Starting phenix.real_space_refine on Fri Apr 12 10:27:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uis_42303/04_2024/8uis_42303_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uis_42303/04_2024/8uis_42303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uis_42303/04_2024/8uis_42303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uis_42303/04_2024/8uis_42303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uis_42303/04_2024/8uis_42303_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uis_42303/04_2024/8uis_42303_neut.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 79 5.49 5 Mg 1 5.21 5 S 242 5.16 5 C 25147 2.51 5 N 7049 2.21 5 O 7707 1.98 5 H 39727 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1433": "OE1" <-> "OE2" Residue "A GLU 1434": "OE1" <-> "OE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 79960 Number of models: 1 Model: "" Number of chains: 25 Chain: "N" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 855 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "P" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 447 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain: "T" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 1209 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "W" Number of atoms: 6058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 6058 Classifications: {'peptide': 381} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 362} Chain breaks: 4 Chain: "Z" Number of atoms: 4375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 4375 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 3 Chain: "A" Number of atoms: 22549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1415, 22549 Classifications: {'peptide': 1415} Link IDs: {'PCIS': 3, 'PTRANS': 66, 'TRANS': 1345} Chain breaks: 4 Chain: "B" Number of atoms: 18194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 18194 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 4039 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 15, 'TRANS': 239} Chain breaks: 1 Chain: "D" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 2016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 3438 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Chain: "F" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain: "G" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2709 Classifications: {'peptide': 171} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 2333 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1790 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1049 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1862 Classifications: {'peptide': 115} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 753 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "U" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3054 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13875 SG CYS A 71 72.742 55.774 74.279 1.00269.33 S ATOM 13916 SG CYS A 74 69.247 57.219 75.076 1.00267.76 S ATOM 14003 SG CYS A 81 72.312 58.835 75.192 1.00269.02 S ATOM 14487 SG CYS A 111 59.919 68.220 120.445 1.00248.50 S ATOM 14537 SG CYS A 114 57.533 65.779 119.985 1.00248.14 S ATOM 15196 SG CYS A 154 57.803 68.871 122.186 1.00253.18 S ATOM 15234 SG CYS A 184 59.309 65.828 123.441 1.00247.08 S ATOM 52847 SG CYS B1122 58.272 60.279 85.248 1.00268.02 S ATOM 53072 SG CYS B1137 59.549 56.809 83.694 1.00263.26 S ATOM 53113 SG CYS B1140 56.770 56.981 86.689 1.00263.54 S ATOM 55068 SG CYS C 88 92.371 89.733 18.927 1.00177.96 S ATOM 55093 SG CYS C 90 94.240 87.114 21.040 1.00192.26 S ATOM 55153 SG CYS C 94 95.824 89.486 18.465 1.00173.87 S ATOM 55192 SG CYS C 97 94.914 90.928 21.296 1.00168.28 S ATOM 69584 SG CYS I 17 100.155 118.032 139.691 1.00245.98 S ATOM 69626 SG CYS I 20 100.515 115.106 137.768 1.00243.72 S ATOM 69948 SG CYS I 39 97.396 115.736 139.066 1.00249.49 S ATOM 70670 SG CYS I 86 101.610 149.825 107.918 1.00250.73 S ATOM 70719 SG CYS I 89 105.178 150.761 107.024 1.00249.67 S ATOM 71112 SG CYS I 114 103.586 147.666 105.623 1.00245.51 S ATOM 71177 SG CYS I 119 104.082 147.903 109.332 1.00242.06 S ATOM 71400 SG CYS J 7 96.656 115.962 41.007 1.00153.15 S ATOM 71444 SG CYS J 10 95.950 116.779 37.741 1.00156.95 S ATOM 71969 SG CYS J 44 95.106 119.510 40.451 1.00160.18 S ATOM 71979 SG CYS J 45 98.365 118.805 38.771 1.00161.67 S ATOM 74275 SG CYS L 19 122.257 83.488 56.976 1.00172.29 S ATOM 74308 SG CYS L 22 125.423 84.149 55.420 1.00174.83 S ATOM 74538 SG CYS L 36 124.872 80.696 55.993 1.00181.80 S Time building chain proxies: 29.28, per 1000 atoms: 0.37 Number of scatterers: 79960 At special positions: 0 Unit cell: (145.494, 201.39, 161.934, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 242 16.00 P 79 15.00 Mg 1 11.99 O 7707 8.00 N 7049 7.00 C 25147 6.00 H 39727 1.00 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 - 3.50 Amino acid : False - 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: 53.85 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " Number of angles added : 24 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9132 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 56 sheets defined 43.1% alpha, 17.8% beta 28 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 33.02 Creating SS restraints... Processing helix chain 'W' and resid 190 through 195 Processing helix chain 'W' and resid 197 through 215 Processing helix chain 'W' and resid 219 through 232 Proline residue: W 225 - end of helix removed outlier: 3.619A pdb=" N MET W 230 " --> pdb=" O GLU W 226 " (cutoff:3.500A) Processing helix chain 'W' and resid 234 through 250 Processing helix chain 'W' and resid 254 through 272 removed outlier: 3.886A pdb=" N VAL W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 284 Processing helix chain 'W' and resid 285 through 288 Processing helix chain 'W' and resid 289 through 303 Processing helix chain 'W' and resid 306 through 319 Processing helix chain 'W' and resid 324 through 329 removed outlier: 3.959A pdb=" N ILE W 328 " --> pdb=" O PRO W 324 " (cutoff:3.500A) Processing helix chain 'W' and resid 330 through 343 removed outlier: 3.666A pdb=" N LYS W 343 " --> pdb=" O GLN W 339 " (cutoff:3.500A) Processing helix chain 'W' and resid 349 through 366 removed outlier: 4.514A pdb=" N LYS W 355 " --> pdb=" O ASP W 351 " (cutoff:3.500A) Processing helix chain 'W' and resid 382 through 399 Processing helix chain 'W' and resid 405 through 410 Processing helix chain 'W' and resid 410 through 418 Processing helix chain 'W' and resid 420 through 436 Processing helix chain 'W' and resid 450 through 462 removed outlier: 3.919A pdb=" N LEU W 454 " --> pdb=" O VAL W 450 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU W 455 " --> pdb=" O HIS W 451 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP