Starting phenix.real_space_refine on Wed Mar 13 07:43:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn7_33313/03_2024/7xn7_33313.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn7_33313/03_2024/7xn7_33313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn7_33313/03_2024/7xn7_33313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn7_33313/03_2024/7xn7_33313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn7_33313/03_2024/7xn7_33313.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xn7_33313/03_2024/7xn7_33313.pdb" } resolution = 3.1 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 114 5.49 5 Mg 1 5.21 5 S 284 5.16 5 C 41369 2.51 5 N 11490 2.21 5 O 12808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 1228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 1329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 1336": "OE1" <-> "OE2" Residue "q TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 66076 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1404, 11064 Classifications: {'peptide': 1404} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1337} Chain breaks: 5 Chain: "B" Number of atoms: 9284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9284 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 52, 'TRANS': 1111} Chain breaks: 4 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 12, 'TRANS': 250} Chain: "D" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1349 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 1 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1741 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1325 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 554 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "N" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 854 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Chain: "P" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 404 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 4, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 14} Chain: "T" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1090 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "V" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "W" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4232 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Chain breaks: 2 Chain: "m" Number of atoms: 9730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9730 Classifications: {'peptide': 1187} Link IDs: {'PTRANS': 45, 'TRANS': 1141} Chain breaks: 3 Chain: "n" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "q" Number of atoms: 7552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7552 Classifications: {'peptide': 930} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 910} Chain: "r" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2139 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 259} Chain breaks: 2 Chain: "u" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1707 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "v" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2878 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 22, 'TRANS': 326} Chain breaks: 3 Chain: "x" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 79.248 90.958 84.617 1.00137.78 S ATOM 549 SG CYS A 70 82.856 89.875 85.175 1.00125.97 S ATOM 594 SG CYS A 77 81.820 93.477 85.902 1.00115.20 S ATOM 829 SG CYS A 107 81.346 115.803 43.073 1.00200.98 S ATOM 851 SG CYS A 110 83.301 112.764 41.877 1.00205.43 S ATOM 1157 SG CYS A 148 83.562 116.038 40.040 1.00234.14 S ATOM 1229 SG CYS A 168 80.157 114.161 40.043 1.00240.65 S ATOM 19880 SG CYS B1163 92.577 91.076 71.603 1.00119.09 S ATOM 19898 SG CYS B1166 90.609 94.263 71.279 1.00123.05 S ATOM 20021 SG CYS B1182 88.782 90.990 71.984 1.00127.92 S ATOM 20044 SG CYS B1185 90.373 91.723 68.557 1.00124.95 S ATOM 20989 SG CYS C 85 95.159 102.787 151.749 1.00179.13 S ATOM 21002 SG CYS C 87 91.761 101.582 150.559 1.00200.73 S ATOM 21037 SG CYS C 91 91.986 103.451 153.676 1.00171.81 S ATOM 21060 SG CYS C 94 92.676 105.437 150.563 1.00156.37 S ATOM 29206 SG CYS I 78 85.487 196.450 95.584 1.00322.27 S ATOM 29422 SG CYS I 103 86.229 192.080 94.983 1.00249.38 S ATOM 28659 SG CYS I 10 62.158 175.877 56.185 1.00131.65 S ATOM 28822 SG CYS I 29 66.090 176.372 53.934 1.00118.35 S ATOM 28847 SG CYS I 32 64.242 178.033 53.375 1.00119.48 S ATOM 29563 SG CYS J 7 95.592 136.173 140.604 1.00101.86 S ATOM 29586 SG CYS J 10 98.351 135.333 143.180 1.00 95.79 S ATOM 29862 SG CYS J 44 98.680 138.353 140.771 1.00102.01 S ATOM 29868 SG CYS J 45 96.410 138.275 143.774 1.00110.14 S ATOM 31039 SG CYS L 33 55.190 121.680 129.816 1.00118.34 S ATOM 31054 SG CYS L 36 53.356 122.172 133.133 1.00128.69 S ATOM 31164 SG CYS L 50 52.316 119.367 130.757 1.00123.95 S ATOM 31188 SG CYS L 53 51.808 123.005 129.739 1.00132.14 S ATOM 31445 SG CYS M 25 54.025 138.000 45.622 1.00174.96 S ATOM 31470 SG CYS M 28 54.203 134.267 45.772 1.00184.61 S ATOM 31628 SG CYS M 49 57.090 136.188 44.207 1.00170.04 S ATOM 31652 SG CYS M 52 53.594 135.853 42.482 1.00194.20 S ATOM 34248 SG CYS V 12 25.898 105.615 59.653 1.00181.95 S ATOM 34270 SG CYS V 15 26.931 108.711 57.880 1.00169.99 S ATOM 34372 SG CYS V 29 23.408 108.570 58.784 1.00202.62 S ATOM 34393 SG CYS V 32 24.672 106.327 56.030 1.00221.15 S Time building chain proxies: 27.25, per 1000 atoms: 0.41 Number of scatterers: 66076 At special positions: 0 Unit cell: (216.664, 219.632, 204.792, 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 10 29.99 S 284 16.00 P 114 15.00 Mg 1 11.99 O 12808 8.00 