Starting phenix.real_space_refine on Wed Apr 10 10:55:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/04_2024/7q4v_13818_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/04_2024/7q4v_13818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/04_2024/7q4v_13818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/04_2024/7q4v_13818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/04_2024/7q4v_13818_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4v_13818/04_2024/7q4v_13818_neut_updated.pdb" } resolution = 4.7 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 66 7.16 5 Zn 2 6.06 5 P 4 5.49 5 S 224 5.16 5 C 12049 2.51 5 N 3247 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 160": "OD1" <-> "OD2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 465": "OD1" <-> "OD2" Residue "E ASP 535": "OD1" <-> "OD2" Residue "E GLU 562": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 268": "OE1" <-> "OE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F GLU 414": "OE1" <-> "OE2" Residue "F ASP 436": "OD1" <-> "OD2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F ASP 564": "OD1" <-> "OD2" Residue "F GLU 569": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19303 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4442 Classifications: {'peptide': 583} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 556} Chain: "B" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4510 Classifications: {'peptide': 599} Link IDs: {'PCIS': 4, 'PTRANS': 26, 'TRANS': 568} Chain: "C" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1188 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 148} Chain: "E" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4442 Classifications: {'peptide': 583} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 556} Chain: "F" Number of atoms: 3513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3513 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 445} Chain: "G" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 60 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 100 Unusual residues: {' ZN': 1, 'FMN': 1, 'NAD': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1485 SG CYS A 197 70.799 91.196 81.836 1.00114.62 S ATOM 1466 SG CYS A 194 71.092 94.046 85.545 1.00116.20 S ATOM 1204 SG CYS A 158 67.194 96.742 81.275 1.00105.56 S ATOM 1444 SG CYS A 191 73.838 95.843 79.905 1.00128.70 S ATOM 1178 SG CYS A 154 64.154 89.680 78.163 1.00 69.55 S ATOM 1152 SG CYS A 151 61.636 85.936 79.356 1.00 60.00 S ATOM 1515 SG CYS A 201 66.391 83.672 79.654 1.00 87.71 S ATOM 1130 SG CYS A 148 64.018 85.289 73.798 1.00 70.72 S ATOM 790 SG CYS A 103 71.148 75.565 77.957 1.00115.02 S ATOM 770 SG CYS A 100 67.501 71.551 75.898 1.00 96.97 S ATOM 770 SG CYS A 100 67.501 71.551 75.898 1.00 96.97 S ATOM 838 SG CYS A 109 65.503 74.712 80.128 1.00 97.73 S ATOM 388 SG CYS A 50 48.990 80.433 83.418 1.00142.31 S ATOM 483 SG CYS A 64 48.422 84.133 83.937 1.00157.42 S ATOM 278 SG CYS A 36 52.843 83.344 82.937 1.00119.08 S ATOM 363 SG CYS A 47 52.829 80.534 81.077 1.00122.36 S ATOM 3802 SG CYS A 502 73.343 93.657 93.673 1.00158.69 S ATOM 2683 SG CYS A 356 78.767 92.887 93.347 1.00161.42 S ATOM 2683 SG CYS A 356 78.767 92.887 93.347 1.00161.42 S ATOM 4532 SG CYS B 11 27.502 106.296 44.948 1.00482.94 S ATOM 4557 SG CYS B 16 29.690 105.471 42.423 1.00505.00 S ATOM 4798 SG CYS B 48 27.021 102.447 48.119 1.00439.72 S ATOM 4827 SG CYS B 52 29.580 101.368 45.457 1.00441.51 S ATOM 8830 SG CYS B 581 56.750 72.617 31.765 1.00356.24 S ATOM 8868 SG CYS B 587 53.659 76.720 27.427 1.00356.64 S ATOM 8680 SG CYS B 561 59.481 75.496 27.259 1.00385.72 S ATOM 8853 SG CYS B 584 56.942 79.370 31.882 1.00336.56 S ATOM 8614 SG CYS B 551 49.989 72.987 17.593 1.00411.99 S ATOM 8633 SG CYS B 554 52.305 78.816 15.379 1.00429.49 S ATOM 8651 SG CYS B 557 54.018 76.203 21.176 1.00441.33 S ATOM 8896 SG CYS B 591 48.235 78.512 20.115 1.00388.68 S ATOM 7754 SG CYS B 440 42.575 73.507 44.414 1.00229.29 S ATOM 8480 SG CYS B 533 43.848 72.587 41.006 1.00238.07 S ATOM 8509 SG CYS B 538 46.387 73.384 43.725 1.00244.76 S ATOM 7933 SG CYS B 463 47.529 84.586 66.184 1.00108.71 S ATOM 7894 SG CYS B 457 48.184 89.756 69.169 1.00126.70 S ATOM 7913 SG CYS B 460 48.122 83.004 71.033 1.00107.95 S ATOM 8237 SG CYS B 503 44.760 88.554 68.682 1.00120.75 S ATOM 9600 SG CYS C 83 42.046 95.787 47.172 1.00369.74 S ATOM 9630 SG CYS C 88 40.605 93.884 44.354 1.00321.96 S ATOM 9600 SG CYS C 83 42.046 95.787 47.172 1.00369.74 S ATOM 9900 SG CYS C 124 40.889 94.436 51.174 1.00332.85 S ATOM 9922 SG CYS C 128 37.894 95.554 48.814 1.00357.46 S ATOM 11606 SG CYS E 194 66.735 41.064 84.318 1.00 86.56 S ATOM 11584 SG CYS E 191 63.762 38.863 79.672 1.00117.23 S ATOM 11344 SG CYS E 158 70.228 38.276 81.148 1.00126.73 S ATOM 11606 SG CYS E 194 66.735 41.064 84.318 1.00 86.56 S ATOM 11625 SG CYS E 197 65.863 43.644 81.909 1.00 86.39 S ATOM 11318 SG CYS E 154 73.026 45.099 77.895 1.00101.23 S ATOM 11292 SG CYS E 151 76.715 49.899 79.648 1.00 83.64 S ATOM 11655 SG CYS E 201 70.817 50.931 79.182 1.00 92.09 S ATOM 11270 SG CYS E 148 73.644 50.276 73.762 1.00 94.22 S ATOM 10978 SG CYS E 109 71.845 60.071 80.542 1.00111.20 S ATOM 10930 SG CYS E 103 67.189 61.207 76.132 1.00103.92 S ATOM 10910 SG CYS E 100 69.659 64.737 76.057 1.00 98.54 S ATOM 10930 SG CYS E 103 67.189 61.207 76.132 1.00103.92 S ATOM 10418 SG CYS E 36 85.018 52.094 83.051 1.00133.43 S ATOM 10528 SG CYS E 50 88.376 54.327 83.584 1.00178.99 S ATOM 10623 SG CYS E 64 88.236 50.562 84.699 1.00178.45 S ATOM 10418 SG CYS E 36 85.018 52.094 83.051 1.00133.43 S ATOM 10503 SG CYS E 47 84.361 54.606 80.960 1.00139.83 S ATOM 10528 SG CYS E 50 88.376 54.327 83.584 1.00178.99 S ATOM 13942 SG CYS E 502 63.853 40.742 94.292 1.00162.85 S ATOM 12823 SG CYS E 356 58.710 42.337 93.067 1.00163.54 S ATOM 12823 SG CYS E 356 58.710 42.337 93.067 1.00163.54 S ATOM 13963 SG CYS E 506 59.949 41.094 96.427 1.00150.14 S ATOM 17823 SG CYS F 561 77.834 59.548 27.194 1.00334.23 S ATOM 18011 SG CYS F 587 83.935 58.778 27.591 1.00331.25 S ATOM 17996 SG CYS F 584 80.345 56.290 32.290 1.00311.46 S ATOM 17973 SG CYS F 581 80.523 63.047 30.126 1.00319.19 S ATOM 17776 SG CYS F 554 85.422 56.183 16.459 1.00368.00 S ATOM 18039 SG CYS F 591 89.247 57.170 20.580 1.00364.96 S ATOM 17794 SG CYS F 557 83.270 58.936 21.772 1.00364.31 S ATOM 17757 SG CYS F 551 88.195 61.586 17.798 1.00341.27 S ATOM 16897 SG CYS F 440 94.068 61.551 44.758 1.00248.55 S ATOM 17623 SG CYS F 533 93.210 63.031 41.366 1.00269.77 S ATOM 17652 SG CYS F 538 90.259 62.250 43.844 1.00276.58 S ATOM 17380 SG CYS F 503 92.781 47.339 68.700 1.00172.63 S ATOM 17076 SG CYS F 463 90.045 50.533 66.202 1.00163.03 S ATOM 17056 SG CYS F 460 89.153 52.070 71.104 1.00147.81 S ATOM 17037 SG CYS F 457 88.395 45.178 69.565 1.00157.98 S ATOM 18743 SG CYS G 83 86.905 39.189 39.642 1.00739.93 S ATOM 18773 SG CYS G 88 88.065 41.996 38.126 1.00747.26 S ATOM 18986 SG CYS G 124 92.328 38.672 41.510 1.00682.29 S ATOM 19008 SG CYS G 128 93.679 39.734 38.665 1.00759.78 S Time building chain proxies: 10.44, per 1000 atoms: 0.54 Number of scatterers: 19303 At special positions: 0 Unit cell: (138.43, 138.43, 130.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 66 26.01 S 224 16.00 P 4 15.00 O 3711 8.00 N 3247 7.00 C 12049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.44 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 604 " pdb="FE2 FES A 604 " - pdb=" SG CYS A 47 " pdb="FE1 FES A 604 " - pdb=" SG CYS A 50 " pdb="FE2 FES A 604 " - pdb=" SG CYS A 36 " pdb="FE1 FES A 604 " - pdb=" SG CYS A 64 " pdb=" FES B 601 " pdb="FE1 FES B 601 " - pdb=" SG CYS B 16 " pdb="FE2 FES B 601 " - pdb=" SG CYS B 48 " pdb="FE2 FES B 601 " - pdb=" SG CYS B 52 " pdb="FE1 FES B 601 " - pdb=" SG CYS B 11 " pdb=" FES C 201 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 88 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 128 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 83 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 124 " pdb=" FES E 604 " pdb="FE2 FES E 604 " - pdb=" SG CYS E 47 " pdb="FE1 FES E 604 " - pdb=" SG CYS E 50 " pdb="FE2 FES E 604 " - pdb=" SG CYS E 36 " pdb="FE1 FES E 604 " - pdb=" SG CYS E 64 " pdb=" FES G 201 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 124 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 88 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 128 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 83 " pdb=" SF4 A 601 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 194 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 197 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 158 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 191 " pdb=" SF4 A 602 " pdb="FE2 SF4 A 602 " - pdb=" SG CYS A 151 " pdb="FE4 SF4 A 602 " - pdb=" SG CYS A 148 " pdb="FE1 SF4 A 602 " - pdb=" SG CYS A 154 " pdb="FE3 SF4 A 602 " - pdb=" SG CYS A 201 " pdb=" SF4 A 603 " pdb="FE2 SF4 A 603 " - pdb=" SG CYS A 100 " pdb="FE4 SF4 A 603 " - pdb=" SG CYS A 109 " pdb="FE1 SF4 A 603 " - pdb=" SG CYS A 103 " pdb="FE3 SF4 A 603 " - pdb=" NE2 HIS A 96 " pdb=" SF4 A 605 " pdb="FE2 SF4 A 605 " - pdb=" SG CYS A 356 " pdb="FE1 SF4 A 605 " - pdb=" SG CYS A 502 " pdb="FE3 SF4 A 605 " - pdb=" SG CYS A 506 " pdb=" SF4 B 602 " pdb="FE4 SF4 B 602 " - pdb=" SG CYS B 584 " pdb="FE3 SF4 B 602 " - pdb=" SG CYS B 561 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 587 " pdb="FE1 