237 0.035 - 0.069: 565 0.069 - 0.104: 200 0.104 - 0.139: 64 0.139 - 0.173: 3 Chirality restraints: 2069 Sorted by residual: chirality pdb=" CA ARG B 303 " pdb=" N ARG B 303 " pdb=" C ARG B 303 " pdb=" CB ARG B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" C2B FAD A1005 " pdb=" C1B FAD A1005 " pdb=" C3B FAD A1005 " pdb=" O2B FAD A1005 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA TYR A 120 " pdb=" N TYR A 120 " pdb=" C TYR A 120 " pdb=" CB TYR A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 2066 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 304 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO B 305 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 460 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C CYS B 460 " 0.036 2.00e-02 2.50e+03 pdb=" O CYS B 460 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG B 461 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 136 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO C 137 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 137 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 137 " 0.026 5.00e-02 4.00e+02 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 983 2.74 - 3.28: 12662 3.28 - 3.82: 21982 3.82 - 4.36: 27690 4.36 - 4.90: 47552 Nonbonded interactions: 110869 Sorted by model distance: nonbonded pdb=" OG1 THR A 794 " pdb=" O ILE A 909 " model vdw 2.196 3.040 nonbonded pdb=" O LEU A 918 " pdb=" OH TYR A 922 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP B 198 " pdb=" OG SER B 426 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP A 474 " pdb=" OG SER A 480 " model vdw 2.267 3.040 nonbonded pdb=" OE1 GLU B 585 " pdb=" OG1 THR C 136 " model vdw 2.278 3.040 ... (remaining 110864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 : 0.005 0.106 13692 Z= 0.221 Angle : 0.972 36.831 18605 Z= 0.315 Chirality : 0.045 0.173 2069 Planarity : 0.005 0.052 2340 Dihedral : 11.624 137.301 5176 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.47 % Allowed : 5.57 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1684 helix: 0.05 (0.20), residues: 642 sheet: -0.22 (0.32), residues: 261 loop : -0.89 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 468 HIS 0.004 0.001 HIS A 99 PHE 0.017 0.002 PHE B 108 TYR 0.028 0.002 TYR A 120 ARG 0.004 0.000 ARG A 759 Details of bonding type rmsd hydrogen bonds : bond 0.17281 ( 553) hydrogen bonds : angle 7.22025 ( 1566) metal coordination : bond 0.01424 ( 45) metal coordination : angle 10.36200 ( 102) covalent geometry : bond 0.00511 (13646) covalent geometry : angle 0.59777 (18503) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7172 (tm-30) REVERT: A 367 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8281 (ptp90) REVERT: A 382 LEU cc_start: 0.9032 (mt) cc_final: 0.8796 (mm) REVERT: A 387 LYS cc_start: 0.8709 (tppt) cc_final: 0.8385 (tppp) REVERT: A 389 ILE cc_start: 0.8914 (mm) cc_final: 0.8492 (mt) REVERT: A 424 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.7175 (mtp85) REVERT: A 800 GLU cc_start: 0.7916 (mp0) cc_final: 0.7539 (mm-30) REVERT: B 61 ASN cc_start: 0.8799 (p0) cc_final: 0.8454 (p0) REVERT: B 62 GLU cc_start: 0.7971 (pt0) cc_final: 0.7567 (pm20) REVERT: B 79 GLU cc_start: 0.8239 (tt0) cc_final: 0.8010 (tt0) REVERT: B 84 ASN cc_start: 0.8771 (m110) cc_final: 0.8470 (m110) REVERT: B 104 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8741 (mmmt) REVERT: B 452 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 101 GLN cc_start: 0.8223 (mt0) cc_final: 0.7843 (mt0) REVERT: C 107 LEU cc_start: 0.8945 (tp) cc_final: 0.8640 (tm) REVERT: C 138 ASP cc_start: 0.8167 (t70) cc_final: 0.7609 (t0) outliers start: 35 outliers final: 11 residues processed: 296 average time/residue: 1.6588 time to fit residues: 525.3403 Evaluate side-chains 218 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 500 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.055825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.043986 restraints weight = 26661.728| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 1.59 r_work: 0.2293 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2176 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13692 Z= 0.245 Angle : 1.015 34.091 18605 Z= 0.349 Chirality : 0.047 0.175 2069 Planarity : 0.006 0.063 2340 Dihedral : 7.096 91.301 1919 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.95 % Allowed : 13.67 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1684 helix: 0.22 (0.20), residues: 642 sheet: -0.29 (0.32), residues: 259 loop : -0.95 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 468 HIS 0.005 0.001 HIS A 99 PHE 0.026 0.002 PHE A 783 TYR 0.026 0.002 TYR A 120 ARG 0.006 0.001 ARG A 837 Details of bonding type rmsd hydrogen bonds : bond 0.05319 ( 553) hydrogen bonds : angle 5.84864 ( 1566) metal coordination : bond 0.01872 ( 45) metal coordination : angle 10.54888 ( 102) covalent geometry : bond 0.00595 (13646) covalent geometry : angle 0.64963 (18503) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8597 (tp30) cc_final: 0.8209 (tp30) REVERT: A 46 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: A 299 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 367 