N 11490 7.00 C 41369 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: 22.92 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " Number of angles added : 45 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15070 Finding SS restraints... Secondary structure from input PDB file: 324 helices and 70 sheets defined 48.2% alpha, 14.2% beta 50 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 17.08 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.723A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.527A pdb=" N THR A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 286 through 306 removed outlier: 3.701A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.710A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.525A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.890A pdb=" N SER A 477 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.678A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.504A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.769A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.581A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.725A pdb=" N ILE A 671 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.617A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.728A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 924 through 947 Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.683A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1099 through 1109 Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.569A pdb=" N LEU A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1223 Processing helix chain 'A' and resid 1259 through 1274 Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.625A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.636A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.986A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 removed outlier: 3.514A pdb=" N SER A1404 " --> pdb=" O LEU A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.811A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1451 through 1455 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.663A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 314 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.648A pdb=" N ARG B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 430 removed outlier: 4.199A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.618A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.207A pdb=" N ARG B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.346A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.575A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.621A pdb=" N ILE B 698 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.620A pdb=" N GLN B 708 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.745A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.553A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.535A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.508A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 921 through 926 removed outlier: 4.147A pdb=" N GLU B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 926 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 removed outlier: 3.655A pdb=" N MET B 999 " --> pdb=" O HIS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.632A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.961A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.532A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.610A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.979A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.996A pdb=" N THR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 117 through 131 removed outlier: 3.606A pdb=" N SER D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 removed outlier: 3.671A pdb=" N VAL D 136 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.716A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 161 through 166 removed outlier: 4.194A pdb=" N ALA D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 166' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.589A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.585A pdb=" N VAL E 140 " --> pdb=" O SER E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.641A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.708A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.528A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.573A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.892A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.817A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'M' and resid 65 through 78 Processing helix chain 'V' and resid 20 through 28 Processing helix chain 'V' and resid 31 through 35 removed outlier: 4.047A pdb=" N SER V 34 " --> pdb=" O ASN V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 Processing helix chain 'W' and resid 304 through 310 removed outlier: 4.207A pdb=" N ASP W 308 " --> pdb=" O VAL W 304 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 452 Processing helix chain 'W' and resid 453 through 455 No H-bonds generated for 'chain 'W' and resid 453 through 455' Processing helix chain 'W' and resid 461 through 475 Processing helix chain 'W' and resid 515 through 520 Processing helix chain 'W' and resid 692 through 695 Processing helix chain 'W' and resid 760 through 764 removed outlier: 4.298A pdb=" N TYR W 763 " --> pdb=" O GLN W 760 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS W 764 " --> pdb=" O GLY W 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 760 through 764' Processing helix