W 456 " --> pdb=" O LEU W 452 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU W 457 " --> pdb=" O ALA W 453 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR W 460 " --> pdb=" O ASP W 456 " (cutoff:3.500A) Processing helix chain 'W' and resid 465 through 477 removed outlier: 4.657A pdb=" N LYS W 475 " --> pdb=" O GLN W 471 " (cutoff:3.500A) Processing helix chain 'W' and resid 485 through 506 Processing helix chain 'W' and resid 509 through 522 Processing helix chain 'W' and resid 526 through 541 Processing helix chain 'W' and resid 546 through 558 removed outlier: 4.818A pdb=" N LEU W 552 " --> pdb=" O ASP W 548 " (cutoff:3.500A) Proline residue: W 555 - end of helix Processing helix chain 'W' and resid 574 through 584 Processing helix chain 'Z' and resid 630 through 633 removed outlier: 3.815A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing helix chain 'Z' and resid 639 through 641 No H-bonds generated for 'chain 'Z' and resid 639 through 641' Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 150 removed outlier: 4.166A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.627A pdb=" N CYS A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.828A pdb=" N MET A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.607A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 7.913A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 856 Processing helix chain 'A' and resid 858 through 868 removed outlier: 3.532A pdb=" N LYS A 866 " --> pdb=" O ARG A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.654A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.727A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.100A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.569A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1097 through 1102 removed outlier: 3.968A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1097 through 1102' Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.642A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1160 removed outlier: 3.567A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1197 removed outlier: 3.509A pdb=" N GLN A1190 " --> pdb=" O VAL A1186 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.560A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.727A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1362 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.905A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.692A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 removed outlier: 3.605A pdb=" N VAL A1438 " --> pdb=" O GLU A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.806A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1470 removed outlier: 3.821A pdb=" N CYS A1470 " --> pdb=" O GLY A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.597A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 38 removed outlier: 4.120A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.578A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 425 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.736A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.593A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 489 through 494 removed outlier: 3.932A pdb=" N LYS B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 564 removed outlier: 3.530A pdb=" N ALA B 560 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 564 " --> pdb=" O ILE B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.519A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.562A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.736A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.596A pdb=" N PHE B 740 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N HIS B 741 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.730A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.859A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.552A pdb=" N ILE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 removed outlier: 4.202A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 269 Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.715A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.930A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.649A pdb=" N CYS D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.968A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.505A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.547A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 137' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 4.121A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 52 removed outlier: 3.997A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.690A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'S' and resid 138 through 153 Processing helix chain 'S' and resid 156 through 162 Processing helix chain 'S' and resid 164 through 181 Processing helix chain 'S' and resid 184 through 200 Processing helix chain 'S' and resid 203 through 212 removed outlier: 4.033A pdb=" N ARG S 207 " --> pdb=" O ASN S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 222 removed outlier: 3.629A pdb=" N ARG S 222 " --> pdb=" O ASP S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 231 through 249 removed outlier: 3.674A pdb=" N ARG S 246 " --> pdb=" O LYS S 242 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU S 247 " --> pdb=" O GLU S 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 18 Processing helix chain 'U' and resid 34 through 45 removed outlier: 5.455A pdb=" N ARG U 42 " --> pdb=" O ILE U 38 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU U 43 " --> pdb=" O ASP U 39 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS U 44 " --> pdb=" O ASN U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 49 through 63 removed outlier: 3.543A pdb=" N THR U 60 " --> pdb=" O LEU U 56 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU U 61 " --> pdb=" O LEU U 57 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU U 63 " --> pdb=" O GLY U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 71 Processing helix chain 'U' and resid 71 through 83 Processing helix chain 'U' and resid 87 through 97 removed outlier: 3.580A pdb=" N LEU U 91 " --> pdb=" O ASP U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 104 Processing helix chain 'U' and resid 114 through 131 removed outlier: 4.653A pdb=" N GLU U 126 " --> pdb=" O GLY U 122 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 144 removed outlier: 3.765A pdb=" N TYR U 143 " --> pdb=" O GLU U 140 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU U 144 " --> pdb=" O CYS U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 152 Processing helix chain 'U' and resid 169 through 188 removed outlier: 4.075A pdb=" N LYS U 181 " --> pdb=" O GLU