Starting phenix.real_space_refine on Fri Sep 19 10:13:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ktl_62562/09_2025/9ktl_62562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ktl_62562/09_2025/9ktl_62562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ktl_62562/09_2025/9ktl_62562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ktl_62562/09_2025/9ktl_62562.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ktl_62562/09_2025/9ktl_62562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ktl_62562/09_2025/9ktl_62562.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 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 Mo 2 10.26 5 Fe 48 7.16 5 P 14 5.49 5 S 224 5.16 5 C 15750 2.51 5 N 4530 2.21 5 O 4800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25368 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7222 Classifications: {'peptide': 951} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 896} Chain: "G" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 477 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "F" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1096 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 143} Chain: "H" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 477 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "C" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3671 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 466} Chain: "E" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1096 Classifications: {'peptide': 149} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 143} Chain: "B" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7222 Classifications: {'peptide': 951} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 896} Chain: "D" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3671 Classifications: {'peptide': 496} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 466} Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Ad-hoc single atom residues: {'6MO': 1} Unusual residues: {'FES': 1, 'MGD': 2, 'SF4': 4} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 130 Ad-hoc single atom residues: {'6MO': 1} Unusual residues: {'FES': 1, 'MGD': 2, 'SF4': 4} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2845 SG CYS A 386 107.544 107.881 74.020 1.00 26.97 S ATOM 361 SG CYS A 57 70.805 109.165 52.792 1.00 13.59 S ATOM 433 SG CYS A 68 68.131 106.494 51.764 1.00 10.14 S ATOM 458 SG CYS A 71 65.100 108.754 55.665 1.00 9.18 S ATOM 559 SG CYS A 85 67.804 111.040 56.410 1.00 11.45 S ATOM 896 SG CYS A 130 75.390 96.166 48.583 1.00 4.82 S ATOM 839 SG CYS A 121 73.393 91.655 44.422 1.00 4.71 S ATOM 860 SG CYS A 124 79.531 93.309 44.931 1.00 5.70 S ATOM 1327 SG CYS A 185 76.441 106.118 50.104 1.00 5.52 S ATOM 1306 SG CYS A 182 79.146 106.020 44.213 1.00 7.58 S ATOM 1679 SG CYS A 234 80.910 102.069 49.292 1.00 2.32 S ATOM 1652 SG CYS A 230 87.745 105.182 51.894 1.00 10.50 S ATOM 1618 SG CYS A 224 92.230 107.934 51.366 1.00 9.89 S ATOM 1637 SG CYS A 227 90.437 107.782 56.538 1.00 5.27 S ATOM 1352 SG CYS A 188 85.620 109.038 51.738 1.00 35.58 S ATOM 1381 SG CYS A 192 86.702 111.655 52.775 1.00 27.02 S ATOM 1858 SG CYS A 258 96.409 99.992 66.248 1.00 3.81 S ATOM 2118 SG CYS A 293 96.706 104.817 62.277 1.00 3.87 S ATOM 1881 SG CYS A 261 98.428 105.703 68.156 1.00 6.03 S ATOM 1902 SG CYS A 265 92.243 104.356 67.425 1.00 6.49 S ATOM 8283 SG CYS F 77 66.800 130.369 26.394 1.00 13.57 S ATOM 8319 SG CYS F 82 64.830 131.837 23.954 1.00 23.34 S ATOM 8564 SG CYS F 116 64.830 132.710 30.690 1.00 18.85 S ATOM 8590 SG CYS F 120 62.246 134.043 29.208 1.00 14.09 S ATOM 12451 SG CYS C 429 74.092 59.768 44.368 1.00 2.97 S ATOM 12488 SG CYS C 435 78.547 62.371 40.132 1.00 5.46 S ATOM 12762 SG CYS C 473 79.757 58.009 44.575 1.00 6.37 S ATOM 12468 SG CYS C 432 78.708 64.667 45.103 1.00 4.79 S ATOM 13527 SG CYS E 77 78.324 48.199 26.377 1.00 13.20 S ATOM 13563 SG CYS E 82 80.267 46.714 23.980 1.00 23.16 S ATOM 13808 SG CYS E 116 80.352 45.793 30.746 1.00 19.74 S ATOM 13834 SG CYS E 120 82.884 44.516 29.229 1.00 14.42 S ATOM 16884 SG CYS B 386 37.684 70.594 74.132 1.00 27.37 S ATOM 14400 SG CYS B 57 74.270 69.381 52.792 1.00 12.22 S ATOM 14472 SG CYS B 68 76.942 72.059 51.766 1.00 9.64 S ATOM 14497 SG CYS B 71 79.980 69.817 55.674 1.00 9.40 S ATOM 14598 SG CYS B 85 77.275 67.524 56.409 1.00 11.91 S ATOM 14935 SG CYS B 130 69.692 82.401 48.569 1.00 5.04 S ATOM 14878 SG CYS B 121 71.688 86.904 44.418 1.00 5.04 S ATOM 14899 SG CYS B 124 65.557 85.251 44.929 1.00 6.02 S ATOM 15366 SG CYS B 185 68.665 72.452 50.127 1.00 5.20 S ATOM 15345 SG CYS B 182 65.926 72.541 44.209 1.00 7.51 S ATOM 15718 SG CYS B 234 64.170 76.508 49.329 1.00 2.13 S ATOM 15391 SG CYS B 188 62.942 70.242 49.189 1.00 2.05 S ATOM 15691 SG CYS B 230 57.660 72.702 51.917 1.00 3.48 S ATOM 15657 SG CYS B 224 52.133 70.980 51.061 1.00 8.26 S ATOM 15676 SG CYS B 227 54.575 70.959 57.232 1.00 4.17 S ATOM 15420 SG CYS B 192 56.517 66.568 53.583 1.00 5.71 S ATOM 15897 SG CYS B 258 48.672 78.567 66.250 1.00 3.91 S ATOM 16157 SG CYS B 293 48.374 73.738 62.276 1.00 3.75 S ATOM 15920 SG CYS B 261 46.650 72.858 68.157 1.00 6.54 S ATOM 15941 SG CYS B 265 52.842 74.222 67.420 1.00 6.58 S ATOM 24440 SG CYS D 429 70.973 118.817 44.339 1.00 3.18 S ATOM 24477 SG CYS D 435 66.504 116.205 40.129 1.00 5.50 S ATOM 24751 SG CYS D 473 65.326 120.548 44.584 1.00 5.73 S ATOM 24457 SG CYS D 432 66.371 113.892 45.106 1.00 4.96 S Time building chain proxies: 6.43, per 1000 atoms: 0.25 Number of scatterers: 25368 At special positions: 0 Unit cell: (146.01, 179.49, 111.6, 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) Mo 2 41.97 Fe 48 26.01 S 224 16.00 P 14 15.00 O 4800 8.00 N 4530 7.00 C 15750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1004 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 71 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 68 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 57 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 85 " pdb=" FES B1004 " pdb="FE2 FES B1004 " - pdb=" SG CYS B 71 " pdb="FE1 FES B1004 " - pdb=" SG CYS B 68 " pdb="FE1 FES B1004 " - pdb=" SG CYS B 57 " pdb="FE2 FES B1004 " - pdb=" SG CYS B 85 " pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 120 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 82 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 77 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 116 " pdb=" FES F 201 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 120 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 116 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 82 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 77 " pdb=" SF4 A1005 " pdb="FE4 SF4 A1005 " - pdb=" ND1 HIS A 117 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 130 " pdb="FE3 SF4 A1005 " - pdb=" SG CYS A 124 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 121 " pdb=" SF4 A1006 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 234 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 182 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 185 " pdb=" SF4 A1007 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 230 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 227 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 224 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 192 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 188 " pdb=" SF4 A1008 " pdb="FE4 SF4 A1008 " - pdb=" SG CYS A 265 " pdb="FE3 SF4 A1008 " - pdb=" SG CYS A 261 " pdb="FE1 SF4 A1008 " - pdb=" SG CYS A 258 " pdb="FE2 SF4 A1008 " - pdb=" SG CYS A 293 " pdb=" SF4 B1005 " pdb="FE4 SF4 B1005 " - pdb=" ND1 HIS B 117 " pdb="FE1 SF4 B1005 " - pdb=" SG CYS B 130 " pdb="FE3 SF4 B1005 " - pdb=" SG CYS B 124 " pdb="FE2 SF4 B1005 " - pdb=" SG CYS B 121 " pdb=" SF4 B1006 " pdb="FE4 SF4 B1006 " - pdb=" SG