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.7842 (ttp80) REVERT: A 389 ILE cc_start: 0.9222 (mm) cc_final: 0.8951 (mt) REVERT: A 396 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: A 600 ARG cc_start: 0.8737 (ptt90) cc_final: 0.8258 (ptt180) REVERT: A 677 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7435 (mmm160) REVERT: A 800 GLU cc_start: 0.8407 (mp0) cc_final: 0.8075 (mm-30) REVERT: A 861 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 961 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: B 452 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7723 (mm-30) REVERT: C 62 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8445 (ptm-80) outliers start: 56 outliers final: 21 residues processed: 242 average time/residue: 1.6785 time to fit residues: 434.1454 Evaluate side-chains 226 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 0.0050 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 ASN B 84 ASN B 102 GLN C 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.057639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.045649 restraints weight = 26952.687| |-----------------------------------------------------------------------------| r_work (start): 0.2459 rms_B_bonded: 1.63 r_work: 0.2348 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2232 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13692 Z= 0.134 Angle : 0.939 31.454 18605 Z= 0.296 Chirality : 0.044 0.165 2069 Planarity : 0.005 0.052 2340 Dihedral : 6.537 81.865 1914 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.75 % Allowed : 15.64 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1684 helix: 0.65 (0.21), residues: 641 sheet: -0.41 (0.31), residues: 259 loop : -0.88 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 468 HIS 0.003 0.001 HIS A 308 PHE 0.010 0.001 PHE A 175 TYR 0.023 0.001 TYR A 120 ARG 0.006 0.000 ARG A 837 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 553) hydrogen bonds : angle 5.32308 ( 1566) metal coordination : bond 0.01118 ( 45) metal coordination : angle 10.22182 ( 102) covalent geometry : bond 0.00313 (13646) covalent geometry : angle 0.55685 (18503) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ILE cc_start: 0.9206 (mm) cc_final: 0.8919 (mt) REVERT: A 396 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8298 (pt0) REVERT: A 398 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7586 (tm-30) REVERT: A 600 ARG cc_start: 0.8672 (ptt90) cc_final: 0.8183 (ptt180) REVERT: A 602 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8421 (mtpp) REVERT: A 677 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7412 (mmm160) REVERT: A 800 GLU cc_start: 0.8410 (mp0) cc_final: 0.8146 (mm-30) REVERT: A 861 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8049 (tm-30) REVERT: A 961 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: B 452 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 548 THR cc_start: 0.7281 (OUTLIER) cc_final: 0.6971 (t) REVERT: B 556 MET cc_start: 0.6310 (mtt) cc_final: 0.6036 (ttm) outliers start: 39 outliers final: 15 residues processed: 243 average time/residue: 1.6320 time to fit residues: 424.7775 Evaluate side-chains 228 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.057564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.045798 restraints weight = 26838.511| |-----------------------------------------------------------------------------| r_work (start): 0.2457 rms_B_bonded: 1.61 r_work: 0.2348 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2233 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13692 Z= 0.143 Angle : 0.931 29.724 18605 Z= 0.301 Chirality : 0.044 0.160 2069 Planarity : 0.005 0.049 2340 Dihedral : 6.134 78.009 1905 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.66 % Allowed : 16.77 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1684 helix: 0.77 (0.21), residues: 643 sheet: -0.43 (0.32), residues: 259 loop : -0.88 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 468 HIS 0.003 0.001 HIS A 36 PHE 0.031 0.001 PHE A 783 TYR 0.023 0.002 TYR A 120 ARG 0.006 0.000 ARG A 837 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 553) hydrogen bonds : angle 5.21578 ( 1566) metal coordination : bond 0.01166 ( 45) metal coordination : angle 9.98199 ( 102) covalent geometry : bond 0.00340 (13646) covalent geometry : angle 0.56715 (18503) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8536 (tmtm) cc_final: 0.8312 (tmtm) REVERT: A 396 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8387 (pt0) REVERT: A 602 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8423 (mtpp) REVERT: A 783 PHE cc_start: 0.8369 (t80) cc_final: 0.8168 (t80) REVERT: A 800 GLU cc_start: 0.8394 (mp0) cc_final: 0.8124 (mm-30) REVERT: A 837 ARG cc_start: 0.8735 (mtm-85) cc_final: 0.8476 (mtp180) REVERT: A 859 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8972 (mm) REVERT: A 861 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 961 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: B 388 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8852 (mtmt) REVERT: B 452 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 526 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: B 548 THR