SF4 B 602 " - pdb=" SG CYS B 581 " pdb=" SF4 B 603 " pdb="FE1 SF4 B 603 " - pdb=" SG CYS B 551 " pdb="FE2 SF4 B 603 " - pdb=" SG CYS B 554 " pdb="FE3 SF4 B 603 " - pdb=" SG CYS B 557 " pdb="FE4 SF4 B 603 " - pdb=" SG CYS B 591 " pdb=" SF4 B 606 " pdb="FE1 SF4 B 606 " - pdb=" SG CYS B 463 " pdb="FE2 SF4 B 606 " - pdb=" SG CYS B 457 " pdb="FE3 SF4 B 606 " - pdb=" SG CYS B 460 " pdb="FE4 SF4 B 606 " - pdb=" SG CYS B 503 " pdb=" SF4 E 601 " pdb="FE1 SF4 E 601 " - pdb=" SG CYS E 194 " pdb="FE2 SF4 E 601 " - pdb=" SG CYS E 191 " pdb="FE3 SF4 E 601 " - pdb=" SG CYS E 158 " pdb="FE4 SF4 E 601 " - pdb=" SG CYS E 197 " pdb=" SF4 E 602 " pdb="FE2 SF4 E 602 " - pdb=" SG CYS E 151 " pdb="FE4 SF4 E 602 " - pdb=" SG CYS E 148 " pdb="FE1 SF4 E 602 " - pdb=" SG CYS E 154 " pdb="FE3 SF4 E 602 " - pdb=" SG CYS E 201 " pdb=" SF4 E 603 " pdb="FE3 SF4 E 603 " - pdb=" SG CYS E 103 " pdb="FE4 SF4 E 603 " - pdb=" SG CYS E 100 " pdb="FE2 SF4 E 603 " - pdb=" SG CYS E 109 " pdb="FE1 SF4 E 603 " - pdb=" NE2 HIS E 96 " pdb=" SF4 E 605 " pdb="FE1 SF4 E 605 " - pdb=" SG CYS E 502 " pdb="FE2 SF4 E 605 " - pdb=" SG CYS E 356 " pdb="FE3 SF4 E 605 " - pdb=" SG CYS E 506 " pdb=" SF4 F 601 " pdb="FE2 SF4 F 601 " - pdb=" SG CYS F 587 " pdb="FE1 SF4 F 601 " - pdb=" SG CYS F 561 " pdb="FE3 SF4 F 601 " - pdb=" SG CYS F 584 " pdb="FE4 SF4 F 601 " - pdb=" SG CYS F 581 " pdb=" SF4 F 602 " pdb="FE1 SF4 F 602 " - pdb=" SG CYS F 554 " pdb="FE4 SF4 F 602 " - pdb=" SG CYS F 551 " pdb="FE3 SF4 F 602 " - pdb=" SG CYS F 557 " pdb="FE2 SF4 F 602 " - pdb=" SG CYS F 591 " pdb=" SF4 F 606 " pdb="FE4 SF4 F 606 " - pdb=" SG CYS F 457 " pdb="FE1 SF4 F 606 " - pdb=" SG CYS F 503 " pdb="FE3 SF4 F 606 " - pdb=" SG CYS F 460 " pdb="FE2 SF4 F 606 " - pdb=" SG CYS F 463 " Number of angles added : 196 Zn2+ tetrahedral coordination pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 527 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 533 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 440 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 538 " pdb=" ZN F 603 " pdb="ZN ZN F 603 " - pdb=" NE2 HIS F 527 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 533 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 440 " pdb="ZN ZN F 603 " - pdb=" SG CYS F 538 " Number of angles added : 6 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4556 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 21 sheets defined 39.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 21 through 27 Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 270 through 290 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 313 through 318 Proline residue: A 317 - end of helix Processing helix chain 'A' and resid 325 through 341 removed outlier: 3.809A pdb=" N TYR A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.579A pdb=" N LYS A 360 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 363 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 392 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 413 through 416 No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 525 through 539 Processing helix chain 'A' and resid 550 through 558 Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.800A pdb=" N ILE B 75 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Proline residue: B 76 - end of helix removed outlier: 3.667A pdb=" N VAL B 79 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU B 81 " --> pdb=" O MET B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 152 through 162 removed outlier: 4.204A pdb=" N ILE B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 215 through 229 removed outlier: 3.618A pdb=" N VAL B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 259 removed outlier: 3.774A pdb=" N ASN B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 248 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 331 through 337 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.605A pdb=" N TYR B 381 " --> pdb=" O ARG B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.554A pdb=" N ALA B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.970A pdb=" N ALA B 445 " --> pdb=" O MET B 441 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 478 removed outlier: 5.106A pdb=" N THR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE B 473 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 474 " --> pdb=" O MET B 470 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 477 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 removed outlier: 3.547A pdb=" N GLU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 493 " --> pdb=" O ARG B 489 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 508 removed outlier: 3.940A pdb=" N THR B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 504 through 508' Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.635A pdb=" N SER B 515 " --> pdb=" O PRO B 512 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 516 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 517 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 528 removed outlier: 3.607A pdb=" N GLU B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 556 through 559 No H-bonds generated for 'chain 'B' and resid 556 through 559' Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.083A pdb=" N ALA B 590 " --> pdb=" O ALA B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 43 through 53 Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 86 through 89 No H-bonds generated for 'chain 'C' and resid 86 through 89' Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'E' and resid 21 through 27 Processing helix chain 'E' and resid 79 through 94 removed outlier: 3.815A pdb=" N SER E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 181 through 183 No H-bonds generated for 'chain 'E' and resid 181 through 183' Processing helix chain 'E' and resid 196 through 199 No H-bonds generated for 'chain 'E' and resid 196 through 199' Processing helix chain 'E' and resid 212 through 220 Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 238 through 241 No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 270 through 289 Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 313 through 318 removed outlier: 3.686A pdb=" N ILE E 316 " --> pdb=" O PRO E 313 " (cutoff:3.500A) Proline residue: E 317 - end of helix No H-bonds generated for 'chain 'E' and resid 313 through 318' Processing helix chain 'E' and resid 325 through 341 removed outlier: 3.811A pdb=" N TYR E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA E 338 " --> pdb=" O LYS E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 357 through 364 removed outlier: 3.974A pdb=" N VAL E 363 " --> pdb=" O LYS E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 392 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 413 through 416 No H-bonds generated for 'chain 'E' and resid 413 through 416' Processing helix chain 'E' and resid 423 through 436 Processing helix chain 'E' and resid 476 through 487 Processing helix chain 'E' and resid 506 through 508 No H-bonds generated for 'chain 'E' and resid 506 through 508' Processing helix chain 'E' and resid 517 through 522 removed outlier: 4.045A pdb=" N ASP E 522 " --> pdb=" O LYS E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 538 Processing helix chain 'E' and resid 550 through 558 Processing helix chain 'E' and resid 566 through 571 Processing helix chain 'F' and resid 131 through 137 removed outlier: 3.529A pdb=" N PHE F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.624A pdb=" N LYS F 145 " --> pdb=" O LEU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 162 removed outlier: 3.907A pdb=" N ILE F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL F 159 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 183 removed outlier: 3.585A pdb=" N TRP F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 213 removed outlier: 4.032A pdb=" N VAL F 210 " --> pdb=" O MET F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 229 removed outlier: 3.714A pdb=" N MET F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 259 removed outlier: 4.118A pdb=" N ASN F 247 " --> pdb=" O PRO F 243 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN F 250 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE F 251 " --> pdb=" O ASN F 247 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU F 258 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 287 removed outlier: 3.605A pdb=" N GLY F 287 " --> pdb=" O PHE F 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 284 through 287' Processing helix chain 'F' and resid 289 through 297 removed outlier: 3.950A pdb=" N MET F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 325 through 329 Processing helix chain 'F' and resid 331 through 337 Processing helix chain 'F' and resid 339 through 342 No H-bonds generated for 'chain 'F' and resid 339 through 342' Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.717A pdb=" N TYR F 381 " --> pdb=" O ARG F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 400 through 402 No H-bonds generated for 'chain 'F' and resid 400 through 402' Processing helix chain 'F' and resid 408 through 410 No H-bonds generated for 'chain 'F' and resid 408 through 410' Processing helix chain 'F' and resid 417 through 423 removed outlier: 3.671A pdb=" N ILE F 421 " --> pdb=" O TYR F 417 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA F 422 " --> pdb=" O ASP