CYS B 188 " pdb="FE2 SF4 B1006 " - pdb=" SG CYS B 182 " pdb="FE3 SF4 B1006 " - pdb=" SG CYS B 234 " pdb="FE1 SF4 B1006 " - pdb=" SG CYS B 185 " pdb=" SF4 B1007 " pdb="FE3 SF4 B1007 " - pdb=" SG CYS B 227 " pdb="FE4 SF4 B1007 " - pdb=" SG CYS B 192 " pdb="FE1 SF4 B1007 " - pdb=" SG CYS B 230 " pdb="FE2 SF4 B1007 " - pdb=" SG CYS B 224 " pdb=" SF4 B1008 " pdb="FE4 SF4 B1008 " - pdb=" SG CYS B 265 " pdb="FE3 SF4 B1008 " - pdb=" SG CYS B 261 " pdb="FE1 SF4 B1008 " - pdb=" SG CYS B 258 " pdb="FE2 SF4 B1008 " - pdb=" SG CYS B 293 " pdb=" SF4 C 603 " pdb="FE1 SF4 C 603 " - pdb=" SG CYS C 429 " pdb="FE2 SF4 C 603 " - pdb=" SG CYS C 435 " pdb="FE3 SF4 C 603 " - pdb=" SG CYS C 473 " pdb="FE4 SF4 C 603 " - pdb=" SG CYS C 432 " pdb=" SF4 D 603 " pdb="FE1 SF4 D 603 " - pdb=" SG CYS D 429 " pdb="FE2 SF4 D 603 " - pdb=" SG CYS D 435 " pdb="FE3 SF4 D 603 " - pdb=" SG CYS D 473 " pdb="FE4 SF4 D 603 " - pdb=" SG CYS D 432 " Number of angles added : 138 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6008 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 30 sheets defined 48.9% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.716A pdb=" N ASP A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.521A pdb=" N GLY A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.775A pdb=" N GLU A 209 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.607A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 346 Processing helix chain 'A' and resid 359 through 373 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.671A pdb=" N LYS A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.563A pdb=" N VAL A 410 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 427 through 440 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 472 through 487 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 513 through 516 Processing helix chain 'A' and resid 517 through 526 removed outlier: 4.838A pdb=" N SER A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 542 Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.537A pdb=" N THR A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'A' and resid 591 through 598 removed outlier: 3.546A pdb=" N CYS A 596 " --> pdb=" O VAL A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 625 Processing helix chain 'A' and resid 635 through 646 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 664 through 674 Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 700 through 704 removed outlier: 3.710A pdb=" N LYS A 704 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.832A pdb=" N ILE A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 765 removed outlier: 3.618A pdb=" N ALA A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 762 through 765' Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 839 through 848 removed outlier: 6.239A pdb=" N GLU A 844 " --> pdb=" O ARG A 841 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN A 845 " --> pdb=" O ARG A 842 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 846 " --> pdb=" O THR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 906 through 910 removed outlier: 3.543A pdb=" N VAL A 910 " --> pdb=" O ALA A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 952 Processing helix chain 'G' and resid 5 through 18 Processing helix chain 'G' and resid 23 through 36 Processing helix chain 'G' and resid 37 through 50 Processing helix chain 'G' and resid 56 through 63 Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'F' and resid 4 through 14 Processing helix chain 'F' and resid 20 through 33 Processing helix chain 'F' and resid 36 through 38 No H-bonds generated for 'chain 'F' and resid 36 through 38' Processing helix chain 'F' and resid 39 through 48 Processing helix chain 'F' and resid 50 through 61 Processing helix chain 'F' and resid 79 through 84 Processing helix chain 'F' and resid 86 through 97 Processing helix chain 'F' and resid 137 through 150 Processing helix chain 'H' and resid 5 through 18 Processing helix chain 'H' and resid 23 through 36 Processing helix chain 'H' and resid 37 through 50 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'C' and resid 8 through 15 Processing helix chain 'C' and resid 15 through 31 Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 66 through 74 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 90 through 95 Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 121 through 130 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 192 through 208 removed outlier: 4.036A pdb=" N LEU C 196 " --> pdb=" O ASP C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 238 Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 260 through 269 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 310 removed outlier: 3.615A pdb=" N VAL C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) Proline residue: C 304 - end of helix Processing helix chain 'C' and resid 310 through 316 removed outlier: 3.606A pdb=" N TYR C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 353 Processing helix chain 'C' and resid 379 through 383 Processing helix chain 'C' and resid 388 through 394 Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 432 through 452 removed outlier: 4.609A pdb=" N VAL C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 471 removed outlier: 3.617A pdb=" N LEU C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.741A pdb=" N VAL C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 494 Processing helix chain 'E' and resid 4 through 14 Processing helix chain 'E' and resid 20 through 33 Processing helix chain 'E' and resid 36 through 38 No H-bonds generated for 'chain 'E' and resid 36 through 38' Processing helix chain 'E' and resid 39 through 48 Processing helix chain 'E' and resid 50 through 61 Processing helix chain 'E' and resid 79 through 84 Processing helix chain 'E' and resid 86 through 99 Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.737A pdb=" N ALA E 123 " --> pdb=" O CYS E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 150 Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.701A pdb=" N ASP B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 removed outlier: 3.521A pdb=" N GLY B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 186 through 195 Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.769A pdb=" N GLU B 209 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.601A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 346 removed outlier: 3.576A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 387 through 399 removed outlier: 3.667A pdb=" N LYS B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 413 removed outlier: 3.542A pdb=" N VAL B 410 " --> pdb=" O PHE B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 427 through 440 Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 472 through 487 Processing helix chain 'B' and resid 491 through 499 Processing helix chain 'B' and resid 500 through 512 Processing helix chain 'B' and resid 513 through 516 Processing helix chain 'B' and resid 517 through 526 removed outlier: 4.838A pdb=" N SER B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 Processing helix chain 'B' and resid 550 through 555 removed outlier: 3.543A pdb=" N THR B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 573 Processing helix chain 'B' and resid 591 through 598 removed outlier: 3.570A pdb=" N CYS B 596 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 625 Processing helix chain 'B' and resid 635 through 646 Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 664 through 674 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 700 through 704 removed outlier: 3.765A pdb=" N LYS B 704 " --> pdb=" O PHE B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 Processing helix chain 'B' and resid 749 through 761 removed outlier: 3.826A pdb=" N ILE