U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 262 Processing sheet with id=AA1, first strand: chain 'W' and resid 367 through 370 removed outlier: 6.137A pdb=" N VAL W 367 " --> pdb=" O ILE W 378 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE W 378 " --> pdb=" O VAL W 367 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR W 369 " --> pdb=" O VAL W 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 453 through 454 removed outlier: 3.529A pdb=" N ARG Z 469 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.241A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.313A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 586 through 587 Processing sheet with id=AA6, first strand: chain 'Z' and resid 635 through 638 removed outlier: 6.853A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.671A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.561A pdb=" N VAL A 21 " --> pdb=" O ASP A1449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.392A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 264 through 266 Processing sheet with id=AB3, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.821A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 377 through 380 removed outlier: 7.820A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 377 through 380 removed outlier: 3.577A pdb=" N HIS B1060 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.327A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 526 through 527 Processing sheet with id=AB8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB9, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.299A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.632A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU A 631 " --> pdb=" O LEU A 635 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AC4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AC5, first strand: chain 'A' and resid 1308 through 1310 Processing sheet with id=AC6, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.613A pdb=" N GLN A1299 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.069A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC9, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AD1, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.653A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 66 through 68 removed outlier: 8.933A pdb=" N LYS U 255 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 91 " --> pdb=" O LYS U 255 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AD4, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD5, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.293A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.750A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 531 through 534 removed outlier: 4.419A pdb=" N ARG B 620 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD9, first strand: chain 'B' and resid 550 through 552 removed outlier: 5.365A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.691A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AE3, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.830A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 828 through 829 Processing sheet with id=AE5, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.022A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AE7, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.678A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 121 through 122 removed outlier: 7.466A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.475A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.953A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE G 2 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.953A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE G 2 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.572A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AF5, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AF6, first strand: chain 'G' and resid 104 through 109 removed outlier: 7.240A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 104 through 109 removed outlier: 7.240A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AF9, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AG1, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AG2, first strand: chain 'K' and resid 19 through 23 1770 hydrogen bonds defined for protein. 4938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 37.88 Time building geometry restraints manager: 56.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 39647 1.03 - 1.23: 152 1.23 - 1.43: 16780 1.43 - 1.63: 23886 1.63 - 1.83: 387 Bond restraints: 80852 Sorted by residual: bond pdb=" C3' DT T 19 " pdb=" O3' DT T 19 " ideal model delta sigma weight residual 1.422 1.534 -0.112 3.00e-02 1.11e+03 1.40e+01 bond pdb=" C3' DT T 18 " pdb=" O3' DT T 18 " ideal model delta sigma weight residual 1.422 1.525 -0.103 3.00e-02 1.11e+03 1.17e+01 bond pdb=" C ASN A 997 " pdb=" N PRO A 998 " ideal model delta sigma weight residual 1.334 1.361 -0.027 8.40e-03 1.42e+04 1.05e+01 bond pdb=" C1' DT T 32 " pdb=" N1 DT T 32 " ideal model delta sigma weight residual 1.490 1.583 -0.093 3.00e-02 1.11e+03 9.67e+00 bond pdb=" C5' DT T 19 " pdb=" C4' DT T 19 " ideal model delta sigma weight residual 1.518 1.578 -0.060 2.00e-02 2.50e+03 9.07e+00 ... (remaining 80847 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.82: 1758 105.82 - 113.22: 95872 113.22 - 120.62: 28272 120.62 - 128.03: 20088 128.03 - 135.43: 524 Bond angle restraints: 146514 Sorted by residual: angle pdb=" C GLY W 345 " pdb=" N ALA W 346 " pdb=" CA ALA W 346 " ideal model delta sigma weight residual 121.70 130.68 -8.98 1.80e+00 3.09e-01 2.49e+01 angle pdb=" O3' DC T 31 " pdb=" P DT T 32 " pdb=" OP2 DT T 32 " ideal model delta sigma weight residual 108.00 122.52 -14.52 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C3' DT T 18 " pdb=" O3' DT T 18 " pdb=" P DT T 19 " ideal model delta sigma weight residual 120.20 127.43 -7.23 1.50e+00 4.44e-01 2.33e+01 angle pdb=" C4' A P 12 " pdb=" C3' A P 12 " pdb=" O3' A P 12 " ideal model delta sigma weight residual 109.40 116.62 -7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" C ARG I 40 " pdb=" N ASN I 41 " pdb=" CA ASN I 41 " ideal model delta sigma weight residual 121.54 130.46 -8.92 1.91e+00 2.74e-01 2.18e+01 ... (remaining 146509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.84: 36034 32.84 - 65.67: 1424 65.67 - 98.50: 92 98.50 - 131.34: 2 131.34 - 164.17: 3 Dihedral angle restraints: 37555 sinusoidal: 21430 harmonic: 16125 Sorted by residual: dihedral pdb=" O4' U P 11 " pdb=" C1' U P 11 " pdb=" N1 U P 11 " pdb=" C2 U P 11 " ideal model delta sinusoidal sigma weight residual -160.00 4.17 -164.17 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" C5' A P 12 " pdb=" C4' A P 12 " pdb=" C3' A