cc_start: 0.7246 (OUTLIER) cc_final: 0.6955 (t) REVERT: C 62 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8458 (ptm-80) REVERT: C 64 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8914 (mt-10) REVERT: C 94 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8117 (mm-30) outliers start: 52 outliers final: 24 residues processed: 240 average time/residue: 1.5817 time to fit residues: 407.7664 Evaluate side-chains 236 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 14 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.057563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.045805 restraints weight = 26914.847| |-----------------------------------------------------------------------------| r_work (start): 0.2460 rms_B_bonded: 1.60 r_work: 0.2350 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2234 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13692 Z= 0.146 Angle : 0.896 26.934 18605 Z= 0.301 Chirality : 0.044 0.161 2069 Planarity : 0.005 0.062 2340 Dihedral : 6.004 74.953 1905 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.95 % Allowed : 16.77 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1684 helix: 0.88 (0.21), residues: 637 sheet: -0.59 (0.32), residues: 263 loop : -0.82 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 468 HIS 0.003 0.001 HIS A 36 PHE 0.023 0.001 PHE A 783 TYR 0.023 0.002 TYR A 120 ARG 0.005 0.000 ARG A 837 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 553) hydrogen bonds : angle 5.15380 ( 1566) metal coordination : bond 0.01166 ( 45) metal coordination : angle 9.39001 ( 102) covalent geometry : bond 0.00348 (13646) covalent geometry : angle 0.56749 (18503) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8434 (mtpp) REVERT: A 682 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8325 (mtpp) REVERT: A 787 LYS cc_start: 0.7225 (mppt) cc_final: 0.6844 (mppt) REVERT: A 859 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8968 (mm) REVERT: A 861 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8040 (tm-30) REVERT: A 961 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: B 388 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8849 (mtmt) REVERT: B 452 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 526 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: B 548 THR cc_start: 0.7276 (OUTLIER) cc_final: 0.6989 (t) REVERT: B 556 MET cc_start: 0.6024 (ttm) cc_final: 0.5672 (mtp) REVERT: C 62 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8450 (ptm-80) REVERT: C 138 ASP cc_start: 0.8517 (t0) cc_final: 0.8311 (t0) outliers start: 56 outliers final: 27 residues processed: 244 average time/residue: 1.5489 time to fit residues: 407.2488 Evaluate side-chains 232 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 124 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.057307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.045374 restraints weight = 27013.818| |-----------------------------------------------------------------------------| r_work (start): 0.2452 rms_B_bonded: 1.61 r_work: 0.2343 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2227 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13692 Z= 0.150 Angle : 0.888 26.310 18605 Z= 0.305 Chirality : 0.044 0.161 2069 Planarity : 0.005 0.064 2340 Dihedral : 5.869 71.622 1902 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.95 % Allowed : 17.34 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1684 helix: 0.84 (0.21), residues: 643 sheet: -0.63 (0.32), residues: 263 loop : -0.86 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 468 HIS 0.003 0.001 HIS A 308 PHE 0.011 0.001 PHE A 175 TYR 0.023 0.002 TYR A 120 ARG 0.010 0.000 ARG A 837 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 553) hydrogen bonds : angle 5.14148 ( 1566) metal coordination : bond 0.01196 ( 45) metal coordination : angle 9.16747 ( 102) covalent geometry : bond 0.00359 (13646) covalent geometry : angle 0.57395 (18503) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8066 (tppp) REVERT: A 602 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8437 (mtpp) REVERT: A 677 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7540 (mmm160) REVERT: A 682 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8353 (mtpp) REVERT: A 859 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8979 (mm) REVERT: A 861 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 961 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: B 90 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8447 (t0) REVERT: B 388 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8857 (mtmt) REVERT: B 452 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7739 (mm-30) REVERT: B 548 THR cc_start: 0.7241 (OUTLIER) cc_final: 0.6962 (t) REVERT: C 62 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8462 (ptm-80) REVERT: C 64 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8923 (mt-10) outliers start: 56 outliers final: 29 residues processed: 238 average time/residue: 1.5221 time to fit residues: 389.5487 Evaluate side-chains 242 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 124 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 28 