F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 453 removed outlier: 3.787A pdb=" N PHE F 448 " --> pdb=" O VAL F 444 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU F 449 " --> pdb=" O ALA F 445 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE F 451 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 464 No H-bonds generated for 'chain 'F' and resid 461 through 464' Processing helix chain 'F' and resid 466 through 479 removed outlier: 4.085A pdb=" N MET F 470 " --> pdb=" O GLY F 466 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU F 471 " --> pdb=" O THR F 467 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE F 473 " --> pdb=" O ARG F 469 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 474 " --> pdb=" O MET F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 removed outlier: 4.251A pdb=" N LEU F 493 " --> pdb=" O ARG F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 509 removed outlier: 3.708A pdb=" N THR F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 519 removed outlier: 3.516A pdb=" N ILE F 517 " --> pdb=" O VAL F 513 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 528 Processing helix chain 'F' and resid 539 through 541 No H-bonds generated for 'chain 'F' and resid 539 through 541' Processing helix chain 'F' and resid 556 through 560 Processing helix chain 'F' and resid 586 through 590 removed outlier: 3.587A pdb=" N ALA F 590 " --> pdb=" O ALA F 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 586 through 590' Processing helix chain 'G' and resid 6 through 15 Processing helix chain 'G' and resid 25 through 37 removed outlier: 4.069A pdb=" N GLN G 32 " --> pdb=" O GLN G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 53 Processing helix chain 'G' and resid 58 through 66 Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 94 through 101 Processing helix chain 'G' and resid 128 through 130 No H-bonds generated for 'chain 'G' and resid 128 through 130' Processing sheet with id= A, first strand: chain 'A' and resid 3 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= C, first strand: chain 'A' and resid 168 through 170 Processing sheet with id= D, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.924A pdb=" N ILE A 378 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 455 through 461 removed outlier: 3.888A pdb=" N VAL A 460 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 468 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE A 496 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA A 473 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU A 498 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 41 through 46 removed outlier: 7.389A pdb=" N SER B 6 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N VAL B 44 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 8 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N THR B 46 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE B 10 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 59 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 58 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 60 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR B 65 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 233 through 238 removed outlier: 6.247A pdb=" N ASP B 274 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL B 236 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU B 276 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL B 238 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG B 278 " --> pdb=" O VAL B 238 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 367 through 371 Processing sheet with id= I, first strand: chain 'B' and resid 544 through 546 Processing sheet with id= J, first strand: chain 'C' and resid 78 through 80 Processing sheet with id= K, first strand: chain 'C' and resid 134 through 136 Processing sheet with id= L, first strand: chain 'E' and resid 3 through 8 Processing sheet with id= M, first strand: chain 'E' and resid 141 through 143 Processing sheet with id= N, first strand: chain 'E' and resid 167 through 170 Processing sheet with id= O, first strand: chain 'E' and resid 265 through 268 removed outlier: 7.362A pdb=" N ILE E 378 " --> pdb=" O SER E 352 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 455 through 460 removed outlier: 6.289A pdb=" N PHE E 496 " --> pdb=" O VAL E 471 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA E 473 " --> pdb=" O PHE E 496 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU E 498 " --> pdb=" O ALA E 473 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 322 through 324 removed outlier: 9.042A pdb=" N ASN F 323 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA F 194 " --> pdb=" O ASN F 323 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS F 233 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N CYS F 195 " --> pdb=" O LYS F 233 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR F 235 " --> pdb=" O CYS F 195 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP F 274 " --> pdb=" O GLY F 234 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL F 236 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU F 276 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N VAL F 238 " --> pdb=" O GLU F 276 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG F 278 " --> pdb=" O VAL F 238 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 353 through 357 removed outlier: 3.579A pdb=" N LYS F 354 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 370 " --> pdb=" O LYS F 354 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE F 356 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU F 368 " --> pdb=" O PHE F 356 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'F' and resid 404 through 407 Processing sheet with id= T, first strand: chain 'F' and resid 543 through 546 Processing sheet with id= U, first strand: chain 'G' and resid 81 through 83 removed outlier: 7.184A pdb=" N ASP G 120 " --> pdb=" O ILE G 82 " (cutoff:3.500A) No H-bonds generated for sheet with id= U 530 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.88 Time building geometry restraints manager: 8.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 7604 1.41 - 1.63: 11662 1.63 - 1.85: 219 1.85 - 2.07: 0 2.07 - 2.28: 188 Bond restraints: 19673 Sorted by residual: bond pdb=" CA HIS A 573 " pdb=" C HIS A 573 " ideal model delta sigma weight residual 1.522 1.626 -0.104 1.18e-02 7.18e+03 7.76e+01 bond pdb=" C4 FMN B 605 " pdb=" C4A FMN B 605 " ideal model delta sigma weight residual 1.390 1.554 -0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" C4 FMN F 604 " pdb=" C4A FMN F 604 " ideal model delta sigma weight residual 1.390 1.552 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" CG PRO A 245 " pdb=" CD PRO A 245 " ideal model delta sigma weight residual 1.503 1.232 0.271 3.40e-02 8.65e+02 6.34e+01 bond pdb=" CA ASN A 549 " pdb=" C ASN A 549 " ideal model delta sigma weight residual 1.524 1.614 -0.090 1.26e-02 6.30e+03 5.07e+01 ... (remaining 19668 not shown) Histogram of bond angle deviations from ideal: 73.50 - 86.18: 178 86.18 - 98.85: 4 98.85 - 111.53: 8428 111.53 - 124.20: 17724 124.20 - 136.88: 393 Bond angle restraints: 26727 Sorted by residual: angle pdb=" CA PRO A 245 " pdb=" N PRO A 245 " pdb=" CD PRO A 245 " ideal model delta sigma weight residual 112.00 95.75 16.25 1.40e+00 5.10e-01 1.35e+02 angle pdb=" N PRO A 245 " pdb=" CD PRO A 245 " pdb=" CG PRO A 245 " ideal model delta sigma weight residual 103.20 89.79 13.41 1.50e+00 4.44e-01 7.99e+01 angle pdb=" N THR A 574 " pdb=" CA THR A 574 " pdb=" C THR A 574 " ideal model delta sigma weight residual 109.65 123.39 -13.74 1.56e+00 4.11e-01 7.75e+01 angle pdb=" CA HIS A 96 " pdb=" CB HIS A 96 " pdb=" CG HIS A 96 " ideal model delta sigma weight residual 113.80 105.92 7.88 1.00e+00 1.00e+00 6.21e+01 angle pdb=" N HIS A 573 " pdb=" CA HIS A 573 " pdb=" CB HIS A 573 " ideal model delta sigma weight residual 110.84 100.85 9.99 1.52e+00 4.33e-01 4.32e+01 ... (remaining 26722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 11648 35.13 - 70.26: 221 70.26 - 105.39: 27 105.39 - 140.52: 0 140.52 - 175.65: 2 Dihedral angle restraints: 11898 sinusoidal: 4756 harmonic: 7142 Sorted by residual: dihedral pdb=" CA VAL G 23 " pdb=" C VAL G 23 " pdb=" N PRO G 24 " pdb=" CA PRO G 24 " ideal model delta harmonic sigma weight residual 180.00 141.11 38.89 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" C10 FMN B 605 " pdb=" C1' FMN B 605 " pdb=" N10 FMN B 605 " pdb=" C2' FMN B 605 " ideal model delta sinusoidal sigma weight residual 257.59 81.94 175.65 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C10 FMN F 604 " pdb=" C1' FMN F 604 " pdb=" N10 FMN F 604 " pdb=" C2' FMN F 604 " ideal model delta sinusoidal sigma weight residual 257.59 86.59 171.00 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 11895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2922 0.114 - 0.228: 130 0.228 - 0.342: 12 0.342 - 0.456: 6 0.456 - 0.570: 4 Chirality restraints: 3074 Sorted by residual: chirality pdb=" CA VAL E 228 " pdb=" N VAL E 228 " pdb=" C VAL E 228 " pdb=" CB VAL E 228 " both_signs ideal model delta sigma weight residual False 2.44 1.87 0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CA VAL G 13 " pdb=" N VAL G 13 " pdb=" C VAL G 13 " pdb=" CB VAL G 13 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" CB ILE G 136 " pdb=" CA ILE G 