chain 'W' and resid 792 through 794 No H-bonds generated for 'chain 'W' and resid 792 through 794' Processing helix chain 'm' and resid 230 through 242 Processing helix chain 'm' and resid 244 through 259 removed outlier: 4.415A pdb=" N TRP m 249 " --> pdb=" O THR m 245 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR m 250 " --> pdb=" O ASP m 246 " (cutoff:3.500A) Processing helix chain 'm' and resid 279 through 284 Processing helix chain 'm' and resid 285 through 293 Processing helix chain 'm' and resid 295 through 304 Processing helix chain 'm' and resid 307 through 314 Processing helix chain 'm' and resid 323 through 342 Processing helix chain 'm' and resid 342 through 353 Processing helix chain 'm' and resid 358 through 377 Processing helix chain 'm' and resid 380 through 388 Processing helix chain 'm' and resid 388 through 393 removed outlier: 3.934A pdb=" N ALA m 392 " --> pdb=" O ARG m 388 " (cutoff:3.500A) Processing helix chain 'm' and resid 410 through 442 removed outlier: 3.944A pdb=" N ASP m 429 " --> pdb=" O HIS m 425 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS m 430 " --> pdb=" O SER m 426 " (cutoff:3.500A) Processing helix chain 'm' and resid 447 through 456 removed outlier: 3.603A pdb=" N SER m 456 " --> pdb=" O GLU m 452 " (cutoff:3.500A) Processing helix chain 'm' and resid 459 through 474 Processing helix chain 'm' and resid 474 through 484 Processing helix chain 'm' and resid 518 through 527 Processing helix chain 'm' and resid 529 through 537 removed outlier: 4.044A pdb=" N ALA m 537 " --> pdb=" O VAL m 533 " (cutoff:3.500A) Processing helix chain 'm' and resid 538 through 549 Processing helix chain 'm' and resid 561 through 573 Processing helix chain 'm' and resid 581 through 599 Processing helix chain 'm' and resid 600 through 615 removed outlier: 3.502A pdb=" N ARG m 604 " --> pdb=" O GLU m 600 " (cutoff:3.500A) Processing helix chain 'm' and resid 622 through 629 removed outlier: 3.520A pdb=" N ILE m 629 " --> pdb=" O GLY m 625 " (cutoff:3.500A) Processing helix chain 'm' and resid 633 through 639 removed outlier: 3.719A pdb=" N ASP m 637 " --> pdb=" O PRO m 634 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS m 639 " --> pdb=" O PHE m 636 " (cutoff:3.500A) Processing helix chain 'm' and resid 648 through 651 Processing helix chain 'm' and resid 652 through 665 removed outlier: 3.909A pdb=" N TYR m 656 " --> pdb=" O THR m 652 " (cutoff:3.500A) Processing helix chain 'm' and resid 676 through 689 Processing helix chain 'm' and resid 694 through 748 Proline residue: m 717 - end of helix Processing helix chain 'm' and resid 802 through 815 removed outlier: 3.567A pdb=" N SER m 806 " --> pdb=" O SER m 802 " (cutoff:3.500A) Processing helix chain 'm' and resid 830 through 847 removed outlier: 4.059A pdb=" N LYS m 834 " --> pdb=" O ILE m 830 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU m 835 " --> pdb=" O HIS m 831 " (cutoff:3.500A) Processing helix chain 'm' and resid 878 through 887 removed outlier: 3.749A pdb=" N HIS m 886 " --> pdb=" O ARG m 882 " (cutoff:3.500A) Processing helix chain 'm' and resid 887 through 894 removed outlier: 3.690A pdb=" N SER m 891 " --> pdb=" O SER m 887 " (cutoff:3.500A) Processing helix chain 'm' and resid 898 through 913 Processing helix chain 'm' and resid 913 through 921 Processing helix chain 'm' and resid 922 through 928 removed outlier: 4.124A pdb=" N MET m 925 " --> pdb=" O ASP m 922 " (cutoff:3.500A) Processing helix chain 'm' and resid 938 through 958 Processing helix chain 'm' and resid 961 through 967 Processing helix chain 'm' and resid 967 through 972 Processing helix chain 'm' and resid 973 through 977 Processing helix chain 'm' and resid 981 through 996 Processing helix chain 'm' and resid 1003 through 1008 Processing helix chain 'm' and resid 1012 through 1020 Processing helix chain 'm' and resid 1030 through 1034 removed outlier: 3.951A pdb=" N ARG m1033 " --> pdb=" O ASP m1030 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN m1034 " --> pdb=" O VAL m1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1030 through 1034' Processing helix chain 'm' and resid 1040 through 1045 Processing helix chain 'm' and resid 1048 through 1050 No H-bonds generated for 'chain 'm' and resid 1048 through 1050' Processing helix chain 'm' and resid 1051 through 1064 Processing helix chain 'm' and resid 1072 through 1085 Processing helix chain 'm' and resid 1097 through 1103 Processing helix chain 'm' and resid 1104 through 1117 removed outlier: 3.557A pdb=" N TYR m1108 " --> pdb=" O ILE m1104 " (cutoff:3.500A) Processing helix chain 'm' and resid 1120 through 1133 Processing helix chain 'm' and resid 1146 through 1156 Processing helix chain 'm' and resid 1194 through 1198 removed outlier: 4.376A pdb=" N LEU m1198 " --> pdb=" O ARG m1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1194 through 1198' Processing helix chain 'm' and resid 1205 through 1210 Processing helix chain 'm' and resid 1235 through 1240 Processing helix chain 'm' and resid 1256 through 1273 Processing helix chain 'm' and resid 1290 through 1300 removed outlier: 3.706A pdb=" N ALA m1300 " --> pdb=" O ASP m1296 " (cutoff:3.500A) Processing helix chain 'm' and resid 1358 through 1380 removed outlier: 3.929A pdb=" N ASN m1368 " --> pdb=" O VAL m1364 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN m1369 " --> pdb=" O GLU m1365 " (cutoff:3.500A) Processing helix chain 'm' and resid 1387 through 1402 Processing helix chain 'm' and resid 1453 through 1469 Processing helix chain 'n' and resid 