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.056703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.044678 restraints weight = 27088.226| |-----------------------------------------------------------------------------| r_work (start): 0.2431 rms_B_bonded: 1.62 r_work: 0.2324 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2210 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13692 Z= 0.171 Angle : 0.905 26.209 18605 Z= 0.319 Chirality : 0.045 0.164 2069 Planarity : 0.005 0.065 2340 Dihedral : 5.924 68.875 1902 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.74 % Allowed : 18.04 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1684 helix: 0.76 (0.20), residues: 643 sheet: -0.63 (0.32), residues: 263 loop : -0.89 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 468 HIS 0.004 0.001 HIS A 99 PHE 0.033 0.002 PHE A 783 TYR 0.024 0.002 TYR A 120 ARG 0.004 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 553) hydrogen bonds : angle 5.19189 ( 1566) metal coordination : bond 0.01355 ( 45) metal coordination : angle 9.13788 ( 102) covalent geometry : bond 0.00413 (13646) covalent geometry : angle 0.60243 (18503) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8019 (pp20) REVERT: A 403 LYS cc_start: 0.9217 (ptmm) cc_final: 0.9012 (ptmm) REVERT: A 602 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8438 (mtpp) REVERT: A 677 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7552 (mmm160) REVERT: A 682 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8368 (mtpp) REVERT: A 800 GLU cc_start: 0.8429 (mp0) cc_final: 0.8107 (mm-30) REVERT: A 859 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.9008 (mm) REVERT: A 861 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8075 (tm-30) REVERT: A 961 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: B 90 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8456 (t0) REVERT: B 388 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8838 (mtmt) REVERT: B 452 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7723 (mm-30) REVERT: B 548 THR cc_start: 0.7343 (OUTLIER) cc_final: 0.7049 (t) REVERT: C 62 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8427 (ptm-80) REVERT: C 64 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8918 (mt-10) outliers start: 53 outliers final: 36 residues processed: 241 average time/residue: 1.5222 time to fit residues: 394.4338 Evaluate side-chains 246 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 961 PHE Chi-restraints excluded: chain B residue 33 LYS Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 142 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.057464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.045794 restraints weight = 27442.989| |-----------------------------------------------------------------------------| r_work (start): 0.2452 rms_B_bonded: 1.57 r_work: 0.2346 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2231 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13692 Z= 0.146 Angle : 0.887 26.274 18605 Z= 0.316 Chirality : 0.044 0.158 2069 Planarity : 0.005 0.064 2340 Dihedral : 5.846 67.024 1902 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.24 % Allowed : 19.45 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1684 helix: 0.87 (0.21), residues: 642 sheet: -0.66 (0.32), residues: 263 loop : -0.88 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 336 HIS 0.003 0.001 HIS A 36 PHE 0.029 0.001 PHE A 783 TYR 0.023 0.001 TYR A 120 ARG 0.004 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 553) hydrogen bonds : angle 5.09432 ( 1566) metal coordination : bond 0.01096 ( 45) metal coordination : angle 8.86349 ( 102) covalent geometry : bond 0.00351 (13646) covalent geometry : angle 0.59882 (18503) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.7985 (tppp) REVERT: A 602 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8444 (mtpp) REVERT: A 682 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8383 (mtpp) REVERT: A 859 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8983 (mm) REVERT: A 861 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 388 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8867 (mtmt) REVERT: B 452 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 548 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.7021 (t) REVERT: C 62 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8404 (ptm-80) REVERT: C 64 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8932 (mt-10) REVERT: C 141 ARG cc_start: 0.8926 (tpp-160) cc_final: 0.8718 (tpp-160) outliers start: 46 outliers final: 29 residues processed: 233 average time/residue: 1.6283 time to fit residues: 411.0480 Evaluate side-chains 239 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 117 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.057932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.046116 restraints weight = 26996.401| |-----------------------------------------------------------------------------| r_work (start): 0.2467 rms_B_bonded: 1.61 r_work: 0.2361 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2249 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13692 Z= 0.135 Angle : 0.869 26.164 18605 Z= 0.312 Chirality : 0.043 0.157 2069 Planarity : 0.005 0.065 2340 Dihedral : 5.778 65.932 1901 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.68 % Allowed : 20.23 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1684 helix: 0.97 (0.21), residues: 642 sheet: -0.65 (0.32), residues: 264 loop : -0.85 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 336 HIS 0.003 0.001 HIS A 36 PHE 0.028 0.001 PHE A 783 TYR 0.023 0.001 TYR A 120 ARG 0.004 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 553) hydrogen bonds : angle 5.05964 ( 1566) metal coordination : bond 0.01021 ( 45) metal coordination : angle 8.59490 ( 102) covalent geometry : bond 0.00322 (13646) covalent geometry : angle 0.59336 (18503) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7896 (pp20) REVERT: A 600 ARG cc_start: 0.8698 (ptt90) cc_final: 0.8415 (ptt180) REVERT: A 682 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8376 (mtpp) REVERT: A 861 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 25 GLU cc_start: 0.8788 (mp0) cc_final: 0.8551 (mp0) REVERT: B 388 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8844 (mtmt) REVERT: B 452 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 548 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.7018 (t) REVERT: C 62 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8400 (ptm-80) REVERT: C 64 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8909 (mt-10) outliers start: 38 outliers final: 22 residues processed: 234 average time/residue: 1.5545 time to fit residues: 391.0376 Evaluate side-chains 227 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 3.9990 chunk 101 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 146 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 133 optimal weight: 0.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.058409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.046387 restraints weight = 26931.590| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 1.62 r_work: 0.2377 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2263 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13692 Z= 0.128 Angle : 0.867 25.856 18605 Z= 0.318 Chirality : 0.044 0.154 2069 Planarity : 0.005 0.065 2340 Dihedral : 5.689 65.998 1901 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.11 % Allowed : 21.21 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1684 helix: 1.09 (0.21), residues: 640 sheet: -0.68 (0.32), residues: 264 loop : -0.79 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 336 HIS 0.003 0.001 HIS A 36 PHE 0.028 0.001 PHE A 783 TYR 0.023 0.001 TYR A 120 ARG 0.004 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 553) hydrogen bonds : angle 5.00537 ( 1566) metal coordination : bond 0.00896 ( 45) metal coordination : angle 8.34143 ( 102) covalent geometry : bond 0.00305 (13646) covalent geometry : angle 0.60949 (18503) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 ARG cc_start: 0.8698 (ptt90) cc_final: 0.8407 (ptt180) REVERT: A 682 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8375 (mtpp) REVERT: A 861 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 388 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8875 (mtmt) REVERT: B 432 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8408 (mtp) REVERT: B 452 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 548 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.7015 (t) REVERT: B 556 MET cc_start: 0.4399 (pp-130) cc_final: 0.4039 (ttm) REVERT: C 62 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8406 (ptm-80) REVERT: C 64 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8914 (mt-10) outliers start: 30 outliers final: 20 residues processed: 232 average time/residue: 1.5305 time to fit residues: 382.0178 Evaluate side-chains 227 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 682 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 763 GLN Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 63 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 106 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.058873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.047024 restraints weight = 27283.444| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 1.58 r_work: 0.2398 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2286 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13692 Z= 0.121 Angle : 0.861 25.634 18605 Z= 0.316 Chirality : 0.043 0.152 2069 Planarity : 0.005 0.062 2340 Dihedral : 5.559 66.066 1900 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.90 % Allowed : 21.35 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1684 helix: 1.21 (0.21), residues: 641 sheet: -0.65 (0.32), residues: 264 loop : -0.76 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 336 HIS 0.003 0.001 HIS A 36 PHE 0.026 0.001 PHE A 783 TYR 0.031 0.001 TYR A 906 ARG 0.007 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 553) hydrogen bonds : angle 4.94314 ( 1566) metal coordination : bond 0.00776 ( 45) metal coordination : angle 8.27422 ( 102) covalent geometry : bond 0.00287 (13646) covalent geometry : angle 0.60648 (18503) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10178.11 seconds wall clock time: 175 minutes 45.28 seconds (10545.28 seconds total)