B 753 " --> pdb=" O HIS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 removed outlier: 3.612A pdb=" N ALA B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 765' Processing helix chain 'B' and resid 768 through 776 Processing helix chain 'B' and resid 839 through 848 removed outlier: 6.233A pdb=" N GLU B 844 " --> pdb=" O ARG B 841 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASN B 845 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL B 846 " --> pdb=" O THR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 865 Processing helix chain 'B' and resid 906 through 910 removed outlier: 3.552A pdb=" N VAL B 910 " --> pdb=" O ALA B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 952 Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 15 through 31 Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 66 through 74 Proline residue: D 71 - end of helix Processing helix chain 'D' and resid 90 through 95 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 183 through 192 Processing helix chain 'D' and resid 192 through 208 removed outlier: 4.004A pdb=" N LEU D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 238 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.611A pdb=" N VAL D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 310 through 316 removed outlier: 3.569A pdb=" N TYR D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 353 Processing helix chain 'D' and resid 379 through 383 Processing helix chain 'D' and resid 388 through 394 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 432 through 452 removed outlier: 4.620A pdb=" N VAL D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 471 removed outlier: 3.621A pdb=" N LEU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 479 Processing helix chain 'D' and resid 479 through 490 removed outlier: 3.742A pdb=" N VAL D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 494 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 37 removed outlier: 9.277A pdb=" N VAL A 95 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 28 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.790A pdb=" N GLU A 160 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 257 removed outlier: 6.427A pdb=" N ARG A 272 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 6.788A pdb=" N LEU A 651 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS A 681 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 653 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 466 removed outlier: 6.342A pdb=" N LEU A 444 " --> pdb=" O TRP A 464 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 466 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 446 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA A 545 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ASN A 584 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 547 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 604 through 605 removed outlier: 3.659A pdb=" N ARG A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 706 through 709 Processing sheet with id=AB1, first strand: chain 'A' and resid 823 through 828 removed outlier: 6.070A pdb=" N LEU A 824 " --> pdb=" O VAL A 896 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR A 898 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR A 826 " --> pdb=" O THR A 898 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 899 " --> pdb=" O ARG A 853 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG A 853 " --> pdb=" O THR A 899 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU A 854 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 879 " --> pdb=" O SER A 876 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 104 through 106 removed outlier: 3.715A pdb=" N LEU F 111 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS F 72 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLU F 112 " --> pdb=" O HIS F 72 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE F 74 " --> pdb=" O GLU F 112 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU F 76 " --> pdb=" O ALA F 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 37 through 39 removed outlier: 6.334A pdb=" N ILE C 3 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN C 39 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 5 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ARG C 59 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU C 86 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLY C 61 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 246 through 251 Processing sheet with id=AB5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AB6, first strand: chain 'C' and resid 338 through 343 Processing sheet with id=AB7, first strand: chain 'E' and resid 104 through 106 removed outlier: 3.728A pdb=" N LEU E 111 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N HIS E 72 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLU E 112 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE E 74 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA E 114 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU E 76 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 32 through 37 removed outlier: 9.274A pdb=" N VAL B 95 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR B 28 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.604A pdb=" N GLU B 160 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AC2, first strand: chain 'B' and resid 202 through 204 Processing sheet with id=AC3, first strand: chain 'B' and resid 252 through 257 removed outlier: 6.424A pdb=" N ARG B 272 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 323 through 324 removed outlier: 6.825A pdb=" N LEU B 651 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N HIS B 681 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 653 " --> pdb=" O HIS B 681 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 463 through 466 removed outlier: 6.342A pdb=" N LEU B 444 " --> pdb=" O TRP B 464 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU B 466 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 446 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA B 545 " --> pdb=" O GLY B 582 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ASN B 584 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 547 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 604 through 605 removed outlier: 3.666A pdb=" N ARG B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 706 through 709 Processing sheet with id=AC8, first strand: chain 'B' and resid 823 through 828 removed outlier: 6.038A pdb=" N LEU B 824 " --> pdb=" O VAL B 896 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR B 898 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR B 826 " --> pdb=" O THR B 898 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 899 " --> pdb=" O ARG B 853 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG B 853 " --> pdb=" O THR B 899 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU B 854 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY B 879 " --> pdb=" O SER B 876 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 35 through 39 removed outlier: 6.132A pdb=" N ILE D 3 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASN D 39 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL D 5 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS D 2 " --> pdb=" O GLU D 54 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ARG D 59 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU D 86 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY D 61 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 246 through 251 Processing sheet with id=AD2, first strand: chain 'D' and resid 318 through 319 Processing sheet with id=AD3, first strand: chain 'D' and resid 338 through 343 1186 hydrogen bonds defined for protein. 