136 " pdb=" CG1 ILE G 136 " pdb=" CG2 ILE G 136 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 3071 not shown) Planarity restraints: 3429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD F 605 " -0.050 2.00e-02 2.50e+03 1.09e-01 2.37e+02 pdb=" C2N NAD F 605 " 0.182 2.00e-02 2.50e+03 pdb=" C3N NAD F 605 " 0.082 2.00e-02 2.50e+03 pdb=" C4N NAD F 605 " 0.088 2.00e-02 2.50e+03 pdb=" C5N NAD F 605 " -0.033 2.00e-02 2.50e+03 pdb=" C6N NAD F 605 " -0.098 2.00e-02 2.50e+03 pdb=" C7N NAD F 605 " -0.184 2.00e-02 2.50e+03 pdb=" N1N NAD F 605 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 96 " -0.105 2.00e-02 2.50e+03 8.45e-02 1.07e+02 pdb=" CG HIS A 96 " 0.163 2.00e-02 2.50e+03 pdb=" ND1 HIS A 96 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS A 96 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 HIS A 96 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS A 96 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 573 " -0.044 2.00e-02 2.50e+03 5.65e-02 4.78e+01 pdb=" CG HIS E 573 " -0.003 2.00e-02 2.50e+03 pdb=" ND1 HIS E 573 " 0.094 2.00e-02 2.50e+03 pdb=" CD2 HIS E 573 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS E 573 " -0.083 2.00e-02 2.50e+03 pdb=" NE2 HIS E 573 " -0.002 2.00e-02 2.50e+03 ... (remaining 3426 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 467 2.68 - 3.24: 18706 3.24 - 3.79: 30598 3.79 - 4.35: 39665 4.35 - 4.90: 60883 Nonbonded interactions: 150319 Sorted by model distance: nonbonded pdb=" O ILE G 5 " pdb=" OD1 ASN G 9 " model vdw 2.129 3.040 nonbonded pdb=" O LEU G 31 " pdb=" OG1 THR G 34 " model vdw 2.174 2.440 nonbonded pdb=" CB GLU G 3 " pdb=" OE2 GLU G 8 " model vdw 2.184 3.440 nonbonded pdb=" O CYS A 103 " pdb=" OG SER A 106 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR A 382 " pdb=" O GLY A 511 " model vdw 2.217 2.440 ... (remaining 150314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.790 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 56.120 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.007 0.271 19673 Z= 0.468 Angle : 1.119 18.446 26727 Z= 0.601 Chirality : 0.063 0.570 3074 Planarity : 0.008 0.149 3429 Dihedral : 14.759 175.651 7342 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.57 % Rotamer: Outliers : 1.01 % Allowed : 2.27 % Favored : 96.71 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.13 % 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: -2.14 (0.15), residues: 2506 helix: -2.14 (0.14), residues: 923 sheet: 0.27 (0.36), residues: 199 loop : -1.08 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 304 HIS 0.071 0.004 HIS E 573 PHE 0.040 0.002 PHE A 174 TYR 0.020 0.002 TYR G 61 ARG 0.015 0.001 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 649 time to evaluate : 2.117 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: A 1 MET cc_start: 0.7045 (tmm) cc_final: 0.6821 (tmm) REVERT: A 8 ILE cc_start: 0.9419 (pt) cc_final: 0.8881 (pt) REVERT: A 13 MET cc_start: 0.8483 (mmm) cc_final: 0.8044 (mmm) REVERT: A 39 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8474 (mtmt) REVERT: A 49 MET cc_start: 0.9085 (mmt) cc_final: 0.8729 (mmm) REVERT: A 153 ARG cc_start: 0.8490 (mtm180) cc_final: 0.8154 (mtp85) REVERT: A 212 ILE cc_start: 0.9733 (mp) cc_final: 0.9401 (mp) REVERT: A 261 LEU cc_start: 0.9041 (mt) cc_final: 0.8837 (mt) REVERT: A 267 PHE cc_start: 0.7920 (m-10) cc_final: 0.7644 (m-10) REVERT: A 297 ILE cc_start: 0.9336 (pt) cc_final: 0.8962 (mm) REVERT: A 308 ILE cc_start: 0.9522 (tp) cc_final: 0.9265 (mt) REVERT: A 389 ILE cc_start: 0.9462 (tp) cc_final: 0.9211 (tp) REVERT: A 470 LEU cc_start: 0.9295 (mm) cc_final: 0.8937 (mm) REVERT: A 480 ARG cc_start: 0.9694 (mtt-85) cc_final: 0.9395 (mmm-85) REVERT: A 498 GLU cc_start: 0.8436 (tp30) cc_final: 0.7695 (tp30) REVERT: A 560 LEU cc_start: 0.9370 (mp) cc_final: 0.9090 (tt) REVERT: A 572 LEU cc_start: 0.9588 (mt) cc_final: 0.9340 (mt) REVERT: B 150 MET cc_start: 0.9508 (mmm) cc_final: 0.9253 (tpp) REVERT: B 273 PHE cc_start: 0.8643 (t80) cc_final: 0.8153 (t80) REVERT: B 304 ARG cc_start: 0.8657 (tpt90) cc_final: 0.8332 (tpt90) REVERT: B 305 PRO cc_start: 0.9109 (Cg_exo) cc_final: 0.8584 (Cg_endo) REVERT: B 514 LEU cc_start: 0.9359 (mt) cc_final: 0.9101 (mt) REVERT: C 37 LYS cc_start: 0.9688 (mptt) cc_final: 0.9486 (mmtm) REVERT: C 46 GLN cc_start: 0.9657 (pt0) cc_final: 0.9412 (mp10) REVERT: C 99 LYS cc_start: 0.7599 (tptt) cc_final: 0.7335 (tttm) REVERT: E 1 MET cc_start: 0.6420 (ppp) cc_final: 0.6062 (tmm) REVERT: E 32 ILE cc_start: 0.9066 (mt) cc_final: 0.8477 (mt) REVERT: E 150 LEU cc_start: 0.9314 (mm) cc_final: 0.9074 (mm) REVERT: E 159 ARG cc_start: 0.9106 (ttp-110) cc_final: 0.8742 (ttp-110) REVERT: E 193 ASN cc_start: 0.8712 (m-40) cc_final: 0.8297 (t0) REVERT: E 217 ASP cc_start: 0.9583 (t0) cc_final: 0.9275 (m-30) REVERT: E 242 PHE cc_start: 0.8096 (m-10) cc_final: 0.7777 (m-10) REVERT: E 274 ASP cc_start: 0.8650 (t0) cc_final: 0.8237 (m-30) REVERT: E 384 GLU cc_start: 0.9078 (tp30) cc_final: 0.8842 (tt0) REVERT: E 391 GLU cc_start: 0.9422 (tm-30) cc_final: 0.9168 (tm-30) REVERT: E 404 PHE cc_start: 0.6192 (m-80) cc_final: 0.5873 (m-80) REVERT: E 425 MET cc_start: 0.9457 (mmp) cc_final: 0.9187 (mtt) REVERT: E 470 LEU cc_start: 0.9639 (mm) cc_final: 0.9316 (mm) REVERT: E 496 PHE cc_start: 0.9287 (m-10) cc_final: 0.8492 (m-80) REVERT: E 499 LEU cc_start: 0.9721 (mt) cc_final: 0.9478 (mt) REVERT: F 206 MET cc_start: 0.7347 (mmm) cc_final: 0.7129 (mmm) REVERT: F 342 PHE cc_start: 0.8724 (t80) cc_final: 0.8022 (t80) REVERT: F 427 MET cc_start: 0.7967 (mtt) cc_final: 0.7154 (mmt) REVERT: F 451 PHE cc_start: 0.9572 (t80) cc_final: 0.9304 (t80) REVERT: F 455 GLU cc_start: 0.9459 (mm-30) cc_final: 0.8831 (tp30) REVERT: F 507 GLN cc_start: 0.9266 (pm20) cc_final: 0.8848 (mp10) REVERT: F 524 TYR cc_start: 0.9310 (m-80) cc_final: 0.9041 (m-80) REVERT: G 67 TYR cc_start: 0.8732 (m-80) cc_final: 0.8064 (m-80) outliers start: 21 outliers final: 2 residues processed: 657 average time/residue: 0.3404 time to fit residues: 327.4616 Evaluate side-chains 454 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 452 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 195 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN B 7 GLN B 364 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN E 336 HIS E 469 ASN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19673 Z= 0.240 Angle : 0.673 15.554 26727 Z= 0.347 Chirality : 0.046 0.231 3074 Planarity : 0.006 0.090 3429 Dihedral : 8.990 172.556 2780 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.65 % Rotamer: Outliers : 0.19 % Allowed : 4.74 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % 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: -1.37 (0.16), residues: 2506 helix: -1.29 (0.15), residues: 955 sheet: 0.61 (0.36), residues: 207 loop : -0.77 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 304 HIS 0.009 0.001 HIS E 96 PHE 0.026 0.002 PHE F 180 TYR 0.022 0.001 TYR E 312 ARG 0.006 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 532 time to evaluate : 2.211 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: A 13 MET cc_start: 0.8567 (mmm) cc_final: 0.8047 (mmm) REVERT: A 39 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8094 (mttt) REVERT: A 49 MET cc_start: 0.9288 (mmt) cc_final: 0.8693 (mmm) REVERT: A 93 LEU cc_start: 0.9625 (mt) cc_final: 0.9270 (mt) REVERT: A 142 VAL cc_start: 0.9195 (t) cc_final: 0.8927 (t) REVERT: A 216 TRP cc_start: 0.8955 (m100) cc_final: 0.8740 (m100) REVERT: A 240 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9168 (mm-30) REVERT: A 246 MET cc_start: 0.9332 (mmp) cc_final: 0.8774 (tpp) REVERT: A 263 PHE cc_start: 0.8866 (m-80) cc_final: 0.8641 (m-80) REVERT: A 333 LEU cc_start: 0.9515 (mm) cc_final: 0.9235 (mm) REVERT: A 352 SER cc_start: 0.9388 (p) cc_final: 0.8446 (p) REVERT: A 354 MET cc_start: 0.8225 (mmp) cc_final: 0.7982 (mmp) REVERT: A 470 LEU cc_start: 0.8756 (mm) cc_final: 0.8491 (pp) REVERT: A 500 MET cc_start: 0.8387 (mmp) cc_final: 0.8000 (mmp) REVERT: A 560 LEU cc_start: 0.9384 (mp) cc_final: 0.9027 (tt) REVERT: B 1 MET cc_start: -0.6433 (tpp) cc_final: -0.6653 (tpp) REVERT: B 78 MET cc_start: 0.5518 (mmp) cc_final: 0.5285 (mmp) REVERT: B 150 MET cc_start: 0.9462 (mmm) cc_final: 0.9080 (tpp) REVERT: B 242 TYR cc_start: 0.7026 (m-80) cc_final: 0.6749 (m-80) REVERT: B 273 PHE cc_start: 0.8773 (t80) cc_final: 0.8566 (t80) REVERT: C 99 LYS cc_start: 0.7742 (tptt) cc_final: 0.7453 (tttm) REVERT: E 1 MET cc_start: 0.6502 (ppp) cc_final: 0.5968 (tmm) REVERT: E 123 ILE cc_start: 0.9358 (tp) cc_final: 0.9027 (tp) REVERT: E 192 ILE cc_start: 0.9685 (pt) cc_final: 0.9165 (tp) REVERT: E 193 ASN cc_start: 0.9013 (m-40) cc_final: 0.8476 (t0) REVERT: E 217 ASP cc_start: 0.9642 (t0) cc_final: 0.9353 (m-30) REVERT: E 246 MET cc_start: 0.8748 (mmp) cc_final: 0.8081 (mmp) REVERT: E 306 LYS cc_start: 0.9221 (ttpt) cc_final: 0.9005 (tmmt) REVERT: E 380 ILE cc_start: 0.9688 (pt) cc_final: 0.9485 (pt) REVERT: E 384 GLU cc_start: 0.9236 (tp30) cc_final: 0.8344 (tp30) REVERT: E 391 GLU cc_start: 0.9371 (tm-30) cc_final: 0.8972 (tm-30) REVERT: E 404 PHE cc_start: 0.6263 (m-80) cc_final: 0.5830 (m-80) REVERT: E 496 PHE cc_start: 0.9125 (m-10) cc_final: 0.8316 (m-80) REVERT: E 499 LEU cc_start: 0.9635 (mt) cc_final: 0.9332 (mt) REVERT: F 342 PHE cc_start: 0.8793 (t80) cc_final: 0.8158 (t80) REVERT: F 416 ASP cc_start: 0.7538 (t70) cc_final: 0.7310 (t70) REVERT: F 427 MET cc_start: 0.8211 (mtt) cc_final: 0.7168 (mmt) REVERT: F 441 MET cc_start: 0.8600 (mmp) cc_final: 0.8039 (pmm) REVERT: F 455 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8568 (tp30) REVERT: F 524 TYR cc_start: 0.9219 (m-80) cc_final: 0.8762 (m-80) REVERT: G 67 TYR cc_start: 0.8616 (m-80) cc_final: 0.7772 (m-80) outliers start: 4 outliers final: 2 residues processed: 533 average time/residue: 0.3382 time to fit residues: 269.7068 Evaluate side-chains 431 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 429 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 20.0000 chunk 70 optimal weight: 40.0000 chunk 188 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 62 optimal weight: 50.0000 chunk 226 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 181 optimal weight: 0.0570 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN E 95 ASN ** E 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN E 336 HIS ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 HIS F 337 ASN F 453 GLN G 101 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19673 Z= 0.182 Angle : 0.624 16.975 26727 Z= 0.315 Chirality : 0.045 0.256 3074 Planarity : 0.005 0.081 3429 Dihedral : 8.600 171.493 2780 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.99 % Favored : 95.89 % Rotamer: Outliers : 0.14 % Allowed : 5.03 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % 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: -1.03 (0.16), residues: 2506 helix: -0.93 (0.16), residues: 953 sheet: 0.75 (0.36), residues: 216 loop : -0.65 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 304 HIS 0.004 0.001 HIS E 573 PHE 0.022 0.002 PHE F 180 TYR 0.024 0.001 TYR A 556 ARG 0.008 0.001 ARG F 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 540 time to evaluate : 2.242 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: A 1 MET cc_start: 0.7055 (tmm) cc_final: 0.6723 (tmm) REVERT: A 13 MET cc_start: 0.8580 (mmm) cc_final: 0.8244 (mmm) REVERT: A 39 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7763 (mtmt) REVERT: A 49 MET cc_start: 0.9291 (mmt) cc_final: 0.8837 (mmm) REVERT: A 90 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8393 (tm-30) REVERT: A 177 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8385 (mp10) REVERT: A 216 TRP cc_start: 0.8909 (m100) cc_final: 0.8126 (m100) REVERT: A 240 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9058 (mm-30) REVERT: A 263 PHE cc_start: 0.8948 (m-80) cc_final: 0.8690 (m-80) REVERT: A 267 PHE cc_start: 0.7912 (m-10) cc_final: 0.7672 (m-80) REVERT: A 280 GLU cc_start: 0.9486 (mm-30) cc_final: 0.9085 (mm-30) REVERT: A 296 MET cc_start: 0.8226 (mmp) cc_final: 0.7748 (mmp) REVERT: A 354 MET cc_start: 0.8232 (mmp) cc_final: 0.7935 (mmp) REVERT: A 426 GLU cc_start: 0.9017 (tp30) cc_final: 0.8435 (tp30) REVERT: A 470 LEU cc_start: 0.8896 (mm) cc_final: 0.8594 (pp) REVERT: A 500 MET cc_start: 0.8595 (mmp) cc_final: 0.7971 (mmp) REVERT: B 78 MET cc_start: 0.5712 (mmp) cc_final: 0.5413 (mmp) REVERT: B 150 MET cc_start: 0.9491 (mmm) cc_final: 0.9177 (tpp) REVERT: B 242 TYR cc_start: 0.7010 (m-80) cc_final: 0.6804 (m-80) REVERT: B 273 PHE cc_start: 0.8800 (t80) cc_final: 0.8489 (t80) REVERT: B 275 LEU cc_start: 0.9361 (mm) cc_final: 0.8958 (mm) REVERT: B 372 MET cc_start: 0.7721 (ppp) cc_final: 0.7440 (ppp) REVERT: B 455 GLU cc_start: 0.9178 (tp30) cc_final: 0.8951 (tp30) REVERT: B 471 LEU cc_start: 0.9772 (mt) cc_final: 0.9480 (mt) REVERT: C 34 THR cc_start: 0.8888 (p) cc_final: 0.8422 (p) REVERT: C 93 SER cc_start: 0.9540 (p) cc_final: 0.9313 (p) REVERT: C 99 LYS cc_start: 0.7666 (tptt) cc_final: 0.7407 (tttm) REVERT: E 1 MET cc_start: 0.6505 (ppp) cc_final: 0.5877 (ppp) REVERT: E 99 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8268 (mt-10) REVERT: E 150 LEU cc_start: 0.9347 (mm) cc_final: 0.9130 (mm) REVERT: E 159 ARG cc_start: 0.9201 (ttp-110) cc_final: 0.8993 (ttp-110) REVERT: E 174 PHE cc_start: 0.8472 (m-10) cc_final: 0.8270 (m-80) REVERT: E 192 ILE cc_start: 0.9674 (pt) cc_final: 0.9161 (tp) REVERT: E 193 ASN cc_start: 0.9009 (m-40) cc_final: 0.8402 (t0) REVERT: E 217 ASP cc_start: 0.9624 (t0) cc_final: 0.9345 (m-30) REVERT: E 246 MET cc_start: 0.8808 (mmp) cc_final: 0.8277 (mmp) REVERT: E 304 TRP cc_start: 0.8315 (p-90) cc_final: 0.7603 (p-90) REVERT: E 380 ILE cc_start: 0.9656 (pt) cc_final: 0.9438 (pt) REVERT: E 384 GLU cc_start: 0.9231 (tp30) cc_final: 0.8326 (tp30) REVERT: E 391 GLU cc_start: 0.9363 (tm-30) cc_final: 0.8937 (tm-30) REVERT: E 404 PHE cc_start: 0.6405 (m-80) cc_final: 0.5965 (m-80) REVERT: E 496 PHE cc_start: 0.8888 (m-10) cc_final: 0.8551 (m-80) REVERT: E 499 LEU cc_start: 0.9606 (mt) cc_final: 0.9363 (tp) REVERT: E 518 LYS cc_start: 0.9480 (tppt) cc_final: 0.9173 (tppt) REVERT: E 555 LEU cc_start: 0.9611 (mt) cc_final: 0.9287 (pp) REVERT: F 179 GLN cc_start: 0.9694 (pp30) cc_final: 0.9478 (pp30) REVERT: F 342 PHE cc_start: 0.8781 (t80) cc_final: 0.8129 (t80) REVERT: F 416 ASP cc_start: 0.7895 (t70) cc_final: 0.7346 (t70) REVERT: F 427 MET cc_start: 0.8249 (mtt) cc_final: 0.7159 (mmt) REVERT: F 441 MET cc_start: 0.8473 (mmp) cc_final: 0.8050 (pmm) REVERT: F 446 ARG cc_start: 0.8735 (mtt180) cc_final: 0.8069 (mtt-85) REVERT: F 455 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8663 (tp30) REVERT: G 20 HIS cc_start: 0.8994 (p90) cc_final: 0.8037 (p90) REVERT: G 44 GLU cc_start: 0.9085 (tp30) cc_final: 0.8613 (tp30) REVERT: G 67 TYR cc_start: 0.8584 (m-80) cc_final: 0.7690 (m-80) outliers start: 3 outliers final: 0 residues processed: 541 average time/residue: 0.3373 time to fit residues: 269.7759 Evaluate side-chains 433 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 432 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 108 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 215 optimal weight: 0.3980 chunk 64 optimal weight: 50.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN A 341 ASN A 469 ASN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN E 573 HIS F 337 ASN G 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19673 Z= 0.291 Angle : 0.691 17.862 26727 Z= 0.359 Chirality : 0.047 0.235 3074 Planarity : 0.005 0.081 3429 Dihedral : 8.618 173.661 2780 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 24.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.04 % 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: -0.96 (0.16), residues: 2506 helix: -0.89 (0.15), residues: 971 sheet: 0.66 (0.34), residues: 220 loop : -0.55 (0.18), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 178 HIS 0.012 0.001 HIS E 96 PHE 0.041 0.002 PHE B 180 TYR 0.029 0.002 TYR E 312 ARG 0.009 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 514 time to evaluate : 2.043 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: A 1 MET cc_start: 0.7138 (tmm) cc_final: 0.6730 (tmm) REVERT: A 13 MET cc_start: 0.8716 (mmm) cc_final: 0.8302 (mmm) REVERT: A 49 MET cc_start: 0.9264 (mmt) cc_final: 0.9040 (mmm) REVERT: A 160 ASP cc_start: 0.8649 (t0) cc_final: 0.8418 (t0) REVERT: A 246 MET cc_start: 0.9392 (mmp) cc_final: 0.9025 (mmp) REVERT: A 263 PHE cc_start: 0.9030 (m-80) cc_final: 0.8714 (m-80) REVERT: A 274 ASP cc_start: 0.9350 (t70) cc_final: 0.9072 (m-30) REVERT: A 280 GLU cc_start: 0.9441 (mm-30) cc_final: 0.8958 (mm-30) REVERT: A 297 ILE cc_start: 0.8778 (pt) cc_final: 0.8514 (mm) REVERT: A 333 LEU cc_start: 0.9603 (mm) cc_final: 0.9380 (mm) REVERT: A 353 ILE cc_start: 0.9459 (pt) cc_final: 0.9253 (pt) REVERT: A 381 THR cc_start: 0.9235 (t) cc_final: 0.8776 (t) REVERT: A 383 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8390 (mtt90) REVERT: A 426 GLU cc_start: 0.9041 (tp30) cc_final: 0.8353 (tp30) REVERT: A 470 LEU cc_start: 0.8938 (mm) cc_final: 0.8636 (pp) REVERT: A 480 ARG cc_start: 0.9725 (mmm-85) cc_final: 0.9066 (mmm-85) REVERT: A 500 MET cc_start: 0.8809 (mmp) cc_final: 0.8221 (mmp) REVERT: A 560 LEU cc_start: 0.9469 (mt) cc_final: 0.9137 (tt) REVERT: A 564 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7736 (p0) REVERT: B 78 MET cc_start: 0.6014 (mmp) cc_final: 0.5685 (mmp) REVERT: B 150 MET cc_start: 0.9546 (mmm) cc_final: 0.9030 (tpp) REVERT: B 242 TYR cc_start: 0.7118 (m-80) cc_final: 0.6702 (m-80) REVERT: B 273 PHE cc_start: 0.9034 (t80) cc_final: 0.8798 (t80) REVERT: B 275 LEU cc_start: 0.9410 (mm) cc_final: 0.8974 (mm) REVERT: B 372 MET cc_start: 0.7817 (ppp) cc_final: 0.7536 (ppp) REVERT: B 455 GLU cc_start: 0.9125 (tp30) cc_final: 0.8830 (tp30) REVERT: B 471 LEU cc_start: 0.9728 (mt) cc_final: 0.9483 (mt) REVERT: E 1 MET cc_start: 0.6918 (ppp) cc_final: 0.6138 (ppp) REVERT: E 192 ILE cc_start: 0.9746 (pt) cc_final: 0.9264 (tp) REVERT: E 193 ASN cc_start: 0.9145 (m-40) cc_final: 0.8755 (t0) REVERT: E 217 ASP cc_start: 0.9682 (t0) cc_final: 0.9378 (m-30) REVERT: E 246 MET cc_start: 0.8904 (mmp) cc_final: 0.8178 (mmp) REVERT: E 274 ASP cc_start: 0.8865 (t0) cc_final: 0.8478 (m-30) REVERT: E 380 ILE cc_start: 0.9706 (pt) cc_final: 0.9493 (pt) REVERT: E 384 GLU cc_start: 0.9240 (tp30) cc_final: 0.8539 (tp30) REVERT: E 391 GLU cc_start: 0.9363 (tm-30) cc_final: 0.8917 (tm-30) REVERT: E 404 PHE cc_start: 0.6401 (m-80) cc_final: 0.5744 (m-80) REVERT: E 518 LYS cc_start: 0.9516 (tppt) cc_final: 0.9234 (tppt) REVERT: F 172 PHE cc_start: 0.8775 (t80) cc_final: 0.8520 (t80) REVERT: F 206 MET cc_start: 0.6324 (mmm) cc_final: 0.6020 (mmm) REVERT: F 304 ARG cc_start: 0.9277 (mtm110) cc_final: 0.9047 (mtm110) REVERT: F 342 PHE cc_start: 0.9006 (t80) cc_final: 0.8363 (t80) REVERT: F 416 ASP cc_start: 0.8082 (t70) cc_final: 0.7525 (t70) REVERT: F 427 MET cc_start: 0.8553 (mtt) cc_final: 0.7401 (mmt) REVERT: F 441 MET cc_start: 0.8627 (mmp) cc_final: 0.7902 (pmm) REVERT: F 455 GLU cc_start: 0.9407 (mm-30) cc_final: 0.8664 (tp30) REVERT: G 20 HIS cc_start: 0.8627 (p90) cc_final: 0.7933 (p90) REVERT: G 44 GLU cc_start: 0.9051 (tp30) cc_final: 0.8511 (tp30) REVERT: G 63 VAL cc_start: 0.9051 (t) cc_final: 0.8617 (t) REVERT: G 67 TYR cc_start: 0.8563 (m-80) cc_final: 0.7642 (m-80) outliers start: 2 outliers final: 0 residues processed: 515 average time/residue: 0.3329 time to fit residues: 254.8515 Evaluate side-chains 404 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 403 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 30.0000 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 205 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 216 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN E 29 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 ASN ** F 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS G 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19673 Z= 0.208 Angle : 0.629 16.449 26727 Z= 0.319 Chirality : 0.046 0.282 3074 Planarity : 0.005 0.082 3429 Dihedral : 8.291 172.285 2780 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 0.29 % Allowed : 2.95 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % 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: -0.74 (0.17), residues: 2506 helix: -0.66 (0.16), residues: 985 sheet: 0.80 (0.35), residues: 213 loop : -0.46 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 304 HIS 0.006 0.001 HIS A 96 PHE 0.026 0.001 PHE B 180 TYR 0.022 0.001 TYR E 312 ARG 0.009 0.001 ARG E 393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 526 time to evaluate : 2.206 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: A 1 MET cc_start: 0.7126 (tmm) cc_final: 0.6749 (tmm) REVERT: A 13 MET cc_start: 0.8782 (mmm) cc_final: 0.8391 (mmm) REVERT: A 49 MET cc_start: 0.9426 (mmt) cc_final: 0.8967 (mmm) REVERT: A 229 GLN cc_start: 0.9484 (mp10) cc_final: 0.9280 (mp10) REVERT: A 246 MET cc_start: 0.9348 (mmp) cc_final: 0.9108 (mmp) REVERT: A 263 PHE cc_start: 0.8933 (m-80) cc_final: 0.8684 (m-80) REVERT: A 280 GLU cc_start: 0.9436 (mm-30) cc_final: 0.8938 (mm-30) REVERT: A 297 ILE cc_start: 0.8822 (pt) cc_final: 0.8612 (mm) REVERT: A 327 ASN cc_start: 0.9551 (m110) cc_final: 0.9345 (m110) REVERT: A 333 LEU cc_start: 0.9576 (mm) cc_final: 0.9373 (mm) REVERT: A 383 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8586 (mtt90) REVERT: A 387 ARG cc_start: 0.9277 (mpp80) cc_final: 0.8977 (ptt-90) REVERT: A 426 GLU cc_start: 0.9076 (tp30) cc_final: 0.8439 (tp30) REVERT: A 500 MET cc_start: 0.8734 (mmp) cc_final: 0.8181 (mmp) REVERT: A 531 LYS cc_start: 0.9619 (pttm) cc_final: 0.9416 (pttm) REVERT: A 560 LEU cc_start: 0.9443 (mt) cc_final: 0.9138 (tt) REVERT: B 150 MET cc_start: 0.9582 (mmm) cc_final: 0.9196 (tpp) REVERT: B 242 TYR cc_start: 0.7130 (m-80) cc_final: 0.6800 (m-80) REVERT: B 250 GLN cc_start: 0.9759 (mt0) cc_final: 0.9467 (tp-100) REVERT: B 275 LEU cc_start: 0.9407 (mm) cc_final: 0.8977 (mm) REVERT: B 356 PHE cc_start: 0.9535 (m-80) cc_final: 0.9306 (m-80) REVERT: B 372 MET cc_start: 0.7805 (ppp) cc_final: 0.7566 (ppp) REVERT: B 426 MET cc_start: 0.9612 (mpp) cc_final: 0.9255 (tpt) REVERT: B 435 MET cc_start: 0.9196 (tmm) cc_final: 0.8780 (mpp) REVERT: B 455 GLU cc_start: 0.9178 (tp30) cc_final: 0.8882 (tp30) REVERT: B 471 LEU cc_start: 0.9773 (mt) cc_final: 0.9501 (mt) REVERT: C 28 MET cc_start: 0.9124 (tpt) cc_final: 0.8895 (tpt) REVERT: E 1 MET cc_start: 0.6800 (ppp) cc_final: 0.6012 (ppp) REVERT: E 108 ASN cc_start: 0.9382 (m110) cc_final: 0.8981 (m110) REVERT: E 136 ASP cc_start: 0.8523 (t70) cc_final: 0.8084 (m-30) REVERT: E 192 ILE cc_start: 0.9742 (pt) cc_final: 0.9414 (tp) REVERT: E 193 ASN cc_start: 0.9210 (m-40) cc_final: 0.8636 (t0) REVERT: E 217 ASP cc_start: 0.9681 (t0) cc_final: 0.9365 (m-30) REVERT: E 246 MET cc_start: 0.8883 (mmp) cc_final: 0.8120 (mmp) REVERT: E 274 ASP cc_start: 0.8904 (t0) cc_final: 0.8500 (m-30) REVERT: E 380 ILE cc_start: 0.9678 (pt) cc_final: 0.9475 (pt) REVERT: E 384 GLU cc_start: 0.9198 (tp30) cc_final: 0.8331 (tp30) REVERT: E 393 ARG cc_start: 0.9116 (ptt90) cc_final: 0.8821 (ptm-80) REVERT: E 404 PHE cc_start: 0.6478 (m-80) cc_final: 0.5828 (m-80) REVERT: E 518 LYS cc_start: 0.9510 (tppt) cc_final: 0.9233 (tppt) REVERT: F 172 PHE cc_start: 0.8891 (t80) cc_final: 0.8595 (t80) REVERT: F 173 PRO cc_start: 0.9453 (Cg_endo) cc_final: 0.8996 (Cg_endo) REVERT: F 206 MET cc_start: 0.6415 (mmm) cc_final: 0.6085 (mmm) REVERT: F 342 PHE cc_start: 0.8993 (t80) cc_final: 0.8367 (t80) REVERT: F 419 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6617 (t0) REVERT: F 427 MET cc_start: 0.8517 (mtt) cc_final: 0.7454 (mmm) REVERT: F 441 MET cc_start: 0.8558 (mmp) cc_final: 0.8001 (pmm) REVERT: F 455 GLU cc_start: 0.9395 (mm-30) cc_final: 0.8543 (tp30) REVERT: G 9 ASN cc_start: 0.7282 (m-40) cc_final: 0.6911 (m-40) REVERT: G 44 GLU cc_start: 0.8990 (tp30) cc_final: 0.8457 (tp30) REVERT: G 67 TYR cc_start: 0.8571 (m-80) cc_final: 0.7734 (m-80) outliers start: 6 outliers final: 2 residues processed: 530 average time/residue: 0.3412 time to fit residues: 270.2322 Evaluate side-chains 405 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 402 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 chunk 141 optimal weight: 0.7980 chunk 59 optimal weight: 50.0000 chunk 240 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS G 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19673 Z= 0.207 Angle : 0.631 15.544 26727 Z= 0.322 Chirality : 0.046 0.299 3074 Planarity : 0.005 0.089 3429 Dihedral : 8.193 171.727 2780 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % 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: -0.67 (0.17), residues: 2506 helix: -0.55 (0.16), residues: 991 sheet: 0.78 (0.36), residues: 213 loop : -0.45 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 304 HIS 0.008 0.001 HIS E 96 PHE 0.028 0.002 PHE A 267 TYR 0.020 0.001 TYR E 312 ARG 0.014 0.001 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 508 time to evaluate : 2.040 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: A 1 MET cc_start: 0.7165 (tmm) cc_final: 0.6757 (tmm) REVERT: A 8 ILE cc_start: 0.9368 (pt) cc_final: 0.9068 (pt) REVERT: A 13 MET cc_start: 0.8780 (mmm) cc_final: 0.8378 (mmm) REVERT: A 39 LYS cc_start: 0.7916 (mttt) cc_final: 0.7692 (mttt) REVERT: A 49 MET cc_start: 0.9476 (mmt) cc_final: 0.9054 (mmm) REVERT: A 90 GLU cc_start: 0.9058 (pm20) cc_final: 0.8750 (pm20) REVERT: A 263 PHE cc_start: 0.8884 (m-80) cc_final: 0.8675 (m-80) REVERT: A 267 PHE cc_start: 0.7821 (m-80) cc_final: 0.7458 (m-80) REVERT: A 280 GLU cc_start: 0.9418 (mm-30) cc_final: 0.8944 (mm-30) REVERT: A 333 LEU cc_start: 0.9657 (mm) cc_final: 0.9415 (mm) REVERT: A 387 ARG cc_start: 0.9303 (mpp80) cc_final: 0.8927 (mtm-85) REVERT: A 426 GLU cc_start: 0.9040 (tp30) cc_final: 0.8256 (tp30) REVERT: A 470 LEU cc_start: 0.8829 (mm) cc_final: 0.8557 (pp) REVERT: A 500 MET cc_start: 0.8821 (mmp) cc_final: 0.8262 (mmp) REVERT: A 531 LYS cc_start: 0.9627 (pttm) cc_final: 0.9389 (pttm) REVERT: A 560 LEU cc_start: 0.9450 (mt) cc_final: 0.9120 (tt) REVERT: B 150 MET cc_start: 0.9577 (mmm) cc_final: 0.9187 (tpp) REVERT: B 242 TYR cc_start: 0.7186 (m-80) cc_final: 0.6879 (m-80) REVERT: B 250 GLN cc_start: 0.9754 (mt0) cc_final: 0.9464 (tp-100) REVERT: B 372 MET cc_start: 0.7800 (ppp) cc_final: 0.7549 (ppp) REVERT: B 450 ASP cc_start: 0.9328 (t0) cc_final: 0.8591 (t0) REVERT: B 455 GLU cc_start: 0.9138 (tp30) cc_final: 0.8842 (tp30) REVERT: E 1 MET cc_start: 0.6693 (ppp) cc_final: 0.5923 (ppp) REVERT: E 192 ILE cc_start: 0.9723 (pt) cc_final: 0.9297 (tp) REVERT: E 193 ASN cc_start: 0.9287 (m-40) cc_final: 0.8818 (t0) REVERT: E 217 ASP cc_start: 0.9680 (t0) cc_final: 0.9361 (m-30) REVERT: E 246 MET cc_start: 0.8812 (mmp) cc_final: 0.8007 (mmp) REVERT: E 274 ASP cc_start: 0.8911 (t0) cc_final: 0.8497 (m-30) REVERT: E 278 MET cc_start: 0.9446 (tmm) cc_final: 0.9108 (tmm) REVERT: E 284 LEU cc_start: 0.9287 (mm) cc_final: 0.9035 (mm) REVERT: E 380 ILE cc_start: 0.9647 (pt) cc_final: 0.9411 (pt) REVERT: E 384 GLU cc_start: 0.9197 (tp30) cc_final: 0.8283 (tp30) REVERT: E 404 PHE cc_start: 0.6382 (m-80) cc_final: 0.5733 (m-80) REVERT: E 518 LYS cc_start: 0.9519 (tppt) cc_final: 0.9139 (tppt) REVERT: F 172 PHE cc_start: 0.8954 (t80) cc_final: 0.8644 (t80) REVERT: F 173 PRO cc_start: 0.9453 (Cg_endo) cc_final: 0.8996 (Cg_endo) REVERT: F 179 GLN cc_start: 0.9677 (pp30) cc_final: 0.9458 (pp30) REVERT: F 206 MET cc_start: 0.6400 (mmm) cc_final: 0.6109 (mmm) REVERT: F 342 PHE cc_start: 0.9002 (t80) cc_final: 0.8376 (t80) REVERT: F 427 MET cc_start: 0.8504 (mtt) cc_final: 0.7577 (mmm) REVERT: F 441 MET cc_start: 0.8439 (mmp) cc_final: 0.7929 (pmm) REVERT: F 455 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8508 (tp30) REVERT: F 468 LYS cc_start: 0.9555 (ptmm) cc_final: 0.9192 (ptmm) REVERT: G 21 ARG cc_start: 0.9212 (mtm110) cc_final: 0.8986 (mtm110) REVERT: G 44 GLU cc_start: 0.8892 (tp30) cc_final: 0.8495 (tp30) REVERT: G 63 VAL cc_start: 0.9025 (t) cc_final: 0.8764 (t) REVERT: G 67 TYR cc_start: 0.8593 (m-80) cc_final: 0.7725 (m-80) outliers start: 1 outliers final: 0 