153 through 180 Processing helix chain 'n' and resid 185 through 200 Proline residue: n 192 - end of helix removed outlier: 3.549A pdb=" N ARG n 200 " --> pdb=" O ASP n 196 " (cutoff:3.500A) Processing helix chain 'n' and resid 203 through 211 Processing helix chain 'n' and resid 212 through 221 Processing helix chain 'n' and resid 230 through 244 Processing helix chain 'n' and resid 247 through 255 Processing helix chain 'n' and resid 255 through 266 removed outlier: 4.553A pdb=" N VAL n 259 " --> pdb=" O GLY n 255 " (cutoff:3.500A) Processing helix chain 'n' and resid 270 through 289 Proline residue: n 287 - end of helix Processing helix chain 'q' and resid 5 through 13 removed outlier: 3.879A pdb=" N TYR q 9 " --> pdb=" O ASP q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 20 removed outlier: 3.751A pdb=" N GLU q 20 " --> pdb=" O ASP q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 23 No H-bonds generated for 'chain 'q' and resid 21 through 23' Processing helix chain 'q' and resid 46 through 58 Processing helix chain 'q' and resid 60 through 74 removed outlier: 3.663A pdb=" N TRP q 64 " --> pdb=" O ARG q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 89 Processing helix chain 'q' and resid 90 through 96 Processing helix chain 'q' and resid 97 through 120 removed outlier: 3.873A pdb=" N THR q 101 " --> pdb=" O SER q 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR q 119 " --> pdb=" O GLU q 115 " (cutoff:3.500A) Processing helix chain 'q' and resid 122 through 141 Processing helix chain 'q' and resid 144 through 158 removed outlier: 3.690A pdb=" N GLY q 148 " --> pdb=" O LEU q 144 " (cutoff:3.500A) Processing helix chain 'q' and resid 160 through 175 Processing helix chain 'q' and resid 178 through 192 Processing helix chain 'q' and resid 194 through 209 removed outlier: 3.535A pdb=" N LEU q 201 " --> pdb=" O GLN q 197 " (cutoff:3.500A) Processing helix chain 'q' and resid 215 through 227 removed outlier: 4.129A pdb=" N GLY q 219 " --> pdb=" O ASP q 215 " (cutoff:3.500A) Processing helix chain 'q' and resid 229 through 244 Processing helix chain 'q' and resid 248 through 267 removed outlier: 3.877A pdb=" N LYS q 252 " --> pdb=" O ASN q 248 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER q 267 " --> pdb=" O CYS q 263 " (cutoff:3.500A) Processing helix chain 'q' and resid 269 through 289 Processing helix chain 'q' and resid 294 through 308 removed outlier: 3.601A pdb=" N SER q 303 " --> pdb=" O MET q 299 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR q 304 " --> pdb=" O VAL q 300 " (cutoff:3.500A) Processing helix chain 'q' and resid 310 through 325 Processing helix chain 'q' and resid 328 through 347 removed outlier: 3.552A pdb=" N VAL q 332 " --> pdb=" O ASN q 328 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS q 345 " --> pdb=" O ARG q 341 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS q 346 " --> pdb=" O VAL q 342 " (cutoff:3.500A) Processing helix chain 'q' and resid 348 through 363 Processing helix chain 'q' and resid 366 through 380 removed outlier: 3.544A pdb=" N LYS q 370 " --> pdb=" O ASN q 366 " (cutoff:3.500A) Processing helix chain 'q' and resid 382 through 397 Processing helix chain 'q' and resid 402 through 417 Processing helix chain 'q' and resid 419 through 438 Processing helix chain 'q' and resid 442 through 454 removed outlier: 3.801A pdb=" N TYR q 446 " --> pdb=" O LEU q 442 " (cutoff:3.500A) Processing helix chain 'q' and resid 457 through 473 Processing helix chain 'q' and resid 474 through 476 No H-bonds generated for 'chain 'q' and resid 474 through 476' Processing helix chain 'q' and resid 477 through 491 Processing helix chain 'q' and resid 493 through 508 Processing helix chain 'q' and resid 509 through 511 No H-bonds generated for 'chain 'q' and resid 509 through 511' Processing helix chain 'q' and resid 512 through 535 removed outlier: 4.231A pdb=" N GLU q 517 " --> pdb=" O PRO q 513 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA q 518 " --> pdb=" O GLN q 514 " (cutoff:3.500A) Processing helix chain 'q' and resid 535 through 550 removed outlier: 3.532A pdb=" N ALA q 539 " --> pdb=" O ASN q 535 " (cutoff:3.500A) Processing helix chain 'q' and resid 553 through 569 removed outlier: 4.100A pdb=" N LYS q 557 " --> pdb=" O TYR q 553 " (cutoff:3.500A) Processing helix chain 'q' and resid 572 through 583 Processing helix chain 'q' and resid 586 through 605 removed outlier: 6.251A pdb=" N ARG q 602 " --> pdb=" O LYS q 598 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS q 603 " --> pdb=" O ARG q 599 " (cutoff:3.500A) Processing helix chain 'q' and resid 609 through 622 Processing helix chain 'q' and resid 626 through 644 Processing helix chain 'q' and resid 648 through 673 Processing helix chain 'q' and resid 676 through 690 removed outlier: 3.546A pdb=" N ALA q 680 " --> pdb=" O ASN q 676 " (cutoff:3.500A) Processing helix chain 'q' and resid 692 through 707 Processing helix chain 'q' and resid 709 through 723 Processing helix chain 'q' and resid 725 through 740 Processing helix chain 'q' and resid 745 through 764 removed outlier: 3.789A pdb=" N LEU q 749 " --> pdb=" O ASP q 745 " (cutoff:3.500A) Processing helix chain 'q' and resid 765 through 784 removed outlier: 3.671A pdb=" N TYR q 769 " --> pdb=" O SER q 765 " (cutoff:3.500A) Processing helix chain 'q' and resid 785 through 806 Processing helix chain 'q' and resid 807 through 811 Processing helix chain 'q' and resid 812 through 835 Processing helix chain 'q' and resid 842 through 856 removed outlier: 3.535A