3255 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: 5.70 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 10773 1.42 - 1.64: 14803 1.64 - 1.86: 251 1.86 - 2.07: 1 2.07 - 2.29: 136 Bond restraints: 25964 Sorted by residual: bond pdb=" C4 FMN C 602 " pdb=" C4A FMN C 602 " ideal model delta sigma weight residual 1.485 1.378 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C4 FMN D 602 " pdb=" C4A FMN D 602 " ideal model delta sigma weight residual 1.485 1.402 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" O5' FMN C 602 " pdb=" P FMN C 602 " ideal model delta sigma weight residual 1.676 1.595 0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C4A FMN C 602 " pdb=" N5 FMN C 602 " ideal model delta sigma weight residual 1.300 1.374 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C10 FMN C 602 " pdb=" C4A FMN C 602 " ideal model delta sigma weight residual 1.443 1.375 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 25959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 34776 2.25 - 4.49: 581 4.49 - 6.74: 82 6.74 - 8.99: 16 8.99 - 11.23: 7 Bond angle restraints: 35462 Sorted by residual: angle pdb=" C TYR F 115 " pdb=" N CYS F 116 " pdb=" CA CYS F 116 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C GLY D 400 " pdb=" N HIS D 401 " pdb=" CA HIS D 401 " ideal model delta sigma weight residual 121.02 114.81 6.21 1.48e+00 4.57e-01 1.76e+01 angle pdb=" C CYS A 188 " pdb=" CA CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sigma weight residual 110.85 103.98 6.87 1.70e+00 3.46e-01 1.63e+01 angle pdb=" C CYS F 122 " pdb=" N ALA F 123 " pdb=" CA ALA F 123 " ideal model delta sigma weight residual 120.97 131.73 -10.76 2.84e+00 1.24e-01 1.43e+01 angle pdb=" C11 MGD A1002 " pdb=" C10 MGD A1002 " pdb=" O3A MGD A1002 " ideal model delta sigma weight residual 107.91 119.14 -11.23 3.00e+00 1.11e-01 1.40e+01 ... (remaining 35457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.69: 14490 27.69 - 55.38: 978 55.38 - 83.07: 108 83.07 - 110.75: 16 110.75 - 138.44: 2 Dihedral angle restraints: 15594 sinusoidal: 6184 harmonic: 9410 Sorted by residual: dihedral pdb=" CA LYS D 278 " pdb=" C LYS D 278 " pdb=" N PRO D 279 " pdb=" CA PRO D 279 " ideal model delta harmonic sigma weight residual 180.00 152.46 27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA LYS C 278 " pdb=" C LYS C 278 " pdb=" N PRO C 279 " pdb=" CA PRO C 279 " ideal model delta harmonic sigma weight residual 180.00 152.61 27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA HIS C 401 " pdb=" C HIS C 401 " pdb=" N ALA C 402 " pdb=" CA ALA C 402 " ideal model delta harmonic sigma weight residual -180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 15591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2946 0.054 - 0.107: 896 0.107 - 0.161: 125 0.161 - 0.215: 7 0.215 - 0.268: 2 Chirality restraints: 3976 Sorted by residual: chirality pdb=" C11 MGD A1002 " pdb=" C10 MGD A1002 " pdb=" C12 MGD A1002 " pdb=" O11 MGD A1002 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C11 MGD B1002 " pdb=" C10 MGD B1002 " pdb=" C12 MGD B1002 " pdb=" O11 MGD B1002 " both_signs ideal model delta sigma weight residual False 2.43 2.17 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C23 MGD A1001 " pdb=" C14 MGD A1001 " pdb=" N22 MGD A1001 " pdb=" O11 MGD A1001 " both_signs ideal model delta sigma weight residual False 2.33 2.12 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3973 not shown) Planarity restraints: 4618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 278 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO D 279 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO D 279 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 279 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 278 " 0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO C 279 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 279 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 279 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 399 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C VAL C 399 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL C 399 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY C 400 " 0.014 2.00e-02 2.50e+03 ... (remaining 4615 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4318 2.76 - 3.30: 24266 3.30 - 3.83: 48074 3.83 - 4.37: 60905 4.37 - 4.90: 98479 Nonbonded interactions: 236042 Sorted by model distance: nonbonded pdb=" O GLY C 148 " pdb=" N7N NAI C 601 " model vdw 2.227 3.120 nonbonded pdb=" O GLY D 148 " pdb=" N7N NAI D 601 " model vdw 2.294 3.120 nonbonded pdb=" O2N NAI D 601 " pdb=" O2' FMN D 602 " model vdw 2.377 3.040 nonbonded pdb=" O ALA B 335 " pdb=" OD1 ASN B 339 " model vdw 2.443 3.040 nonbonded pdb=" C5' MGD B1002 " pdb=" O3B MGD B1002 " model vdw 2.485 2.752 ... (remaining 236037 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 2.080 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: 0.040 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.660 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.153 26020 Z= 0.319 Angle : 1.002 48.317 35600 Z= 0.369 Chirality : 0.049 0.268 3976 Planarity : 0.006 0.082 4618 Dihedral : 17.543 138.443 9586 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 2.82 % Allowed : 21.22 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.14), residues: 3308 helix: 0.41 (0.14), residues: 1344 sheet: -0.97 (0.23), residues: 440 loop : -0.49 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 853 TYR 0.022 0.002 TYR E 115 PHE 0.029 0.003 PHE C 419 TRP 0.032 0.002 TRP B 780 HIS 0.006 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00743 (25964) covalent geometry : angle 0.72219 (35462) hydrogen bonds : bond 0.13755 ( 1186) hydrogen bonds : angle 7.31155 ( 3255) metal coordination : bond 0.03815 ( 56) metal coordination : angle 11.17526 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 270 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7621 (p0) cc_final: 0.7405 (p0) REVERT: A 657 ASP cc_start: 0.8204 (t0) cc_final: 0.7992 (t0) REVERT: A 952 ARG cc_start: 0.8622 (mtt-85) cc_final: 0.8380 (mtt-85) REVERT: D 189 ILE cc_start: 0.8782 (tt) cc_final: 0.8581 (tt) outliers start: 72 outliers final: 48 residues processed: 331 average time/residue: 0.2085 time to fit residues: 102.3486 Evaluate side-chains 257 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain F residue 8 ARG Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 8 ARG Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 934 SER Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.7980 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 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN D 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.077742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.061193 restraints weight = 46509.827| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.07 r_work: 0.2598 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 26020 Z= 0.136 Angle : 0.938 51.101 35600 Z= 0.286 Chirality : 0.042 0.170 3976 Planarity : 0.005 0.062 4618 Dihedral : 9.631 132.824 4116 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 2.78 % Allowed : 19.53 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.15), residues: 3308 helix: 1.11 (0.14), residues: 1356 sheet: -0.79 (0.23), residues: 430 loop : -0.17 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 18 TYR 0.013 0.001 TYR A 834 PHE 0.020 0.001 PHE D 419 TRP 0.017 0.001 TRP B 780 HIS 0.006 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00296 (25964) covalent geometry : angle 0.54116 (35462) hydrogen bonds : bond 0.03966 ( 1186) hydrogen bonds : angle 5.58010 ( 3255) metal coordination : bond 0.02430 ( 56) metal coordination : angle 12.30925 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 235 