P 12 " pdb=" O3' A P 12 " ideal model delta sinusoidal sigma weight residual 147.00 110.65 36.35 1 8.00e+00 1.56e-02 2.92e+01 dihedral pdb=" CA ALA S 251 " pdb=" C ALA S 251 " pdb=" N LYS S 252 " pdb=" CA LYS S 252 " ideal model delta harmonic sigma weight residual 180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 37552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 5670 0.080 - 0.160: 623 0.160 - 0.240: 12 0.240 - 0.320: 2 0.320 - 0.400: 2 Chirality restraints: 6309 Sorted by residual: chirality pdb=" P DT T 32 " pdb=" OP1 DT T 32 " pdb=" OP2 DT T 32 " pdb=" O5' DT T 32 " both_signs ideal model delta sigma weight residual True 2.35 -2.75 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C3' A P 12 " pdb=" C4' A P 12 " pdb=" O3' A P 12 " pdb=" C2' A P 12 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" P DT T 20 " pdb=" OP1 DT T 20 " pdb=" OP2 DT T 20 " pdb=" O5' DT T 20 " both_signs ideal model delta sigma weight residual True 2.35 -2.65 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 6306 not shown) Planarity restraints: 11605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN W 306 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.70e+00 pdb=" N PRO W 307 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO W 307 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO W 307 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 13 " 0.035 2.00e-02 2.50e+03 1.77e-02 8.61e+00 pdb=" N1 DC N 13 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DC N 13 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC N 13 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC N 13 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC N 13 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC N 13 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DC N 13 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC N 13 " -0.017 2.00e-02 2.50e+03 pdb=" H5 DC N 13 " 0.006 2.00e-02 2.50e+03 pdb=" H6 DC N 13 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 49 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C TRP C 49 " -0.045 2.00e-02 2.50e+03 pdb=" O TRP C 49 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 50 " 0.015 2.00e-02 2.50e+03 ... (remaining 11602 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 406 1.95 - 2.61: 93459 2.61 - 3.27: 250045 3.27 - 3.94: 318442 3.94 - 4.60: 497286 Nonbonded interactions: 1159638 Sorted by model distance: nonbonded pdb="HG23 THR A 73 " pdb="ZN ZN A2001 " model vdw 1.287 1.930 nonbonded pdb=" HB2 CYS I 42 " pdb="ZN ZN I 201 " model vdw 1.591 1.930 nonbonded pdb=" OP1 DC T 26 " pdb="HH12 ARG B 812 " model vdw 1.671 1.850 nonbonded pdb=" H GLN B1068 " pdb=" O GLN B1073 " model vdw 1.673 1.850 nonbonded pdb=" O THR D 64 " pdb=" HG1 THR D 68 " model vdw 1.675 1.850 ... (remaining 1159633 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 7.810 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: 0.850 Extract box with map and model: 28.260 Check model and map are aligned: 0.970 Set scattering table: 0.550 Process input model: 262.690 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 305.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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 : 0.006 0.112 41125 Z= 0.361 Angle : 0.851 14.521 55887 Z= 0.456 Chirality : 0.048 0.400 6309 Planarity : 0.006 0.074 6956 Dihedral : 15.724 164.175 15960 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.58 % Allowed : 4.74 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.12), residues: 4779 helix: 0.22 (0.12), residues: 1744 sheet: -1.23 (0.18), residues: 646 loop : -0.95 (0.13), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 453 HIS 0.008 0.001 HIS Z 737 PHE 0.036 0.002 PHE B 918 TYR 0.020 0.002 TYR W 356 ARG 0.011 0.001 ARG A1416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 348 time to evaluate : 4.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 244 MET cc_start: 0.2622 (mmp) cc_final: 0.1524 (mtp) REVERT: Z 474 MET cc_start: -0.0519 (ppp) cc_final: -0.2375 (ppp) REVERT: A 355 MET cc_start: 0.9183 (mmt) cc_final: 0.8927 (mmt) REVERT: A 388 MET cc_start: 0.8893 (mmt) cc_final: 0.8422 (mmt) REVERT: A 493 ASN cc_start: 0.9715 (t0) cc_final: 0.9470 (t0) REVERT: A 775 LYS cc_start: 0.9557 (tppt) cc_final: 0.9338 (tppp) REVERT: A 849 ASP cc_start: 0.9228 (m-30) cc_final: 0.8998 (m-30) REVERT: A 1102 MET cc_start: 0.9095 (ptp) cc_final: 0.8773 (ptt) REVERT: A 1344 MET cc_start: 0.8722 (tpt) cc_final: 0.8471 (tpp) REVERT: A 1412 MET cc_start: 0.8944 (ttp) cc_final: 0.7815 (tmm) REVERT: B 297 MET cc_start: 0.9238 (mmm) cc_final: 0.8831 (tpp) REVERT: B 368 MET cc_start: 0.9335 (mtp) cc_final: 0.9098 (ttt) REVERT: B 908 MET cc_start: 0.7987 (ppp) cc_final: 0.7684 (tmm) REVERT: B 1075 MET cc_start: 0.7400 (ptt) cc_final: 0.6932 (ppp) REVERT: I 100 HIS cc_start: 0.9197 (t-90) cc_final: 0.8748 (t-170) REVERT: S 148 LEU cc_start: 0.8538 (tt) cc_final: 0.7840 (tt) REVERT: U 22 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7774 (tt0) outliers start: 25 outliers final: 11 residues processed: 371 average time/residue: 1.2083 time to fit residues: 712.7631 Evaluate side-chains 271 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 260 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain W residue 274 HIS Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain Z residue 718 LYS Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain S residue 235 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 3.9990 chunk 366 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 378 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 281 optimal weight: 0.0170 chunk 438 optimal weight: 7.9990 overall best weight: 2.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 196 GLN W 442 GLN ** Z 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN F 72 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 41125 Z= 0.247 Angle : 0.585 8.659 55887 Z= 0.318 Chirality : 0.041 0.274 6309 Planarity : 0.004 0.079 6956 Dihedral : 14.626 163.743 6227 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 0.70 % Allowed : 7.29 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.12), residues: 4779 helix: 0.71 (0.12), residues: 1786 sheet: -1.26 (0.19), residues: 623 loop : -0.80 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1067 HIS 0.005 0.001 HIS K 65 PHE 0.020 0.001 PHE A 592 TYR 0.018 0.001 TYR W 508 ARG 0.005 0.000 ARG W 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 264 time to evaluate : 4.