pdb=" N THR q 856 " --> pdb=" O MET q 852 " (cutoff:3.500A) Processing helix chain 'q' and resid 856 through 930 removed outlier: 3.780A pdb=" N ARG q 883 " --> pdb=" O LEU q 879 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG q 884 " --> pdb=" O ARG q 880 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS q 885 " --> pdb=" O THR q 881 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU q 917 " --> pdb=" O ILE q 913 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU q 918 " --> pdb=" O LYS q 914 " (cutoff:3.500A) Processing helix chain 'r' and resid 197 through 204 removed outlier: 3.802A pdb=" N ILE r 204 " --> pdb=" O ASP r 200 " (cutoff:3.500A) Processing helix chain 'r' and resid 207 through 215 Processing helix chain 'r' and resid 219 through 225 Processing helix chain 'r' and resid 287 through 289 No H-bonds generated for 'chain 'r' and resid 287 through 289' Processing helix chain 'r' and resid 295 through 310 Processing helix chain 'r' and resid 315 through 332 Processing helix chain 'r' and resid 335 through 350 Processing helix chain 'r' and resid 353 through 374 Processing helix chain 'r' and resid 378 through 391 removed outlier: 3.611A pdb=" N ARG r 382 " --> pdb=" O GLU r 378 " (cutoff:3.500A) Processing helix chain 'r' and resid 398 through 433 removed outlier: 3.829A pdb=" N ARG r 420 " --> pdb=" O ASN r 416 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU r 428 " --> pdb=" O MET r 424 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS r 429 " --> pdb=" O ALA r 425 " (cutoff:3.500A) Processing helix chain 'r' and resid 486 through 490 Processing helix chain 'r' and resid 492 through 497 Processing helix chain 'r' and resid 498 through 505 Processing helix chain 'u' and resid 122 through 129 Processing helix chain 'u' and resid 135 through 149 Processing helix chain 'u' and resid 228 through 242 removed outlier: 3.624A pdb=" N GLN u 242 " --> pdb=" O LEU u 238 " (cutoff:3.500A) Processing helix chain 'u' and resid 258 through 282 Processing helix chain 'v' and resid 32 through 35 Processing helix chain 'v' and resid 36 through 45 Processing helix chain 'v' and resid 47 through 58 Processing helix chain 'v' and resid 64 through 71 removed outlier: 3.574A pdb=" N ASP v 68 " --> pdb=" O GLU v 65 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY v 69 " --> pdb=" O THR v 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP v 71 " --> pdb=" O ASP v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 73 through 77 removed outlier: 3.608A pdb=" N ILE v 77 " --> pdb=" O TYR v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 85 through 94 Processing helix chain 'v' and resid 103 through 109 Processing helix chain 'v' and resid 158 through 172 Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 218 through 221 Processing helix chain 'v' and resid 225 through 233 Processing helix chain 'v' and resid 244 through 249 Processing helix chain 'v' and resid 271 through 284 Processing helix chain 'v' and resid 345 through 347 No H-bonds generated for 'chain 'v' and resid 345 through 347' Processing helix chain 'v' and resid 348 through 353 Processing helix chain 'v' and resid 368 through 380 Processing helix chain 'x' and resid 136 through 145 Processing helix chain 'x' and resid 153 through 157 removed outlier: 4.066A pdb=" N LEU x 156 " --> pdb=" O ASN x 153 " (cutoff:3.500A) Processing helix chain 'x' and resid 164 through 175 Processing helix chain 'x' and resid 224 through 230 Processing helix chain 'x' and resid 275 through 280 removed outlier: 3.547A pdb=" N TYR x 278 " --> pdb=" O LYS x 275 " (cutoff:3.500A) Processing helix chain 'x' and resid 290 through 295 removed outlier: 3.647A pdb=" N GLN x 293 " --> pdb=" O LYS x 290 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS x 295 " --> pdb=" O TRP x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 301 through 309 Processing helix chain 'x' and resid 322 through 327 Processing helix chain 'x' and resid 341 through 361 removed outlier: 4.390A pdb=" N GLN x 345 " --> pdb=" O PHE x 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.780A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.613A pdb=" N LYS A 344 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.692A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.967A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.329A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.953A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.740A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 3.969A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 Processing sheet with id=AB7, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 4.334A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR A1156 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS I 42 " --> pdb=" O TYR A1156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 62 removed outlier: 4.937A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.950A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 removed outlier: 3.966A pdb=" N GLU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 644 through 645 current: chain 'B' and resid 740 through 741 Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.659A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 572 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B 574 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 796 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 853 through 862 current: chain 'B' and resid 947 through 956 removed outlier: 