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8686 (p0) cc_final: 0.8218 (p0) REVERT: A 135 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.9242 (mpp) REVERT: A 148 LYS cc_start: 0.9135 (tttm) cc_final: 0.8933 (tttm) REVERT: A 187 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8503 (ttp-170) REVERT: A 245 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: A 271 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.7870 (mmm) REVERT: A 657 ASP cc_start: 0.8976 (t0) cc_final: 0.8576 (t70) REVERT: A 675 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8278 (mtt) REVERT: F 80 GLU cc_start: 0.8996 (mp0) cc_final: 0.8661 (mp0) REVERT: C 114 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8559 (mt0) REVERT: C 138 GLU cc_start: 0.9292 (OUTLIER) cc_final: 0.8957 (tp30) REVERT: E 104 GLU cc_start: 0.8843 (tt0) cc_final: 0.8597 (tt0) REVERT: B 135 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.9272 (mpp) REVERT: B 186 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8584 (mpp) REVERT: B 675 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8218 (mtt) REVERT: B 944 TYR cc_start: 0.8324 (t80) cc_final: 0.8013 (t80) REVERT: D 138 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8961 (tp30) outliers start: 71 outliers final: 23 residues processed: 288 average time/residue: 0.1819 time to fit residues: 79.9197 Evaluate side-chains 256 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 684 PHE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 307 optimal weight: 0.6980 chunk 319 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 294 optimal weight: 5.9990 chunk 320 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN F 72 HIS F 91 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.059446 restraints weight = 47122.957| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 2.07 r_work: 0.2530 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 26020 Z= 0.185 Angle : 0.960 55.280 35600 Z= 0.286 Chirality : 0.043 0.187 3976 Planarity : 0.005 0.077 4618 Dihedral : 8.844 129.109 4051 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.22 % Rotamer: Outliers : 2.75 % Allowed : 19.45 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.15), residues: 3308 helix: 1.31 (0.14), residues: 1358 sheet: -0.72 (0.23), residues: 430 loop : -0.06 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 666 TYR 0.018 0.001 TYR F 115 PHE 0.021 0.001 PHE C 419 TRP 0.013 0.001 TRP B 322 HIS 0.003 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00416 (25964) covalent geometry : angle 0.54751 (35462) hydrogen bonds : bond 0.03861 ( 1186) hydrogen bonds : angle 5.31540 ( 3255) metal coordination : bond 0.03009 ( 56) metal coordination : angle 12.68143 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 230 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8699 (p0) cc_final: 0.8235 (p0) REVERT: A 135 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9269 (mpp) REVERT: A 148 LYS cc_start: 0.9138 (tttm) cc_final: 0.8924 (tttm) REVERT: A 271 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.7944 (mmm) REVERT: A 675 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8296 (mtt) REVERT: A 830 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9028 (pp) REVERT: A 873 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8039 (ttm110) REVERT: F 80 GLU cc_start: 0.9017 (mp0) cc_final: 0.8665 (mp0) REVERT: F 83 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8832 (mt0) REVERT: C 114 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: C 138 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8911 (tp30) REVERT: C 465 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8930 (t0) REVERT: C 473 CYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9053 (p) REVERT: B 135 MET cc_start: 0.9561 (OUTLIER) cc_final: 0.9280 (mpp) REVERT: B 675 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: B 867 ARG cc_start: 0.8901 (ttm-80) cc_final: 0.8583 (ttm-80) REVERT: D 138 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.8912 (tp30) outliers start: 70 outliers final: 31 residues processed: 285 average time/residue: 0.1975 time to fit residues: 84.8078 Evaluate side-chains 264 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain C residue 473 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 60 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 199 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 59 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.0010 chunk 118 optimal weight: 1.9990 overall best weight: 1.6090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 HIS B 387 HIS B 638 ASN D 114 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.059890 restraints weight = 47051.393| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.03 r_work: 0.2543 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2405 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 26020 Z= 0.165 Angle : 0.968 59.212 35600 Z= 0.279 Chirality : 0.042 0.189 3976 Planarity : 0.004 0.080 4618 Dihedral : 8.673 128.026 4048 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.22 % Rotamer: Outliers : 3.06 % Allowed : 19.61 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.15), residues: 3308 helix: 1.46 (0.14), residues: 1358 sheet: -0.70 (0.23), residues: 430 loop : 0.00 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 410 TYR 0.014 0.001 TYR F 115 PHE 0.019 0.001 PHE C 419 TRP 0.008 0.001 TRP B 780 HIS 0.004 0.001 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00373 (25964) covalent geometry : angle 0.53352 (35462) hydrogen bonds : bond 0.03629 ( 1186) hydrogen bonds : angle 5.14559 ( 3255) metal coordination : bond 0.02683 ( 56) metal coordination : angle 12.98512 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 232 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8700 (p0) cc_final: 0.8242 (p0) REVERT: A 135 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9288 (mpp) REVERT: A 246 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8544 (mp0) REVERT: A 271 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.7957 (mmm) REVERT: A 675 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8308 (mtt) REVERT: A 687 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8881 (mm-30) REVERT: A 830 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9058 (pp) REVERT: A 873 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7998 (ttm110) REVERT: G 26 GLU cc_start: 0.7490 (mp0) cc_final: 0.7269 (mp0) REVERT: F 15 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: F 83 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8856 (mt0) REVERT: C 114 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8600 (mt0) REVERT: C 138 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.8892 (tp30) REVERT: C 473 CYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9024 (p) REVERT: E 15 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: B 135 MET cc_start: 0.9560 (OUTLIER) cc_final: 0.9296 (mpp) REVERT: B 186 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.8516 (mpp) REVERT: B 675 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8240 (mtt) REVERT: B 867 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8565 (ttm-80) REVERT: B 944 TYR cc_start: 0.8269 (t80) cc_final: 0.7999 (t80) REVERT: D 65 MET cc_start: 0.9245 (mmm) cc_final: 0.8900 (mmm) REVERT: D 138 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8890 (tp30) REVERT: D 465 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8897 (t0) REVERT: D 473 CYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9000 (p) outliers start: 78 outliers final: 42 residues processed: 288 average time/residue: 0.1985 time to fit residues: 86.6523 Evaluate side-chains 278 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 473 CYS Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain D residue 473 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 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 = 0.3064 r_free = 0.3064 target = 0.077177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.060801 restraints weight = 46775.435| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.07 r_work: 0.2570 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 26020 Z= 0.123 Angle : 0.924 53.688 35600 Z= 0.264 Chirality : 0.041 0.166 3976 Planarity : 0.004 0.081 4618 Dihedral : 8.453 126.007 4048 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 2.86 % Allowed : 19.53 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.15), residues: 3308 helix: 1.58 (0.14), residues: 1358 sheet: -0.67 (0.23), residues: 430 loop : 0.09 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 79 TYR 0.012 0.001 TYR B 834 PHE 0.016 0.001 PHE D 419 TRP 0.009 0.001 TRP B 322 HIS 0.005 0.001 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00276 (25964) covalent geometry : angle 0.50519 (35462) hydrogen bonds : bond 0.03396 ( 1186) hydrogen bonds : angle 5.01153 ( 3255) metal coordination : bond 0.01991 ( 56) metal coordination : angle 12.43198 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 231 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8696 (p0) cc_final: 0.8234 (p0) REVERT: A 135 MET cc_start: 0.9541 (OUTLIER) cc_final: 0.9271 (mpp) REVERT: A 148 LYS cc_start: 0.9044 (tttm) cc_final: 0.8809 (tptp) REVERT: A 246 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8588 (mm-30) REVERT: A 271 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.7968 (mmm) REVERT: A 687 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8918 (mm-30) REVERT: A 830 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9085 (pp) REVERT: A 873 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8032 (ttm110) REVERT: G 26 GLU cc_start: 0.7587 (mp0) cc_final: 0.7317 (mp0) REVERT: F 15 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: F 83 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8813 (mt0) REVERT: C 138 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.8857 (tp30) REVERT: C 190 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: E 15 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: E 83 GLN cc_start: 0.9062 (mt0) cc_final: 0.8800 (mt0) REVERT: B 135 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.9271 (mpp) REVERT: B 186 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.8509 (mpp) REVERT: B 271 MET cc_start: 0.8826 (mmm) cc_final: 0.8437 (mmm) REVERT: B 675 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8234 (mtt) REVERT: B 867 ARG cc_start: 0.8881 (ttm-80) cc_final: 0.8567 (ttm-80) REVERT: B 944 TYR cc_start: 0.8278 (t80) cc_final: 0.8035 (t80) REVERT: D 65 MET cc_start: 0.9254 (mmm) cc_final: 0.8927 (mmm) REVERT: D 138 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8841 (tp30) REVERT: D 465 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8880 (t0) outliers start: 73 outliers final: 43 residues processed: 284 average time/residue: 0.1913 time to fit residues: 83.1389 Evaluate side-chains 281 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 892 SER Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 465 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 129 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 258 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 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 = 0.3038 r_free = 0.3038 target = 0.075820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.059670 restraints weight = 47462.044| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.04 r_work: 0.2542 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2406 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 26020 Z= 0.173 Angle : 0.997 65.120 35600 Z= 0.282 Chirality : 0.042 0.206 3976 Planarity : 0.004 0.081 4618 Dihedral : 8.457 126.340 4045 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % Rotamer: Outliers : 2.94 % Allowed : 19.29 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.15), residues: 3308 helix: 1.64 (0.14), residues: 1358 sheet: -0.63 (0.23), residues: 430 loop : 0.11 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 79 TYR 0.016 0.001 TYR F 115 PHE 0.019 0.001 PHE C 419 TRP 0.009 0.001 TRP D 46 HIS 0.003 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00393 (25964) covalent geometry : angle 0.53584 (35462) hydrogen bonds : bond 0.03584 ( 1186) hydrogen bonds : angle 5.00165 ( 3255) metal coordination : bond 0.02919 ( 56) metal coordination : angle 13.51847 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 222 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8711 (p0) cc_final: 0.8246 (p0) REVERT: A 135 MET cc_start: 0.9550 (OUTLIER) cc_final: 0.9303 (mpp) REVERT: A 148 LYS cc_start: 0.9020 (tttm) cc_final: 0.8773 (tptp) REVERT: A 246 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8565 (mm-30) REVERT: A 271 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.7987 (mmm) REVERT: A 675 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8332 (mtt) REVERT: A 687 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8948 (mm-30) REVERT: A 830 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9071 (pp) REVERT: A 873 ARG cc_start: 0.8386 (ttm110) cc_final: 0.8038 (ttm110) REVERT: G 26 GLU cc_start: 0.7574 (mp0) cc_final: 0.7372 (mp0) REVERT: F 15 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: C 138 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8836 (tp30) REVERT: C 190 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: C 473 CYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9010 (p) REVERT: E 15 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: E 104 GLU cc_start: 0.8832 (tt0) cc_final: 0.8585 (pt0) REVERT: E 138 ASP cc_start: 0.8576 (m-30) cc_final: 0.8101 (m-30) REVERT: B 135 MET cc_start: 0.9556 (OUTLIER) cc_final: 0.9266 (mpp) REVERT: B 186 MET cc_start: 0.9453 (OUTLIER) cc_final: 0.8536 (mpp) REVERT: B 261 CYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8690 (p) REVERT: B 271 MET cc_start: 0.8921 (mmm) cc_final: 0.8524 (mmm) REVERT: B 412 ASP cc_start: 0.9089 (m-30) cc_final: 0.8774 (m-30) REVERT: B 675 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8269 (mtt) REVERT: B 687 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8959 (mm-30) REVERT: B 867 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8541 (ttm-80) REVERT: B 935 ASN cc_start: 0.9002 (m-40) cc_final: 0.8183 (t0) REVERT: D 65 MET cc_start: 0.9252 (mmm) cc_final: 0.8941 (mmm) REVERT: D 138 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.8800 (tp30) REVERT: D 328 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9234 (mt) REVERT: D 465 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8879 (t0) REVERT: D 473 CYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8994 (p) outliers start: 75 outliers final: 43 residues processed: 275 average time/residue: 0.1922 time to fit residues: 80.4940 Evaluate side-chains 279 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 473 CYS Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain D residue 473 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 272 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.076321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.060244 restraints weight = 46790.761| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.03 r_work: 0.2557 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2422 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 26020 Z= 0.145 Angle : 0.971 63.880 35600 Z= 0.273 Chirality : 0.042 0.174 3976 Planarity : 0.004 0.081 4618 Dihedral : 8.366 125.807 4045 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 2.90 % Allowed : 19.53 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.15), residues: 