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 244 MET cc_start: 0.2615 (mmp) cc_final: 0.1551 (mtp) REVERT: W 411 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7233 (tp) REVERT: Z 474 MET cc_start: -0.0337 (ppp) cc_final: -0.2210 (ppp) REVERT: A 355 MET cc_start: 0.9201 (mmt) cc_final: 0.8815 (mmt) REVERT: A 388 MET cc_start: 0.8723 (mmt) cc_final: 0.8353 (mmt) REVERT: A 775 LYS cc_start: 0.9604 (tppt) cc_final: 0.9321 (tppp) REVERT: A 849 ASP cc_start: 0.9261 (m-30) cc_final: 0.9047 (m-30) REVERT: A 1412 MET cc_start: 0.8898 (ttp) cc_final: 0.7801 (tmm) REVERT: A 1428 MET cc_start: 0.9492 (mmp) cc_final: 0.9277 (mmp) REVERT: A 1484 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8112 (pmm) REVERT: B 239 MET cc_start: 0.9403 (ttm) cc_final: 0.9103 (tpp) REVERT: B 368 MET cc_start: 0.9358 (mtp) cc_final: 0.9121 (ttt) REVERT: B 603 MET cc_start: 0.8109 (mpp) cc_final: 0.7666 (mpp) REVERT: B 791 GLU cc_start: 0.9217 (mm-30) cc_final: 0.9011 (mm-30) REVERT: B 908 MET cc_start: 0.8195 (ppp) cc_final: 0.7977 (tmm) REVERT: B 1075 MET cc_start: 0.7300 (ptt) cc_final: 0.6890 (ppp) REVERT: B 1151 MET cc_start: 0.9523 (ptm) cc_final: 0.8757 (ptp) REVERT: E 94 MET cc_start: 0.8753 (mmm) cc_final: 0.8358 (mmm) REVERT: I 100 HIS cc_start: 0.9238 (t-90) cc_final: 0.8758 (t-170) REVERT: L 44 MET cc_start: 0.9194 (mmm) cc_final: 0.8923 (mmm) REVERT: U 22 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7729 (tt0) outliers start: 30 outliers final: 16 residues processed: 286 average time/residue: 1.0973 time to fit residues: 512.5819 Evaluate side-chains 261 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 243 time to evaluate : 4.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 274 HIS Chi-restraints excluded: chain W residue 336 LEU Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain W residue 479 THR Chi-restraints excluded: chain Z residue 718 LYS Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1484 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain S residue 236 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 365 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 439 optimal weight: 7.9990 chunk 474 optimal weight: 0.6980 chunk 391 optimal weight: 6.9990 chunk 435 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 352 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 41125 Z= 0.277 Angle : 0.569 8.797 55887 Z= 0.309 Chirality : 0.040 0.193 6309 Planarity : 0.004 0.064 6956 Dihedral : 14.325 167.754 6216 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.77 % Allowed : 8.37 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4779 helix: 0.90 (0.12), residues: 1798 sheet: -1.28 (0.19), residues: 628 loop : -0.79 (0.13), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 203 HIS 0.005 0.001 HIS A 84 PHE 0.024 0.001 PHE A 592 TYR 0.022 0.001 TYR W 508 ARG 0.011 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 241 time to evaluate : 4.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 474 MET cc_start: -0.0229 (ppp) cc_final: -0.0678 (ppp) REVERT: A 355 MET cc_start: 0.9195 (mmt) cc_final: 0.8679 (mmt) REVERT: A 501 MET cc_start: 0.8613 (mtp) cc_final: 0.7814 (mtp) REVERT: A 775 LYS cc_start: 0.9585 (tppt) cc_final: 0.9339 (tppp) REVERT: A 1412 MET cc_start: 0.8883 (ttp) cc_final: 0.7773 (tmm) REVERT: A 1428 MET cc_start: 0.9526 (mmp) cc_final: 0.9306 (mmp) REVERT: A 1459 MET cc_start: 0.9362 (mtm) cc_final: 0.8774 (mtt) REVERT: B 239 MET cc_start: 0.9420 (ttm) cc_final: 0.9126 (tpp) REVERT: B 368 MET cc_start: 0.9358 (mtp) cc_final: 0.9153 (ttt) REVERT: B 603 MET cc_start: 0.8048 (mpp) cc_final: 0.7593 (mpp) REVERT: B 791 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9114 (mm-30) REVERT: B 796 MET cc_start: 0.8705 (mtp) cc_final: 0.8119 (mtp) REVERT: B 908 MET cc_start: 0.8171 (ppp) cc_final: 0.7919 (tmm) REVERT: B 1056 ASP cc_start: 0.9364 (m-30) cc_final: 0.9055 (p0) REVERT: B 1075 MET cc_start: 0.7223 (ptt) cc_final: 0.6781 (ppp) REVERT: B 1125 MET cc_start: 0.9254 (ppp) cc_final: 0.8832 (tmm) REVERT: B 1151 MET cc_start: 0.9509 (ptm) cc_final: 0.8847 (ptp) REVERT: E 94 MET cc_start: 0.8765 (mmm) cc_final: 0.8357 (mmm) REVERT: H 123 MET cc_start: 0.7716 (tmm) cc_final: 0.6918 (tmm) REVERT: I 100 HIS cc_start: 0.9262 (t-90) cc_final: 0.8754 (t-170) REVERT: S 167 GLU cc_start: 0.7561 (tp30) cc_final: 0.7302 (mm-30) REVERT: U 22 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7759 (tt0) REVERT: U 71 MET cc_start: 0.5226 (mtt) cc_final: 0.4927 (ttm) outliers start: 33 outliers final: 25 residues processed: 268 average time/residue: 1.0822 time to fit residues: 469.6801 Evaluate side-chains 255 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 4.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 274 HIS Chi-restraints excluded: chain W residue 336 LEU Chi-restraints excluded: chain W residue 479 THR Chi-restraints excluded: chain W residue 503 LEU Chi-restraints excluded: chain Z residue 718 LYS Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain S residue 236 MET Chi-restraints excluded: chain U residue 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 4.9990 chunk 330 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 440 optimal weight: 8.9990 chunk 466 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 417 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 GLN A 493 ASN A 757 GLN B 245 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 41125 Z= 0.334 Angle : 0.580 8.765 55887 Z= 0.316 Chirality : 0.040 0.177 6309 Planarity : 0.004 0.052 6956 Dihedral : 14.322 176.373 6214 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.22 % Allowed : 9.16 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4779 helix: 0.84 (0.12), residues: 1815 sheet: -1.28 (0.19), residues: 643 loop : -0.85 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 203 HIS 0.005 0.001 HIS A 84 PHE 0.024 0.001 PHE A 592 TYR 0.014 0.001 TYR A1197 ARG 0.008 0.000 ARG Z 711 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 239 time to evaluate : 4.