8.660A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 962 through 972 current: chain 'L' and resid 39 through 42 Processing sheet with id=AC8, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AC9, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.004A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.424A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.538A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD4, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD5, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.589A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.731A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 156 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE C 50 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL C 48 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS C 160 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY C 162 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.671A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.475A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 5 through 6 current: chain 'G' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 48 current: chain 'G' and resid 68 through 79 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE2, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.470A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.521A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.118A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.589A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.736A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'M' and resid 16 through 21 removed outlier: 3.901A pdb=" N VAL M 34 " --> pdb=" O THR M 21 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF3, first strand: chain 'V' and resid 81 through 86 removed outlier: 6.968A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 337 through 339 Processing sheet with id=AF5, first strand: chain 'W' and resid 349 through 354 removed outlier: 4.663A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 522 through 526 removed outlier: 7.776A pdb=" N ILE W 506 " --> pdb=" O VAL W 501 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL W 501 " --> pdb=" O ILE W 506 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER W 508 " --> pdb=" O SER W 499 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 572 through 576 removed outlier: 6.042A pdb=" N ILE W 565 " --> pdb=" O ILE W 554 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE W 554 " --> pdb=" O ILE W 565 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 601 through 603 removed outlier: 6.872A pdb=" N ASP W 621 " --> pdb=" O ILE W 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 650 through 651 removed outlier: 3.560A pdb=" N ALA W 650 " --> pdb=" O VAL W 658 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 697 through 701 removed outlier: 6.907A pdb=" N PHE W 683 " --> pdb=" O VAL W 679 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL W 679 " --> pdb=" O PHE W 683 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE W 685 " --> pdb=" O LEU W 677 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 787 through 791 removed outlier: 4.574A pdb=" N LYS W 787 " --> pdb=" O LEU W 782 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 396 through 397 Processing sheet with id=AG4, first strand: chain 'm' and resid 644 through 645 Processing sheet with id=AG5, first strand: chain 'm' and resid 790 through 796 removed outlier: 3.833A pdb=" N SER m 792 " --> pdb=" O PHE m 783 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU m 766 " --> pdb=" O GLY m 824 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'm' and resid 959 through 960 removed outlier: 6.877A pdb=" N VAL m 959 " --> pdb=" O TYR m1024 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'm' and resid 1167 through 1175 removed outlier: 6.712A pdb=" N SER m1181 " --> pdb=" O ARG m1173 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL m1175 " --> pdb=" O TYR m1179 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR m1179 " --> pdb=" O VAL m1175 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS m1230 " --> pdb=" O ALA m1189 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLN m1193 " --> pdb=" O LEU m1232 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER m1233 " --> pdb=" O ILE m1220 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE m1220 " --> pdb=" O SER m1233 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'm' and resid 1306 through 1310 removed outlier: 6.746A pdb=" N LEU m1328 " --> pdb=" O VAL m1324 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 1407 through 1412 Processing sheet with id=AH1, first strand: chain 'q' and resid 25 through 29 Processing sheet with id=AH2, first strand: chain 'r' and resid 228 through 232 removed outlier: 4.020A pdb=" N LEU r 229 " --> pdb=" O VAL r 246 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL r 246 " --> pdb=" O LEU r 229 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL r 248 " --> pdb=" O ALA r 275 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA r 275 " --> pdb=" O VAL r 248 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'r' and resid 259 through 260 Processing sheet with id=AH4, first strand: chain 'u' and resid 87 through 91 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 87 through 91 current: chain 'u' and resid 178 through 182 removed outlier: 4.925A pdb=" N TYR u 178 " --> pdb=" O MET u 189 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 185 through 193 current: chain 'u' and resid 208 