3308 helix: 1.68 (0.15), residues: 1346 sheet: -0.58 (0.23), residues: 430 loop : 0.17 (0.17), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 79 TYR 0.014 0.001 TYR F 115 PHE 0.017 0.001 PHE C 419 TRP 0.008 0.001 TRP B 940 HIS 0.003 0.001 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00327 (25964) covalent geometry : angle 0.51870 (35462) hydrogen bonds : bond 0.03443 ( 1186) hydrogen bonds : angle 4.96829 ( 3255) metal coordination : bond 0.02439 ( 56) metal coordination : angle 13.19602 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 228 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8707 (p0) cc_final: 0.8245 (p0) REVERT: A 135 MET cc_start: 0.9541 (OUTLIER) cc_final: 0.9296 (mpp) REVERT: A 148 LYS cc_start: 0.9008 (tttm) cc_final: 0.8749 (tptp) REVERT: A 261 CYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8690 (p) REVERT: A 271 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.7999 (mmm) REVERT: A 675 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8343 (mtt) REVERT: A 687 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8967 (mm-30) REVERT: A 830 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9080 (pp) REVERT: A 873 ARG cc_start: 0.8404 (ttm110) cc_final: 0.7982 (ttm110) REVERT: G 26 GLU cc_start: 0.7653 (mp0) cc_final: 0.7419 (mp0) REVERT: F 15 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: F 101 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8852 (mmtp) REVERT: C 138 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.8778 (tp30) REVERT: C 328 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9206 (mt) REVERT: C 473 CYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9015 (p) REVERT: E 15 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: E 83 GLN cc_start: 0.9072 (mt0) cc_final: 0.8862 (mt0) REVERT: E 104 GLU cc_start: 0.8799 (tt0) cc_final: 0.8550 (pt0) REVERT: E 138 ASP cc_start: 0.8550 (m-30) cc_final: 0.8064 (m-30) REVERT: B 135 MET cc_start: 0.9547 (OUTLIER) cc_final: 0.9300 (mpp) REVERT: B 261 CYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8675 (p) REVERT: B 271 MET cc_start: 0.8902 (mmm) cc_final: 0.8482 (mmm) REVERT: B 412 ASP cc_start: 0.9076 (m-30) cc_final: 0.8755 (m-30) REVERT: B 675 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8270 (mtt) REVERT: B 687 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8956 (mm-30) REVERT: B 867 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8549 (ttm-80) REVERT: B 935 ASN cc_start: 0.8974 (m-40) cc_final: 0.8168 (t0) REVERT: D 65 MET cc_start: 0.9254 (mmm) cc_final: 0.8946 (mmm) REVERT: D 138 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.8779 (tp30) REVERT: D 328 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9235 (mt) REVERT: D 465 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8877 (t0) REVERT: D 473 CYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9000 (p) outliers start: 74 outliers final: 49 residues processed: 281 average time/residue: 0.1906 time to fit residues: 82.5335 Evaluate side-chains 288 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 473 CYS Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain D residue 473 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 102 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 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 = 0.3023 r_free = 0.3023 target = 0.074935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.058397 restraints weight = 48012.698| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.08 r_work: 0.2515 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2378 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 26020 Z= 0.200 Angle : 0.988 61.065 35600 Z= 0.286 Chirality : 0.043 0.193 3976 Planarity : 0.004 0.084 4618 Dihedral : 8.434 127.073 4045 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 2.55 % Allowed : 19.84 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.15), residues: 3308 helix: 1.67 (0.14), residues: 1346 sheet: -0.55 (0.23), residues: 418 loop : 0.13 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 79 TYR 0.017 0.001 TYR F 115 PHE 0.021 0.001 PHE C 419 TRP 0.008 0.001 TRP A 917 HIS 0.003 0.001 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00456 (25964) covalent geometry : angle 0.54816 (35462) hydrogen bonds : bond 0.03663 ( 1186) hydrogen bonds : angle 5.00232 ( 3255) metal coordination : bond 0.02894 ( 56) metal coordination : angle 13.22239 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8728 (p0) cc_final: 0.8275 (p0) REVERT: A 135 MET cc_start: 0.9566 (OUTLIER) cc_final: 0.9287 (mpp) REVERT: A 148 LYS cc_start: 0.9008 (tttm) cc_final: 0.8744 (tptp) REVERT: A 187 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8649 (mtp180) REVERT: A 261 CYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8698 (p) REVERT: A 271 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.7947 (mmm) REVERT: A 675 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8373 (mtt) REVERT: A 687 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8924 (mm-30) REVERT: A 830 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9058 (pp) REVERT: A 873 ARG cc_start: 0.8417 (ttm110) cc_final: 0.7925 (ttm110) REVERT: G 26 GLU cc_start: 0.7690 (mp0) cc_final: 0.7428 (mp0) REVERT: F 15 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: C 328 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9220 (mt) REVERT: C 473 CYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9015 (p) REVERT: E 15 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: E 104 GLU cc_start: 0.8821 (tt0) cc_final: 0.8607 (pt0) REVERT: E 138 ASP cc_start: 0.8577 (m-30) cc_final: 0.8064 (m-30) REVERT: B 135 MET cc_start: 0.9570 (OUTLIER) cc_final: 0.9293 (mpp) REVERT: B 261 CYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8713 (p) REVERT: B 412 ASP cc_start: 0.9092 (m-30) cc_final: 0.8806 (m-30) REVERT: B 675 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8312 (mtt) REVERT: B 867 ARG cc_start: 0.8860 (ttm-80) cc_final: 0.8557 (ttm-80) REVERT: B 935 ASN cc_start: 0.8990 (m-40) cc_final: 0.8210 (t0) REVERT: D 65 MET cc_start: 0.9258 (mmm) cc_final: 0.8957 (mmm) REVERT: D 328 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9266 (mt) REVERT: D 465 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8876 (t0) REVERT: D 473 CYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8998 (p) outliers start: 65 outliers final: 45 residues processed: 270 average time/residue: 0.1950 time to fit residues: 80.2194 Evaluate side-chains 280 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 473 CYS Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain D residue 473 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 112 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.075826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.059365 restraints weight = 47884.954| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.09 r_work: 0.2538 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2401 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 26020 Z= 0.158 Angle : 0.967 60.127 35600 Z= 0.276 Chirality : 0.042 0.177 3976 Planarity : 0.004 0.082 4618 Dihedral : 8.333 126.934 4045 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.60 % Favored : 97.34 % Rotamer: Outliers : 2.63 % Allowed : 19.88 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.15), residues: 3308 helix: 1.69 (0.14), residues: 1346 sheet: -0.57 (0.23), residues: 430 loop : 0.17 (0.17), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 289 TYR 0.014 0.001 TYR F 115 PHE 0.018 0.001 PHE C 419 TRP 0.008 0.001 TRP A 322 HIS 0.006 0.001 HIS D 401 Details of bonding type rmsd covalent geometry : bond 0.00359 (25964) covalent geometry : angle 0.52857 (35462) hydrogen bonds : bond 0.03509 ( 1186) hydrogen bonds : angle 4.96271 ( 