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 474 MET cc_start: -0.0040 (ppp) cc_final: -0.0483 (ppp) REVERT: A 355 MET cc_start: 0.9204 (mmt) cc_final: 0.8584 (mmt) REVERT: A 501 MET cc_start: 0.8469 (mtp) cc_final: 0.8005 (mtt) REVERT: A 775 LYS cc_start: 0.9589 (tppt) cc_final: 0.9329 (tppp) REVERT: A 849 ASP cc_start: 0.9291 (m-30) cc_final: 0.8958 (m-30) REVERT: A 1412 MET cc_start: 0.8893 (ttp) cc_final: 0.7752 (tmm) REVERT: A 1428 MET cc_start: 0.9528 (mmp) cc_final: 0.9321 (mmp) REVERT: A 1459 MET cc_start: 0.9346 (mtm) cc_final: 0.8769 (mtt) REVERT: B 239 MET cc_start: 0.9407 (ttm) cc_final: 0.9096 (tpp) REVERT: B 791 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9180 (mm-30) REVERT: B 1048 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.9076 (m-10) REVERT: B 1056 ASP cc_start: 0.9340 (m-30) cc_final: 0.9109 (p0) REVERT: B 1075 MET cc_start: 0.7142 (ptt) cc_final: 0.6693 (ppp) REVERT: B 1125 MET cc_start: 0.9280 (ppp) cc_final: 0.8916 (tmm) REVERT: B 1151 MET cc_start: 0.9505 (ptm) cc_final: 0.8886 (ptp) REVERT: B 1161 GLU cc_start: 0.9263 (tt0) cc_final: 0.9030 (tt0) REVERT: H 123 MET cc_start: 0.7960 (tmm) cc_final: 0.7106 (tmm) REVERT: I 100 HIS cc_start: 0.9285 (t-90) cc_final: 0.8766 (t-170) REVERT: L 44 MET cc_start: 0.9105 (mmm) cc_final: 0.8840 (mmm) REVERT: U 22 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7851 (tt0) REVERT: U 71 MET cc_start: 0.5576 (mtt) cc_final: 0.5344 (ttm) outliers start: 52 outliers final: 37 residues processed: 280 average time/residue: 1.0650 time to fit residues: 485.4331 Evaluate side-chains 271 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 274 HIS Chi-restraints excluded: chain W residue 336 LEU Chi-restraints excluded: chain W residue 479 THR Chi-restraints excluded: chain W residue 491 GLU Chi-restraints excluded: chain W residue 503 LEU Chi-restraints excluded: chain Z residue 718 LYS Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1388 PHE Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 90 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 347 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 419 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 704 ASN A1077 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 41125 Z= 0.280 Angle : 0.548 7.796 55887 Z= 0.298 Chirality : 0.040 0.171 6309 Planarity : 0.004 0.052 6956 Dihedral : 14.276 176.555 6214 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.24 % Allowed : 9.72 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4779 helix: 0.99 (0.12), residues: 1817 sheet: -1.15 (0.19), residues: 637 loop : -0.85 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 453 HIS 0.005 0.001 HIS A 84 PHE 0.019 0.001 PHE A 592 TYR 0.015 0.001 TYR W 356 ARG 0.009 0.000 ARG Z 711 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 237 time to evaluate : 4.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 474 MET cc_start: 0.0012 (ppp) cc_final: -0.0445 (ppp) REVERT: A 355 MET cc_start: 0.9174 (mmt) cc_final: 0.8494 (mmt) REVERT: A 501 MET cc_start: 0.8439 (mtp) cc_final: 0.7994 (mtt) REVERT: A 775 LYS cc_start: 0.9585 (tppt) cc_final: 0.9332 (tppp) REVERT: A 1412 MET cc_start: 0.8876 (ttp) cc_final: 0.7696 (tmm) REVERT: A 1428 MET cc_start: 0.9512 (mmp) cc_final: 0.9289 (mmp) REVERT: A 1459 MET cc_start: 0.9331 (mtm) cc_final: 0.8744 (mtt) REVERT: B 239 MET cc_start: 0.9405 (ttm) cc_final: 0.9094 (tpp) REVERT: B 791 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9189 (mm-30) REVERT: B 1056 ASP cc_start: 0.9320 (m-30) cc_final: 0.9110 (p0) REVERT: B 1075 MET cc_start: 0.7131 (ptt) cc_final: 0.6656 (ppp) REVERT: B 1125 MET cc_start: 0.9286 (ppp) cc_final: 0.8954 (tmm) REVERT: B 1151 MET cc_start: 0.9514 (ptm) cc_final: 0.8895 (ptp) REVERT: B 1161 GLU cc_start: 0.9258 (tt0) cc_final: 0.9024 (tt0) REVERT: H 123 MET cc_start: 0.8100 (tmm) cc_final: 0.7209 (tmm) REVERT: I 100 HIS cc_start: 0.9298 (t-90) cc_final: 0.8783 (t-170) REVERT: S 146 GLU cc_start: 0.8282 (pp20) cc_final: 0.8050 (mm-30) REVERT: S 236 MET cc_start: 0.8792 (tpt) cc_final: 0.8552 (tmm) REVERT: U 22 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7816 (tt0) outliers start: 53 outliers final: 43 residues processed: 281 average time/residue: 1.0363 time to fit residues: 476.5518 Evaluate side-chains 274 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 231 time to evaluate : 4.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 192 SER Chi-restraints excluded: chain W residue 274 HIS Chi-restraints excluded: chain W residue 336 LEU Chi-restraints excluded: chain W residue 479 THR Chi-restraints excluded: chain W residue 503 LEU Chi-restraints excluded: chain Z residue 718 LYS Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1485 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1119 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 90 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 1.9990 chunk 420 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 467 optimal weight: 3.9990 chunk 387 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 38 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41125 Z= 0.234 Angle : 0.530 8.862 55887 Z= 0.286 Chirality : 0.040 0.171 6309 Planarity : 0.004 0.050 6956 Dihedral : 14.240 176.471 6214 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.26 % Allowed : 10.42 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 4779 helix: 1.14 (0.12), residues: 1812 sheet: -1.13 (0.19), residues: 649 loop : -0.79 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 453 HIS 0.005 0.001 HIS A 84 PHE 0.019 0.001 PHE A 592 TYR 0.019 0.001 TYR W 508 ARG 0.009 0.000 ARG Z 711 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 239 time to evaluate : 5.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 415 TYR cc_start: 0.3799 (m-10) cc_final: 0.3590 (m-10) REVERT: Z 474 MET cc_start: -0.0017 (ppp) cc_final: -0.0459 (ppp) REVERT: A 355 MET cc_start: 0.9170 (mmt) cc_final: 0.8470 (mmt) REVERT: A 501 MET cc_start: 0.8450 (mtp) cc_final: 0.8007 (mtt) REVERT: A 775 LYS cc_start: 0.9578 (tppt) cc_final: 0.9315 (tppp) REVERT: A 986 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8628 (mpt) REVERT: A 1412 MET cc_start: 0.8871 (ttp) cc_final: 0.7695 (tmm) REVERT: A 1428 MET cc_start: 0.9511 (mmp) cc_final: 0.9304 (mmp) REVERT: A 1459 MET cc_start: 0.9326 (mtm) cc_final: 0.8735 (mtt) REVERT: B 239 MET cc_start: 0.9406 (ttm) cc_final: 0.9095 (tpp) REVERT: B 791 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9178 (mm-30) REVERT: B 1056 ASP cc_start: 0.9291 (m-30) cc_final: 0.9090 (p0) REVERT: B 1075 MET cc_start: 0.7142 (ptt) cc_final: 0.6665 (ppp) REVERT: B 1125 MET cc_start: 0.9272 (ppp) cc_final: 0.8953 (tmm) REVERT: B 1151 MET cc_start: 0.9519 (ptm) cc_final: 0.8887 (ptp) REVERT: B 1161 GLU cc_start: 0.9255 (tt0) cc_final: 0.9016 (tt0) REVERT: H 123 MET cc_start: 0.8131 (tmm) cc_final: 0.7212 (tmm) REVERT: I 100 HIS cc_start: 0.9303 (t-90) cc_final: 0.8786 (t-170) REVERT: L 44 MET cc_start: 0.9041 (mmm) cc_final: 0.8729 (mmm) REVERT: S 146 GLU cc_start: 0.8229 (pp20) cc_final: 0.8027 (mm-30) REVERT: S 228 MET cc_start: 0.7881 (ptp) cc_final: 0.7505 (ptt) REVERT: S 236 MET cc_start: 0.8781 (tpt) cc_final: 0.8554 (tmm) REVERT: U 22 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7825 (tt0) REVERT: U 89 TRP cc_start: 0.5055 (m-10) cc_final: 0.4748 (m-10) outliers start: 54 outliers final: 46 residues processed: 283 average time/residue: 1.0367 time to fit residues: 481.1461 Evaluate side-chains 281 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 234 time to evaluate : 4.