through 223 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 208 through 223 current: chain 'v' and resid 263 through 268 removed outlier: 6.449A pdb=" N ILE v 264 " --> pdb=" O ASP v 302 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP v 302 " --> pdb=" O ILE v 264 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU v 266 " --> pdb=" O ILE v 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 295 through 309 current: chain 'v' and resid 327 through 333 Processing sheet with id=AH5, first strand: chain 'u' and resid 116 through 120 removed outlier: 4.465A pdb=" N TRP u 152 " --> pdb=" O ASN u 117 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU u 119 " --> pdb=" O TRP u 152 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR u 154 " --> pdb=" O GLU u 119 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'v' and resid 29 through 30 Processing sheet with id=AH7, first strand: chain 'x' and resid 247 through 252 removed outlier: 5.935A pdb=" N ILE x 210 " --> pdb=" O VAL x 266 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE x 209 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE x 285 " --> pdb=" O ILE x 209 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL x 211 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE x 312 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE x 285 " --> pdb=" O PHE x 312 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE x 314 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY x 311 " --> pdb=" O LYS x 331 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU x 333 " --> pdb=" O GLY x 311 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR x 313 " --> pdb=" O LEU x 333 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE x 335 " --> pdb=" O TYR x 313 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS x 315 " --> pdb=" O ILE x 335 " (cutoff:3.500A) 3049 hydrogen bonds defined for protein. 8643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 126 hydrogen bonds 252 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 29.44 Time building geometry restraints manager: 24.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14840 1.33 - 1.45: 14280 1.45 - 1.57: 37720 1.57 - 1.69: 224 1.69 - 1.81: 462 Bond restraints: 67526 Sorted by residual: bond pdb=" C1' G P 10 " pdb=" N9 G P 10 " ideal model delta sigma weight residual 1.475 1.369 0.106 1.50e-02 4.44e+03 4.95e+01 bond pdb=" C1' G P 6 " pdb=" N9 G P 6 " ideal model delta sigma weight residual 1.475 1.374 0.101 1.50e-02 4.44e+03 4.55e+01 bond pdb=" C1' U P -7 " pdb=" N1 U P -7 " ideal model delta sigma weight residual 1.470 1.563 -0.093 1.50e-02 4.44e+03 3.84e+01 bond pdb=" C1' C P -5 " pdb=" N1 C P -5 " ideal model delta sigma weight residual 1.470 1.552 -0.082 1.50e-02 4.44e+03 2.98e+01 bond pdb=" C1' U P 2 " pdb=" N1 U P 2 " ideal model delta sigma weight residual 1.480 1.562 -0.082 1.50e-02 4.44e+03 2.97e+01 ... (remaining 67521 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.63: 1364 104.63 - 111.98: 33346 111.98 - 119.32: 23134 119.32 - 126.67: 32799 126.67 - 134.01: 1012 Bond angle restraints: 91655 Sorted by residual: angle pdb=" N VAL A1001 " pdb=" CA VAL A1001 " pdb=" C VAL A1001 " ideal model delta sigma weight residual 112.96 107.25 5.71 1.00e+00 1.00e+00 3.26e+01 angle pdb=" O4' U P -3 " pdb=" C4' U P -3 " pdb=" C3' U P -3 " ideal model delta sigma weight residual 104.00 109.12 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" C2' U P -3 " pdb=" C1' U P -3 " pdb=" N1 U P -3 " ideal model delta sigma weight residual 112.00 119.48 -7.48 1.50e+00 4.44e-01 2.49e+01 angle pdb=" O3' DC N -54 " pdb=" C3' DC N -54 " pdb=" C2' DC N -54 " ideal model delta sigma weight residual 111.50 104.42 7.08 1.50e+00 4.44e-01 2.23e+01 angle pdb=" O3' C P -4 " pdb=" C3' C P -4 " pdb=" C2' C P -4 " ideal model delta sigma weight residual 109.50 115.55 -6.05 1.50e+00 4.44e-01 1.63e+01 ... (remaining 91650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.09: 40110 34.09 - 68.18: 1024 68.18 - 102.27: 64 102.27 - 136.36: 2 136.36 - 170.45: 1 Dihedral angle restraints: 41201 sinusoidal: 17963 harmonic: 23238 Sorted by residual: dihedral pdb=" O4' C P -4 " pdb=" C1' C P -4 " pdb=" N1 C P -4 " pdb=" C2 C P -4 " ideal model delta sinusoidal sigma weight residual 232.00 61.55 170.45 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' U P -3 " pdb=" C1' U P -3 " pdb=" N1 U P -3 " pdb=" C2 U P -3 " ideal model delta sinusoidal sigma weight residual 200.00 91.95 108.05 1 1.50e+01 4.44e-03 5.59e+01 dihedral pdb=" C3' G P -2 " pdb=" C4' G P -2 " pdb=" O4' G P -2 " pdb=" C1' G P -2 " ideal model delta sinusoidal sigma weight residual 20.00 -19.08 39.08 1 8.00e+00 1.56e-02 3.36e+01 ... (remaining 41198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 8130 0.049 - 0.097: 1636 0.097 - 0.146: 419 0.146 - 0.195: 15 0.195 - 0.243: 3 Chirality restraints: 10203 Sorted by residual: chirality pdb=" C1' U P -3 " pdb=" O4' U P -3 " pdb=" C2' U P -3 " pdb=" N1 U P -3 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' DG T 47 " pdb=" O4' DG T 47 " pdb=" C2' DG T 47 " pdb=" N9 DG T 47 " both_signs ideal model delta sigma weight residual False 2.42 2.21 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C1' G P 10 " pdb=" O4' G P 10 " pdb=" C2' G P 10 " pdb=" N9 G P 10 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.51e-01 ... (remaining 10200 not shown) Planarity restraints: 11489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C P -4 " -0.177 2.00e-02 2.50e+03 8.30e-02 1.55e+02 pdb=" N1 C P -4 " 0.066 2.00e-02 