residues processed: 508 average time/residue: 0.3284 time to fit residues: 248.7869 Evaluate side-chains 405 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN E 339 GLN ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19673 Z= 0.199 Angle : 0.631 15.645 26727 Z= 0.321 Chirality : 0.046 0.317 3074 Planarity : 0.005 0.085 3429 Dihedral : 8.046 171.160 2780 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2506 helix: -0.49 (0.16), residues: 988 sheet: 0.76 (0.36), residues: 213 loop : -0.48 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 304 HIS 0.007 0.001 HIS A 96 PHE 0.019 0.001 PHE B 180 TYR 0.018 0.001 TYR E 312 ARG 0.009 0.001 ARG E 393 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 506 time to evaluate : 2.288 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: A 1 MET cc_start: 0.7193 (tmm) cc_final: 0.6814 (tmm) REVERT: A 8 ILE cc_start: 0.9365 (pt) cc_final: 0.9116 (pt) REVERT: A 13 MET cc_start: 0.8762 (mmm) cc_final: 0.8465 (mpp) REVERT: A 49 MET cc_start: 0.9487 (mmt) cc_final: 0.9075 (mmm) REVERT: A 181 VAL cc_start: 0.8791 (t) cc_final: 0.8543 (t) REVERT: A 246 MET cc_start: 0.9254 (mmp) cc_final: 0.8928 (mmp) REVERT: A 267 PHE cc_start: 0.7910 (m-80) cc_final: 0.7348 (m-80) REVERT: A 280 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8967 (mm-30) REVERT: A 327 ASN cc_start: 0.9515 (m110) cc_final: 0.9247 (m110) REVERT: A 333 LEU cc_start: 0.9677 (mm) cc_final: 0.9428 (mm) REVERT: A 426 GLU cc_start: 0.9025 (tp30) cc_final: 0.8143 (tp30) REVERT: A 500 MET cc_start: 0.8839 (mmp) cc_final: 0.8209 (mmp) REVERT: A 560 LEU cc_start: 0.9422 (mt) cc_final: 0.9105 (tt) REVERT: B 150 MET cc_start: 0.9588 (mmm) cc_final: 0.9211 (tpp) REVERT: B 236 VAL cc_start: 0.9615 (p) cc_final: 0.9245 (m) REVERT: B 250 GLN cc_start: 0.9755 (mt0) cc_final: 0.9463 (tp-100) REVERT: B 273 PHE cc_start: 0.8967 (t80) cc_final: 0.8665 (t80) REVERT: B 275 LEU cc_start: 0.9385 (mm) cc_final: 0.9005 (mm) REVERT: B 356 PHE cc_start: 0.9506 (m-80) cc_final: 0.9273 (m-80) REVERT: B 372 MET cc_start: 0.7780 (ppp) cc_final: 0.7537 (ppp) REVERT: B 450 ASP cc_start: 0.8914 (t0) cc_final: 0.8581 (t0) REVERT: B 455 GLU cc_start: 0.9225 (tp30) cc_final: 0.8923 (tp30) REVERT: E 1 MET cc_start: 0.6800 (ppp) cc_final: 0.6039 (ppp) REVERT: E 108 ASN cc_start: 0.9310 (m110) cc_final: 0.8930 (m110) REVERT: E 159 ARG cc_start: 0.9218 (ttp-110) cc_final: 0.9016 (ttp-110) REVERT: E 192 ILE cc_start: 0.9721 (pt) cc_final: 0.9304 (tp) REVERT: E 193 ASN cc_start: 0.9290 (m-40) cc_final: 0.8778 (t0) REVERT: E 217 ASP cc_start: 0.9678 (t0) cc_final: 0.9372 (m-30) REVERT: E 229 GLN cc_start: 0.9109 (mp-120) cc_final: 0.8871 (mp10) REVERT: E 246 MET cc_start: 0.8777 (mmp) cc_final: 0.7947 (mmp) REVERT: E 254 MET cc_start: 0.9448 (ptp) cc_final: 0.8970 (ptp) REVERT: E 274 ASP cc_start: 0.8942 (t0) cc_final: 0.8607 (m-30) REVERT: E 278 MET cc_start: 0.9469 (tmm) cc_final: 0.9181 (tmm) REVERT: E 284 LEU cc_start: 0.9305 (mm) cc_final: 0.8820 (mm) REVERT: E 351 VAL cc_start: 0.9808 (p) cc_final: 0.9487 (p) REVERT: E 380 ILE cc_start: 0.9629 (pt) cc_final: 0.9374 (pt) REVERT: E 384 GLU cc_start: 0.9190 (tp30) cc_final: 0.8273 (tp30) REVERT: E 518 LYS cc_start: 0.9532 (tppt) cc_final: 0.9059 (tppt) REVERT: F 172 PHE cc_start: 0.9015 (t80) cc_final: 0.8737 (t80) REVERT: F 173 PRO cc_start: 0.9425 (Cg_endo) cc_final: 0.8940 (Cg_endo) REVERT: F 179 GLN cc_start: 0.9675 (pp30) cc_final: 0.9464 (pp30) REVERT: F 206 MET cc_start: 0.6436 (mmm) cc_final: 0.6142 (mmm) REVERT: F 304 ARG cc_start: 0.9209 (mtm110) cc_final: 0.8983 (mtm110) REVERT: F 342 PHE cc_start: 0.9012 (t80) cc_final: 0.8428 (t80) REVERT: F 427 MET cc_start: 0.8473 (mtt) cc_final: 0.7582 (mmm) REVERT: F 441 MET cc_start: 0.8390 (mmp) cc_final: 0.8031 (pmm) REVERT: F 455 GLU cc_start: 0.9383 (mm-30) cc_final: 0.8417 (tp30) REVERT: F 468 LYS cc_start: 0.9490 (ptmm) cc_final: 0.9217 (ptmt) REVERT: G 44 GLU cc_start: 0.8896 (tp30) cc_final: 0.8455 (tp30) REVERT: G 67 TYR cc_start: 0.8514 (m-80) cc_final: 0.7562 (m-80) outliers start: 1 outliers final: 0 residues processed: 506 average time/residue: 0.3332 time to fit residues: 250.4413 Evaluate side-chains 397 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 46 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 22 optimal weight: 30.0000 chunk 188 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 GLN E 469 ASN ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 HIS ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19673 Z= 0.196 Angle : 0.636 15.625 26727 Z= 0.324 Chirality : 0.046 0.334 3074 Planarity : 0.005 0.091 3429 Dihedral : 7.979 171.939 2780 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.71 % Favored : 95.21 % Rotamer: Outliers : 0.05 % Allowed : 1.16 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % 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: -0.62 (0.17), residues: 2506 helix: -0.46 (0.16), residues: 981 sheet: 0.77 (0.36), residues: 213 loop : -0.46 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 178 HIS 0.006 0.001 HIS A 96 PHE 0.018 0.001 PHE A 174 TYR 0.023 0.001 TYR F 242 ARG 0.009 0.001 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 506 time to evaluate : 2.304 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: A 1 MET cc_start: 0.7249 (tmm) cc_final: 0.6887 (tmm) REVERT: A 8 ILE cc_start: 0.9373 (pt) cc_final: 0.9134 (pt) REVERT: A 13 MET cc_start: 0.8727 (mmm) cc_final: 0.8466 (mpp) REVERT: A 39 LYS cc_start: 0.7902 (mttt) cc_final: 0.7667 (mttp) REVERT: A 49 MET cc_start: 0.9499 (mmt) cc_final: 0.9020 (mmm) REVERT: A 181 VAL cc_start: 0.8754 (t) cc_final: 0.8513 (t) REVERT: A 246 MET cc_start: 0.9295 (mmp) cc_final: 0.8904 (mmp) REVERT: A 280 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8899 (mm-30) REVERT: A 304 TRP cc_start: 0.8957 (p-90) cc_final: 0.8722 (p-90) REVERT: A 308 ILE cc_start: 0.9810 (pt) cc_final: 0.9597 (pt) REVERT: A 333 LEU cc_start: 0.9698 (mm) cc_final: 0.9450 (mm) REVERT: A 354 MET cc_start: 0.8227 (mmp) cc_final: 0.7968 (mmp) REVERT: A 426 GLU cc_start: 0.8983 (tp30) cc_final: 0.8150 (tp30) REVERT: A 470 LEU cc_start: 0.8964 (mm) cc_final: 0.8605 (pp) REVERT: A 500 MET cc_start: 0.8873 (mmp) cc_final: 0.8143 (mmp) REVERT: A 560 LEU cc_start: 0.9406 (mt) cc_final: 0.9109 (tt) REVERT: B 150 MET cc_start: 0.9603 (mmm) cc_final: 0.9287 (tpp) REVERT: B 236 VAL cc_start: 0.9619 (p) cc_final: 0.9259 (m) REVERT: B 250 GLN cc_start: 0.9754 (mt0) cc_final: 0.9423 (tp-100) REVERT: B 275 LEU cc_start: 0.9334 (mm) cc_final: 0.8951 (mm) REVERT: B 302 GLU cc_start: 0.8933 (pp20) cc_final: 0.8612 (pp20) REVERT: B 372 MET cc_start: 0.7772 (ppp) cc_final: 0.7548 (ppp) REVERT: B 455 GLU cc_start: 0.9226 (tp30) cc_final: 0.8964 (tp30) REVERT: E 1 MET cc_start: 0.6803 (ppp) cc_final: 0.6011 (ppp) REVERT: E 108 ASN cc_start: 0.9262 (m110) cc_final: 0.8771 (m110) REVERT: E 192 ILE cc_start: 0.9727 (pt) cc_final: 0.9280 (tp) REVERT: E 193 ASN cc_start: 0.9301 (m-40) cc_final: 0.8795 (t0) REVERT: E 217 ASP cc_start: 0.9669 (t0) cc_final: 0.9343 (m-30) REVERT: E 235 ARG cc_start: 0.8016 (mpp-170) cc_final: 0.7712 (tmm160) REVERT: E 246 MET cc_start: 0.8807 (mmp) cc_final: 0.7992 (mmp) REVERT: E 274 ASP cc_start: 0.8981 (t0) cc_final: 0.8558 (m-30) REVERT: E 279 GLU cc_start: 0.9588 (tp30) cc_final: 0.9328 (tp30) REVERT: E 283 GLU cc_start: 0.8696 (pm20) cc_final: 0.7771 (pm20) REVERT: E 284 LEU cc_start: 0.9141 (mm) cc_final: 0.8762 (mm) REVERT: E 351 VAL cc_start: 0.9781 (p) cc_final: 0.9518 (p) REVERT: E 380 ILE cc_start: 0.9669 (pt) cc_final: 0.9432 (pt) REVERT: E 384 GLU cc_start: 0.9183 (tp30) cc_final: 0.8270 (tp30) REVERT: E 518 LYS cc_start: 0.9543 (tppt) cc_final: 0.9071 (tppt) REVERT: F 172 PHE cc_start: 0.9080 (t80) cc_final: 0.8853 (t80) REVERT: F 173 PRO cc_start: 0.9384 (Cg_endo) cc_final: 0.8884 (Cg_endo) REVERT: F 206 MET cc_start: 0.6471 (mmm) cc_final: 0.6223 (mmm) REVERT: F 342 PHE cc_start: 0.9022 (t80) cc_final: 0.8449 (t80) REVERT: F 427 MET cc_start: 0.8538 (mtt) cc_final: 0.7607 (mmm) REVERT: F 441 MET cc_start: 0.8389 (mmp) cc_final: 0.7991 (pmm) REVERT: F 455 GLU cc_start: 0.9359 (mm-30) cc_final: 0.8397 (tp30) REVERT: G 21 ARG cc_start: 0.9217 (mtm110) cc_final: 0.8940 (mtm110) REVERT: G 44 GLU cc_start: 0.8914 (tp30) cc_final: 0.8475 (tp30) REVERT: G 67 TYR cc_start: 0.8537 (m-80) cc_final: 0.7653 (m-80) outliers start: 1 outliers final: 0 residues processed: 506 average time/residue: 0.3351 time to fit residues: 253.2947 Evaluate side-chains 391 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 chunk 202 optimal weight: 30.0000 chunk 211 optimal weight: 30.0000 chunk 222 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN E 95 ASN E 326 GLN E 327 ASN ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 HIS ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19673 Z= 0.197 Angle : 0.650 18.312 26727 Z= 0.329 Chirality : 0.047 0.340 3074 Planarity : 0.005 0.090 3429 Dihedral : 7.948 172.392 2780 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 0.10 % Allowed : 0.63 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % 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: -0.61 (0.17), residues: 2506 helix: -0.47 (0.16), residues: 965 sheet: 0.76 (0.36), residues: 215 loop : -0.45 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP F 178 HIS 0.006 0.001 HIS A 96 PHE 0.021 0.001 PHE B 451 TYR 0.018 0.001 TYR F 242 ARG 0.008 