3255) metal coordination : bond 0.02371 ( 56) metal coordination : angle 13.02460 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8723 (p0) cc_final: 0.8272 (p0) REVERT: A 135 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.9315 (mpp) REVERT: A 148 LYS cc_start: 0.9012 (tttm) cc_final: 0.8786 (tptp) REVERT: A 187 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8640 (mtp180) REVERT: A 261 CYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8678 (p) REVERT: A 271 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.7957 (mmm) REVERT: A 675 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8360 (mtt) REVERT: A 687 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8913 (mm-30) REVERT: A 830 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9078 (pp) REVERT: A 873 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7927 (ttm110) REVERT: G 26 GLU cc_start: 0.7754 (mp0) cc_final: 0.7470 (mp0) REVERT: F 15 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: H 26 GLU cc_start: 0.7842 (pm20) cc_final: 0.7642 (pm20) REVERT: C 328 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9215 (mt) REVERT: C 473 CYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9012 (p) REVERT: E 15 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: E 104 GLU cc_start: 0.8796 (tt0) cc_final: 0.8590 (pt0) REVERT: E 138 ASP cc_start: 0.8564 (m-30) cc_final: 0.8085 (m-30) REVERT: B 135 MET cc_start: 0.9553 (OUTLIER) cc_final: 0.9308 (mpp) REVERT: B 186 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8488 (mpp) REVERT: B 261 CYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8694 (p) REVERT: B 412 ASP cc_start: 0.9099 (m-30) cc_final: 0.8778 (m-30) REVERT: B 675 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8296 (mtt) REVERT: B 867 ARG cc_start: 0.8868 (ttm-80) cc_final: 0.8564 (ttm-80) REVERT: B 935 ASN cc_start: 0.8968 (m-40) cc_final: 0.8223 (t0) REVERT: B 944 TYR cc_start: 0.8324 (t80) cc_final: 0.8009 (t80) REVERT: D 65 MET cc_start: 0.9263 (mmm) cc_final: 0.8961 (mmm) REVERT: D 328 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9259 (mt) REVERT: D 465 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8864 (t0) REVERT: D 473 CYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9000 (p) outliers start: 67 outliers final: 46 residues processed: 275 average time/residue: 0.1908 time to fit residues: 79.8869 Evaluate side-chains 284 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 473 CYS Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain D residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 180 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 253 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.074934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.058751 restraints weight = 48412.442| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.05 r_work: 0.2523 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 26020 Z= 0.198 Angle : 1.028 65.896 35600 Z= 0.293 Chirality : 0.043 0.219 3976 Planarity : 0.004 0.083 4618 Dihedral : 8.374 127.679 4045 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 2.51 % Allowed : 20.00 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.15), residues: 3308 helix: 1.67 (0.14), residues: 1346 sheet: -0.52 (0.24), residues: 418 loop : 0.13 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 884 TYR 0.016 0.001 TYR F 115 PHE 0.020 0.001 PHE C 419 TRP 0.009 0.001 TRP C 46 HIS 0.012 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00450 (25964) covalent geometry : angle 0.55729 (35462) hydrogen bonds : bond 0.03681 ( 1186) hydrogen bonds : angle 4.99551 ( 3255) metal coordination : bond 0.03047 ( 56) metal coordination : angle 13.88572 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6616 Ramachandran restraints generated. 3308 Oldfield, 0 Emsley, 3308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8719 (p0) cc_final: 0.8263 (p0) REVERT: A 135 MET cc_start: 0.9565 (OUTLIER) cc_final: 0.9324 (mpp) REVERT: A 148 LYS cc_start: 0.9014 (tttm) cc_final: 0.8788 (tptp) REVERT: A 156 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.9130 (mmm-85) REVERT: A 261 CYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 271 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.7937 (mmm) REVERT: A 675 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8381 (mtt) REVERT: A 687 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8917 (mm-30) REVERT: A 830 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9070 (pp) REVERT: A 873 ARG cc_start: 0.8418 (ttm110) cc_final: 0.8094 (ttm110) REVERT: G 26 GLU cc_start: 0.7749 (mp0) cc_final: 0.7452 (mp0) REVERT: F 15 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: C 328 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9221 (mt) REVERT: C 473 CYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9019 (p) REVERT: E 15 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: E 104 GLU cc_start: 0.8837 (tt0) cc_final: 0.8589 (pt0) REVERT: E 138 ASP cc_start: 0.8580 (m-30) cc_final: 0.8082 (m-30) REVERT: B 135 MET cc_start: 0.9566 (OUTLIER) cc_final: 0.9319 (mpp) REVERT: B 261 CYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8712 (p) REVERT: B 412 ASP cc_start: 0.9086 (m-30) cc_final: 0.8769 (m-30) REVERT: B 675 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8309 (mtt) REVERT: B 867 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8556 (ttm-80) REVERT: B 935 ASN cc_start: 0.8971 (m-40) cc_final: 0.8258 (t0) REVERT: B 944 TYR cc_start: 0.8400 (t80) cc_final: 0.8058 (t80) REVERT: D 65 MET cc_start: 0.9262 (mmm) cc_final: 0.8967 (mmm) REVERT: D 138 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.8774 (tp30) REVERT: D 328 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9257 (mt) REVERT: D 465 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8868 (t0) REVERT: D 473 CYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8984 (p) outliers start: 64 outliers final: 46 residues processed: 263 average time/residue: 0.1956 time to fit residues: 77.9583 Evaluate side-chains 277 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 214 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 662 ASP Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 473 CYS Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 675 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 913 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 398 LEU Chi-restraints excluded: chain D residue 465 ASP Chi-restraints excluded: chain D residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 179 optimal weight: 3.9990 chunk 321 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.058394 restraints weight = 49032.165| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.08 r_work: 0.2512 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2374 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 26020 Z= 0.204 Angle : 1.027 66.031 35600 Z= 0.295 Chirality : 0.043 0.210 3976 Planarity : 0.004 0.083 4618 Dihedral : 8.399 128.471 4045 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % Rotamer: Outliers : 2.39 % Allowed : 20.16 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.15), residues: 3308 helix: 1.63 (0.14), residues: 1346 sheet: -0.58 (0.23), residues: 430 loop : 0.15 (0.17), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 884 TYR 0.016 0.001 TYR F 115 PHE 0.020 0.001 PHE C 419 TRP 0.008 0.001 TRP A 917 HIS 0.008 0.001 HIS F 107 Details of bonding type rmsd covalent geometry : bond 0.00464 (25964) covalent geometry : angle 0.56085 (35462) hydrogen bonds : bond 0.03722 ( 1186) hydrogen bonds : angle 5.01681 ( 3255) metal coordination : bond 0.03191 ( 56) metal coordination : angle 13.83134 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6026.08 seconds wall clock time: 104 minutes 25.27 seconds (6265.27 seconds total)