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 268 PHE Chi-restraints excluded: chain W residue 336 LEU Chi-restraints excluded: chain W residue 479 THR Chi-restraints excluded: chain W residue 491 GLU Chi-restraints excluded: chain W residue 503 LEU Chi-restraints excluded: chain Z residue 718 LYS Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1388 PHE Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1119 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 90 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 1.9990 chunk 52 optimal weight: 30.0000 chunk 266 optimal weight: 0.9990 chunk 341 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 chunk 393 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 465 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41125 Z= 0.217 Angle : 0.514 7.087 55887 Z= 0.278 Chirality : 0.040 0.166 6309 Planarity : 0.003 0.048 6956 Dihedral : 14.178 174.920 6212 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.31 % Allowed : 10.38 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.12), residues: 4779 helix: 1.25 (0.12), residues: 1818 sheet: -1.11 (0.19), residues: 659 loop : -0.73 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 453 HIS 0.006 0.001 HIS W 274 PHE 0.021 0.001 PHE A 592 TYR 0.011 0.001 TYR A1197 ARG 0.010 0.000 ARG Z 711 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 237 time to evaluate : 5.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 415 TYR cc_start: 0.3776 (m-10) cc_final: 0.3566 (m-10) REVERT: Z 474 MET cc_start: -0.0047 (ppp) cc_final: -0.0463 (ppp) REVERT: A 355 MET cc_start: 0.9152 (mmt) cc_final: 0.8467 (mmt) REVERT: A 501 MET cc_start: 0.8456 (mtp) cc_final: 0.7987 (mtt) REVERT: A 775 LYS cc_start: 0.9570 (tppt) cc_final: 0.9300 (tppp) REVERT: A 1412 MET cc_start: 0.8874 (ttp) cc_final: 0.8135 (tmm) REVERT: A 1428 MET cc_start: 0.9509 (mmp) cc_final: 0.9303 (mmp) REVERT: A 1459 MET cc_start: 0.9321 (mtm) cc_final: 0.8714 (mtt) REVERT: B 239 MET cc_start: 0.9400 (ttm) cc_final: 0.9088 (tpp) REVERT: B 298 MET cc_start: 0.9381 (mmm) cc_final: 0.9180 (mmm) REVERT: B 1075 MET cc_start: 0.7181 (ptt) cc_final: 0.6691 (ppp) REVERT: B 1125 MET cc_start: 0.9260 (ppp) cc_final: 0.8955 (tmm) REVERT: B 1151 MET cc_start: 0.9528 (ptm) cc_final: 0.8915 (ptp) REVERT: B 1161 GLU cc_start: 0.9251 (tt0) cc_final: 0.9012 (tt0) REVERT: H 123 MET cc_start: 0.8180 (tmm) cc_final: 0.7274 (tmm) REVERT: I 100 HIS cc_start: 0.9304 (t-90) cc_final: 0.8775 (t-170) REVERT: J 1 MET cc_start: 0.9155 (tpp) cc_final: 0.8416 (tpp) REVERT: S 236 MET cc_start: 0.8753 (tpt) cc_final: 0.8545 (tmm) REVERT: U 22 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7838 (tt0) REVERT: U 89 TRP cc_start: 0.5082 (m-10) cc_final: 0.4842 (m-10) outliers start: 56 outliers final: 53 residues processed: 285 average time/residue: 1.0548 time to fit residues: 492.5036 Evaluate side-chains 284 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 231 time to evaluate : 4.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 192 SER Chi-restraints excluded: chain W residue 268 PHE Chi-restraints excluded: chain W residue 336 LEU Chi-restraints excluded: chain W residue 479 THR Chi-restraints excluded: chain W residue 491 GLU Chi-restraints excluded: chain W residue 503 LEU Chi-restraints excluded: chain Z residue 718 LYS Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 492 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1119 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 295 optimal weight: 4.9990 chunk 317 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 365 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN B1120 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 41125 Z= 0.305 Angle : 0.557 10.036 55887 Z= 0.301 Chirality : 0.040 0.185 6309 Planarity : 0.004 0.049 6956 Dihedral : 14.191 171.423 6212 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.52 % Allowed : 10.52 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 4779 helix: 1.08 (0.12), residues: 1834 sheet: -1.19 (0.19), residues: 681 loop : -0.84 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 203 HIS 0.004 0.001 HIS A 84 PHE 0.021 0.001 PHE A 592 TYR 0.012 0.001 TYR A1197 ARG 0.010 0.000 ARG Z 711 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 234 time to evaluate : 4.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 415 TYR cc_start: 0.3726 (m-10) cc_final: 0.3517 (m-10) REVERT: Z 474 MET cc_start: 0.0011 (ppp) cc_final: -0.0457 (ppp) REVERT: A 355 MET cc_start: 0.9187 (mmt) cc_final: 0.8497 (mmt) REVERT: A 469 MET cc_start: 0.9180 (ttt) cc_final: 0.8909 (ttm) REVERT: A 501 MET cc_start: 0.8437 (mtp) cc_final: 0.7527 (mtp) REVERT: A 775 LYS cc_start: 0.9580 (tppt) cc_final: 0.9318 (tppp) REVERT: A 1412 MET cc_start: 0.8916 (ttp) cc_final: 0.8172 (tmm) REVERT: A 1459 MET cc_start: 0.9326 (mtm) cc_final: 0.8736 (mtt) REVERT: A 1485 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: B 239 MET cc_start: 0.9407 (ttm) cc_final: 0.9036 (tpp) REVERT: B 908 MET cc_start: 0.8126 (tmm) cc_final: 0.7603 (tmm) REVERT: B 1075 MET cc_start: 0.7171 (ptt) cc_final: 0.6676 (ppp) REVERT: B 1125 MET cc_start: 0.9311 (ppp) cc_final: 0.9017 (tmm) REVERT: B 1151 MET cc_start: 0.9535 (ptm) cc_final: 0.8923 (ptp) REVERT: B 1161 GLU cc_start: 0.9243 (tt0) cc_final: 0.9002 (tt0) REVERT: I 100 HIS cc_start: 0.9250 (t-90) cc_final: 0.8685 (t-170) REVERT: J 1 MET cc_start: 0.9166 (tpp) cc_final: 0.8429 (tpp) REVERT: U 22 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7840 (tt0) outliers start: 65 outliers final: 57 residues processed: 289 average time/residue: 1.0549 time to fit residues: 499.5746 Evaluate side-chains 287 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 229 time to evaluate : 4.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 192 SER Chi-restraints excluded: chain W residue 268 PHE Chi-restraints excluded: chain W residue 336 LEU Chi-restraints excluded: chain W residue 479 THR Chi-restraints excluded: chain W residue 491 GLU Chi-restraints excluded: chain W residue 503 LEU Chi-restraints excluded: chain Z residue 526 SER Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1388 PHE Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain A residue 1485 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 990 SER Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1119 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 90 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 10.0000 chunk 445 optimal weight: 1.9990 chunk 406 optimal weight: 0.5980 chunk 433 optimal weight: 0.2980 chunk 261 optimal weight: 0.2980 chunk 188 optimal weight: 8.9990 chunk 340 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 392 optimal weight: 9.9990 chunk 410 optimal weight: 3.9990 chunk 432 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 41125 Z= 0.156 Angle : 0.508 8.892 55887 Z= 0.270 Chirality : 0.040 0.156 6309 Planarity : 0.003 0.043 6956 Dihedral : 14.090 168.587 6208 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.10 % Allowed : 10.89 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.12), residues: 4779 helix: 1.46 (0.12), residues: 1826 sheet: -1.02 (0.19), residues: 661 loop : -0.64 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 236 HIS 0.005 0.001 HIS A 84 PHE 0.018 0.001 PHE A 592 TYR 0.009 0.001 TYR A1197 ARG 0.010 0.000 ARG Z 711 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 236 time to evaluate : 4.