0.001 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 497 time to evaluate : 2.577 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: A 1 MET cc_start: 0.7371 (tmm) cc_final: 0.7016 (tmm) REVERT: A 8 ILE cc_start: 0.9371 (pt) cc_final: 0.9116 (pt) REVERT: A 13 MET cc_start: 0.8645 (mmm) cc_final: 0.8385 (mpp) REVERT: A 49 MET cc_start: 0.9503 (mmt) cc_final: 0.9020 (mmm) REVERT: A 93 LEU cc_start: 0.9664 (mt) cc_final: 0.9432 (mt) REVERT: A 181 VAL cc_start: 0.8699 (t) cc_final: 0.8440 (t) REVERT: A 246 MET cc_start: 0.9279 (mmp) cc_final: 0.8903 (mmp) REVERT: A 280 GLU cc_start: 0.9311 (mm-30) cc_final: 0.8850 (mm-30) REVERT: A 333 LEU cc_start: 0.9718 (mm) cc_final: 0.9470 (mm) REVERT: A 354 MET cc_start: 0.8250 (mmp) cc_final: 0.8003 (mmp) REVERT: A 426 GLU cc_start: 0.9018 (tp30) cc_final: 0.8208 (tp30) REVERT: A 470 LEU cc_start: 0.8893 (mm) cc_final: 0.8552 (pp) REVERT: A 500 MET cc_start: 0.8817 (mmp) cc_final: 0.8058 (mmp) REVERT: A 560 LEU cc_start: 0.9395 (mt) cc_final: 0.9109 (tt) REVERT: B 150 MET cc_start: 0.9603 (mmm) cc_final: 0.9297 (tpp) REVERT: B 167 ARG cc_start: 0.8489 (tpm170) cc_final: 0.8107 (tpm170) REVERT: B 236 VAL cc_start: 0.9587 (p) cc_final: 0.9234 (m) REVERT: B 250 GLN cc_start: 0.9756 (mt0) cc_final: 0.9453 (tp-100) REVERT: B 275 LEU cc_start: 0.9429 (mm) cc_final: 0.9164 (mm) REVERT: E 1 MET cc_start: 0.6879 (ppp) cc_final: 0.6103 (ppp) REVERT: E 28 ASN cc_start: 0.9516 (OUTLIER) cc_final: 0.9069 (m-40) REVERT: E 108 ASN cc_start: 0.9220 (m110) cc_final: 0.8754 (m110) REVERT: E 192 ILE cc_start: 0.9712 (pt) cc_final: 0.9259 (tp) REVERT: E 193 ASN cc_start: 0.9305 (m-40) cc_final: 0.8829 (t0) REVERT: E 217 ASP cc_start: 0.9663 (t0) cc_final: 0.9353 (m-30) REVERT: E 246 MET cc_start: 0.8774 (mmp) cc_final: 0.7971 (mmp) REVERT: E 274 ASP cc_start: 0.9001 (t0) cc_final: 0.8599 (m-30) REVERT: E 279 GLU cc_start: 0.9579 (tp30) cc_final: 0.9348 (tp30) REVERT: E 283 GLU cc_start: 0.8651 (pm20) cc_final: 0.7852 (pm20) REVERT: E 284 LEU cc_start: 0.9200 (mm) cc_final: 0.8615 (mm) REVERT: E 305 ILE cc_start: 0.9512 (pt) cc_final: 0.9168 (pt) REVERT: E 380 ILE cc_start: 0.9683 (pt) cc_final: 0.9394 (pt) REVERT: E 384 GLU cc_start: 0.9203 (tp30) cc_final: 0.8276 (tp30) REVERT: E 518 LYS cc_start: 0.9543 (tppt) cc_final: 0.9072 (tppt) REVERT: E 576 TYR cc_start: 0.7278 (m-80) cc_final: 0.6699 (m-10) REVERT: F 172 PHE cc_start: 0.9098 (t80) cc_final: 0.8847 (t80) REVERT: F 173 PRO cc_start: 0.9418 (Cg_endo) cc_final: 0.8894 (Cg_endo) REVERT: F 206 MET cc_start: 0.6594 (mmm) cc_final: 0.6335 (mmm) REVERT: F 304 ARG cc_start: 0.9171 (mtm110) cc_final: 0.8948 (mtm110) REVERT: F 309 PHE cc_start: 0.9154 (m-80) cc_final: 0.8938 (m-80) REVERT: F 342 PHE cc_start: 0.9039 (t80) cc_final: 0.8465 (t80) REVERT: F 427 MET cc_start: 0.8518 (mtt) cc_final: 0.7560 (mmm) REVERT: F 441 MET cc_start: 0.8354 (mmp) cc_final: 0.7961 (pmm) REVERT: F 455 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8363 (tp30) REVERT: G 21 ARG cc_start: 0.9217 (mtm110) cc_final: 0.8952 (mtm110) REVERT: G 44 GLU cc_start: 0.8869 (tp30) cc_final: 0.8418 (tp30) REVERT: G 67 TYR cc_start: 0.8431 (m-80) cc_final: 0.7472 (m-80) outliers start: 2 outliers final: 0 residues processed: 498 average time/residue: 0.3279 time to fit residues: 244.5875 Evaluate side-chains 397 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 248 optimal weight: 0.6980 chunk 228 optimal weight: 6.9990 chunk 197 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 121 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN E 95 ASN ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN E 573 HIS ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN G 46 GLN G 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19673 Z= 0.164 Angle : 0.647 17.463 26727 Z= 0.323 Chirality : 0.046 0.351 3074 Planarity : 0.005 0.091 3429 Dihedral : 7.751 172.802 2780 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % 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: -0.60 (0.17), residues: 2506 helix: -0.43 (0.17), residues: 967 sheet: 1.00 (0.36), residues: 203 loop : -0.50 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP F 178 HIS 0.004 0.001 HIS E 96 PHE 0.018 0.001 PHE B 451 TYR 0.025 0.001 TYR F 242 ARG 0.013 0.001 ARG F 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 2.381 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: A 1 MET cc_start: 0.7318 (tmm) cc_final: 0.6971 (tmm) REVERT: A 8 ILE cc_start: 0.9375 (pt) cc_final: 0.9105 (pt) REVERT: A 13 MET cc_start: 0.8574 (mmm) cc_final: 0.8373 (mpp) REVERT: A 39 LYS cc_start: 0.8177 (mtmm) cc_final: 0.7380 (mttt) REVERT: A 49 MET cc_start: 0.9412 (mmt) cc_final: 0.8937 (mmm) REVERT: A 181 VAL cc_start: 0.8677 (t) cc_final: 0.8432 (t) REVERT: A 229 GLN cc_start: 0.9428 (mp10) cc_final: 0.8507 (tm-30) REVERT: A 246 MET cc_start: 0.9310 (mmp) cc_final: 0.8898 (mmp) REVERT: A 280 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8827 (mm-30) REVERT: A 296 MET cc_start: 0.8539 (mmp) cc_final: 0.8185 (mmm) REVERT: A 308 ILE cc_start: 0.9797 (pt) cc_final: 0.9592 (pt) REVERT: A 333 LEU cc_start: 0.9660 (mm) cc_final: 0.9416 (mm) REVERT: A 354 MET cc_start: 0.8263 (mmp) cc_final: 0.7395 (mmp) REVERT: A 426 GLU cc_start: 0.8995 (tp30) cc_final: 0.8293 (tp30) REVERT: A 470 LEU cc_start: 0.8867 (mm) cc_final: 0.8523 (pp) REVERT: A 560 LEU cc_start: 0.9372 (mt) cc_final: 0.9081 (tt) REVERT: A 582 LEU cc_start: 0.8273 (mt) cc_final: 0.8024 (tp) REVERT: B 150 MET cc_start: 0.9601 (mmm) cc_final: 0.9238 (tmm) REVERT: B 167 ARG cc_start: 0.8456 (tpm170) cc_final: 0.6763 (tpt-90) REVERT: B 236 VAL cc_start: 0.9590 (p) cc_final: 0.9268 (m) REVERT: B 250 GLN cc_start: 0.9736 (mt0) cc_final: 0.9399 (tp-100) REVERT: B 275 LEU cc_start: 0.9362 (mm) cc_final: 0.9082 (mm) REVERT: B 300 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7250 (tpm170) REVERT: B 356 PHE cc_start: 0.9507 (m-80) cc_final: 0.9150 (m-80) REVERT: B 448 PHE cc_start: 0.9630 (m-80) cc_final: 0.9416 (m-80) REVERT: B 450 ASP cc_start: 0.9607 (m-30) cc_final: 0.9149 (m-30) REVERT: B 453 GLN cc_start: 0.9145 (pp30) cc_final: 0.8854 (pp30) REVERT: C 32 GLN cc_start: 0.9500 (pp30) cc_final: 0.9091 (pp30) REVERT: C 66 PHE cc_start: 0.8526 (t80) cc_final: 0.8156 (t80) REVERT: C 149 ILE cc_start: 0.8680 (mt) cc_final: 0.7799 (mt) REVERT: E 1 MET cc_start: 0.6867 (ppp) cc_final: 0.6227 (ppp) REVERT: E 108 ASN cc_start: 0.9193 (m110) cc_final: 0.8262 (m110) REVERT: E 159 ARG cc_start: 0.9280 (ttp-110) cc_final: 0.9061 (ttp-110) REVERT: E 192 ILE cc_start: 0.9652 (pt) cc_final: 0.9013 (tp) REVERT: E 193 ASN cc_start: 0.9179 (m-40) cc_final: 0.8579 (t0) REVERT: E 214 ARG cc_start: 0.8617 (ptt180) cc_final: 0.8382 (ppt170) REVERT: E 217 ASP cc_start: 0.9645 (t0) cc_final: 0.9337 (m-30) REVERT: E 274 ASP cc_start: 0.8967 (t0) cc_final: 0.8580 (m-30) REVERT: E 278 MET cc_start: 0.9364 (tmm) cc_final: 0.9091 (tmm) REVERT: E 284 LEU cc_start: 0.9168 (mm) cc_final: 0.8734 (mm) REVERT: E 305 ILE cc_start: 0.9538 (pt) cc_final: 0.9185 (pt) REVERT: E 380 ILE cc_start: 0.9668 (pt) cc_final: 0.9369 (pt) REVERT: E 384 GLU cc_start: 0.9166 (tp30) cc_final: 0.8208 (tp30) REVERT: E 518 LYS cc_start: 0.9528 (tppt) cc_final: 0.9016 (tppt) REVERT: E 576 TYR cc_start: 0.7086 (m-80) cc_final: 0.6545 (m-80) REVERT: F 172 PHE cc_start: 0.9087 (t80) cc_final: 0.8825 (t80) REVERT: F 173 PRO cc_start: 0.9388 (Cg_endo) cc_final: 0.8893 (Cg_endo) REVERT: F 206 MET cc_start: 0.6530 (mmm) cc_final: 0.6269 (mmm) REVERT: F 342 PHE cc_start: 0.8971 (t80) cc_final: 0.8392 (t80) REVERT: F 427 MET cc_start: 0.8327 (mtt) cc_final: 0.7406 (mmm) REVERT: F 441 MET cc_start: 0.8260 (mmp) cc_final: 0.8006 (pmm) REVERT: F 455 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8381 (tp30) REVERT: G 21 ARG cc_start: 0.9215 (mtm110) cc_final: 0.8944 (mtm110) REVERT: G 44 GLU cc_start: 0.8961 (tp30) cc_final: 0.8562 (tp30) REVERT: G 67 TYR cc_start: 0.8524 (m-80) cc_final: 0.7511 (m-80) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.3366 time to fit residues: 260.6259 Evaluate side-chains 407 residues out of total 2069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 182 optimal weight: 0.7980 chunk 29 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN E 95 ASN E 108 ASN E 326 GLN E 327 ASN ** E 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 HIS ** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.106091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070534 restraints weight = 66826.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075069 restraints weight = 58368.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.075366 restraints weight = 30615.307| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19673 Z= 0.210 Angle : 0.660 20.251 26727 Z= 0.333 Chirality : 0.047 0.343 3074 Planarity : 0.005 0.090 3429 Dihedral : 7.815 172.683 2780 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.08 % Twisted Proline : 0.85 % 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: -0.56 (0.17), residues: 2506 helix: -0.42 (0.16), residues: 970 sheet: 0.99 (0.36), residues: 205 loop : -0.45 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 304 HIS 0.009 0.001 HIS A 96 PHE 0.022 0.002 PHE A 242 TYR 0.024 0.001 TYR F 242 ARG 0.013 0.001 ARG F 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4921.44 seconds wall clock time: 90 minutes 56.60 seconds (5456.60 seconds total)