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 415 TYR cc_start: 0.3673 (m-10) cc_final: 0.3462 (m-10) REVERT: Z 474 MET cc_start: 0.0039 (ppp) cc_final: -0.0409 (ppp) REVERT: A 355 MET cc_start: 0.9106 (mmt) cc_final: 0.8441 (mmt) REVERT: A 501 MET cc_start: 0.8412 (mtp) cc_final: 0.7941 (mtt) REVERT: A 775 LYS cc_start: 0.9555 (tppt) cc_final: 0.9284 (tppp) REVERT: A 1412 MET cc_start: 0.8874 (ttp) cc_final: 0.8130 (tmm) REVERT: A 1459 MET cc_start: 0.9363 (mtm) cc_final: 0.8760 (mtt) REVERT: B 239 MET cc_start: 0.9398 (ttm) cc_final: 0.9079 (tpp) REVERT: B 908 MET cc_start: 0.7959 (tmm) cc_final: 0.7469 (tmm) REVERT: B 1075 MET cc_start: 0.7161 (ptt) cc_final: 0.6660 (ppp) REVERT: B 1125 MET cc_start: 0.9242 (ppp) cc_final: 0.8946 (tmm) REVERT: B 1151 MET cc_start: 0.9531 (ptm) cc_final: 0.8900 (ptp) REVERT: B 1161 GLU cc_start: 0.9244 (tt0) cc_final: 0.9012 (tt0) REVERT: E 94 MET cc_start: 0.8757 (mmm) cc_final: 0.8320 (mmm) REVERT: I 100 HIS cc_start: 0.9291 (t-90) cc_final: 0.8753 (t-170) REVERT: J 1 MET cc_start: 0.9161 (tpp) cc_final: 0.8415 (tpp) REVERT: U 22 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7912 (tt0) outliers start: 47 outliers final: 44 residues processed: 276 average time/residue: 1.0266 time to fit residues: 463.3920 Evaluate side-chains 274 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 4.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 268 PHE Chi-restraints excluded: chain W residue 336 LEU Chi-restraints excluded: chain W residue 479 THR Chi-restraints excluded: chain W residue 491 GLU Chi-restraints excluded: chain W residue 503 LEU Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1119 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 6.9990 chunk 458 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 318 optimal weight: 7.9990 chunk 481 optimal weight: 8.9990 chunk 442 optimal weight: 3.9990 chunk 383 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 295 optimal weight: 0.8980 chunk 234 optimal weight: 0.0870 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN S 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41125 Z= 0.272 Angle : 0.542 9.616 55887 Z= 0.291 Chirality : 0.039 0.156 6309 Planarity : 0.004 0.048 6956 Dihedral : 14.089 165.322 6208 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.19 % Allowed : 11.05 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.12), residues: 4779 helix: 1.34 (0.12), residues: 1832 sheet: -1.13 (0.19), residues: 685 loop : -0.74 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 203 HIS 0.004 0.001 HIS E 22 PHE 0.023 0.001 PHE A 592 TYR 0.011 0.001 TYR A1197 ARG 0.009 0.000 ARG Z 711 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9558 Ramachandran restraints generated. 4779 Oldfield, 0 Emsley, 4779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 231 time to evaluate : 4.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 415 TYR cc_start: 0.3697 (m-10) cc_final: 0.3482 (m-10) REVERT: Z 474 MET cc_start: 0.0088 (ppp) cc_final: -0.0359 (ppp) REVERT: A 355 MET cc_start: 0.9170 (mmt) cc_final: 0.8499 (mmt) REVERT: A 501 MET cc_start: 0.8426 (mtp) cc_final: 0.7948 (mtt) REVERT: A 775 LYS cc_start: 0.9572 (tppt) cc_final: 0.9309 (tppp) REVERT: A 986 MET cc_start: 0.9031 (mpp) cc_final: 0.8676 (mpt) REVERT: A 1412 MET cc_start: 0.8917 (ttp) cc_final: 0.8169 (tmm) REVERT: A 1459 MET cc_start: 0.9361 (mtm) cc_final: 0.8776 (mtt) REVERT: B 239 MET cc_start: 0.9413 (ttm) cc_final: 0.9048 (tpp) REVERT: B 908 MET cc_start: 0.8038 (tmm) cc_final: 0.7554 (tmm) REVERT: B 1075 MET cc_start: 0.7197 (ptt) cc_final: 0.6688 (ppp) REVERT: B 1125 MET cc_start: 0.9294 (ppp) cc_final: 0.9000 (tmm) REVERT: B 1151 MET cc_start: 0.9538 (ptm) cc_final: 0.8921 (ptp) REVERT: I 100 HIS cc_start: 0.9250 (t-90) cc_final: 0.8664 (t-170) REVERT: J 1 MET cc_start: 0.9168 (tpp) cc_final: 0.8388 (tpp) REVERT: U 22 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7910 (tt0) outliers start: 51 outliers final: 47 residues processed: 274 average time/residue: 1.0296 time to fit residues: 462.1195 Evaluate side-chains 276 residues out of total 4279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 228 time to evaluate : 4.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 268 PHE Chi-restraints excluded: chain W residue 336 LEU Chi-restraints excluded: chain W residue 479 THR Chi-restraints excluded: chain W residue 491 GLU Chi-restraints excluded: chain W residue 503 LEU Chi-restraints excluded: chain Z residue 744 SER Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 1201 ASP Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1430 CYS Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1119 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain I residue 63 ASP Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 83 ASP Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain U residue 22 GLU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 3.9990 chunk 408 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 353 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 383 optimal weight: 0.5980 chunk 160 optimal weight: 8.9990 chunk 394 optimal weight: 5.9990 chunk 48 optimal weight: 0.0970 chunk 70 optimal weight: 10.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1397 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.079621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.058853 restraints weight = 958276.269| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 7.99 r_work: 0.3125 rms_B_bonded: 6.82 restraints_weight: 2.0000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 41125 Z= 0.224 Angle : 0.522 8.701 55887 Z= 0.280 Chirality : 0.040 0.155 6309 Planarity : 0.004 0.045 6956 Dihedral : 14.069 162.523 6208 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.29 % Allowed : 10.89 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 4779 helix: 1.41 (0.12), residues: 1831 sheet: -1.02 (0.19), residues: 660 loop : -0.69 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 89 HIS 0.005 0.001 HIS A 84 PHE 0.023 0.001 PHE A 592 TYR 0.018 0.001 TYR W 356 ARG 0.010 0.000 ARG Z 711 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15573.77 seconds wall clock time: 273 minutes 2.40 seconds (16382.40 seconds total)