2.50e+03 pdb=" C2 C P -4 " 0.043 2.00e-02 2.50e+03 pdb=" O2 C P -4 " 0.053 2.00e-02 2.50e+03 pdb=" N3 C P -4 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C P -4 " -0.009 2.00e-02 2.50e+03 pdb=" N4 C P -4 " -0.108 2.00e-02 2.50e+03 pdb=" C5 C P -4 " 0.051 2.00e-02 2.50e+03 pdb=" C6 C P -4 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G P -2 " -0.081 2.00e-02 2.50e+03 3.89e-02 4.53e+01 pdb=" N9 G P -2 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G P -2 " 0.060 2.00e-02 2.50e+03 pdb=" N7 G P -2 " 0.032 2.00e-02 2.50e+03 pdb=" C5 G P -2 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G P -2 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G P -2 " -0.056 2.00e-02 2.50e+03 pdb=" N1 G P -2 " -0.011 2.00e-02 2.50e+03 pdb=" C2 G P -2 " 0.023 2.00e-02 2.50e+03 pdb=" N2 G P -2 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G P -2 " 0.040 2.00e-02 2.50e+03 pdb=" C4 G P -2 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U P -3 " -0.079 2.00e-02 2.50e+03 3.77e-02 3.21e+01 pdb=" N1 U P -3 " 0.023 2.00e-02 2.50e+03 pdb=" C2 U P -3 " 0.021 2.00e-02 2.50e+03 pdb=" O2 U P -3 " 0.022 2.00e-02 2.50e+03 pdb=" N3 U P -3 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U P -3 " -0.008 2.00e-02 2.50e+03 pdb=" O4 U P -3 " -0.050 2.00e-02 2.50e+03 pdb=" C5 U P -3 " 0.026 2.00e-02 2.50e+03 pdb=" C6 U P -3 " 0.042 2.00e-02 2.50e+03 ... (remaining 11486 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 545 2.60 - 3.17: 54839 3.17 - 3.75: 103445 3.75 - 4.32: 143217 4.32 - 4.90: 235919 Nonbonded interactions: 537965 Sorted by model distance: nonbonded pdb=" OD1 ASP A 484 " pdb="MG MG A1803 " model vdw 2.019 2.170 nonbonded pdb=" OP1 U P 11 " pdb="MG MG A1803 " model vdw 2.168 2.170 nonbonded pdb=" OG1 THR K 57 " pdb=" OE1 GLN K 76 " model vdw 2.169 2.440 nonbonded pdb=" O ILE u 145 " pdb=" OG1 THR u 149 " model vdw 2.173 2.440 nonbonded pdb=" OD2 ASP E 47 " pdb=" NE2 GLN E 53 " model vdw 2.189 2.520 ... (remaining 537960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 7.180 Check model and map are aligned: 0.770 Set scattering table: 0.500 Process input model: 166.070 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.190 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:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 : 0.004 0.106 67526 Z= 0.279 Angle : 0.497 9.666 91655 Z= 0.275 Chirality : 0.042 0.243 10203 Planarity : 0.003 0.083 11489 Dihedral : 14.593 170.455 26131 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.22 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.10), residues: 7841 helix: 2.11 (0.09), residues: 3398 sheet: 0.29 (0.15), residues: 1153 loop : 0.16 (0.11), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 170 HIS 0.009 0.001 HIS A 817 PHE 0.017 0.001 PHE B 363 TYR 0.019 0.001 TYR m 530 ARG 0.004 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 6.063 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: A 64 ASN cc_start: 0.9130 (p0) cc_final: 0.8791 (p0) REVERT: A 65 PHE cc_start: 0.8444 (m-10) cc_final: 0.8139 (m-80) REVERT: A 74 MET cc_start: 0.8845 (ttt) cc_final: 0.8440 (ttp) REVERT: A 108 MET cc_start: 0.9240 (mmm) cc_final: 0.8717 (mmm) REVERT: A 281 GLU cc_start: 0.8971 (tp30) cc_final: 0.8748 (tm-30) REVERT: A 294 GLU cc_start: 0.8569 (pt0) cc_final: 0.8351 (pt0) REVERT: A 308 ASP cc_start: 0.8944 (m-30) cc_final: 0.8346 (p0) REVERT: A 488 MET cc_start: 0.9394 (mtp) cc_final: 0.9115 (mtm) REVERT: A 535 MET cc_start: 0.9552 (ttt) cc_final: 0.9260 (ttp) REVERT: A 548 MET cc_start: 0.9659 (mtm) cc_final: 0.9443 (mtm) REVERT: A 1262 MET cc_start: 0.8461 (tpt) cc_final: 0.8169 (tpp) REVERT: B 237 LYS cc_start: 0.9087 (tppp) cc_final: 0.8800 (pptt) REVERT: B 302 MET cc_start: 0.8513 (ptm) cc_final: 0.7313 (ptp) REVERT: B 305 MET cc_start: 0.9090 (mtp) cc_final: 0.8641 (mtp) REVERT: B 839 MET cc_start: 0.9448 (ptp) cc_final: 0.9229 (ptp) REVERT: B 841 MET cc_start: 0.9653 (ttm) cc_final: 0.9296 (ttm) REVERT: B 968 MET cc_start: 0.8647 (tmm) cc_final: 0.8263 (tmm) REVERT: B 1082 MET cc_start: 0.9243 (tpp) cc_final: 0.8964 (tpt) REVERT: B 1152 MET cc_start: 0.9252 (mmm) cc_final: 0.9018 (mmm) REVERT: E 92 MET cc_start: 0.9623 (tpp) cc_final: 0.9196 (tpp) REVERT: E 136 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8688 (mt-10) REVERT: F 112 GLU cc_start: 0.8773 (mp0) cc_final: 0.8474 (mp0) REVERT: G 55 ASP cc_start: 0.8548 (t0) cc_final: 0.8296 (t0) REVERT: G 102 ASP cc_start: 0.8453 (m-30) cc_final: 0.8161 (m-30) REVERT: H 104 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8289 (tm-30) REVERT: H 105 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8564 (tp30) REVERT: J 26 GLU cc_start: 0.9006 (tp30) cc_final: 0.8530 (tm-30) REVERT: L 48 VAL cc_start: 0.9391 (t) cc_final: 0.9167 (t) REVERT: M 38 LEU cc_start: 0.9065 (pt) cc_final: 0.8630 (pt) REVERT: V 113 ILE cc_start: 0.7692 (tt) cc_final: 0.7448 (mt) REVERT: m 511 MET cc_start: 0.2075 (tmm) cc_final: 0.0496 (tpt) REVERT: m 563 MET cc_start: 0.6003 (tpp) cc_final: 0.5652 (mpp) REVERT: m 570 MET cc_start: -0.0896 (ttm) cc_final: -0.1372 (mmp) REVERT: n 180 GLN cc_start: 0.8978 (mt0) cc_final: 0.8240 (pt0) REVERT: q 1 MET cc_start: 0.5644 (mtt) cc_final: 0.5157 (tpt) REVERT: q 735 ILE cc_start: 0.9052 (mt) cc_final: 0.8838 (tp) REVERT: r 270 MET cc_start: 0.7576 (tpp) cc_final: 0.7284 (tpt) REVERT: r 329 MET cc_start: 0.1996 (tmm) cc_final: 0.1684 (tmm) REVERT: r 336 ASN cc_start: 0.9031 (m-40) cc_final: 0.8663 (t0) outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.6913 time to fit residues: 570.4726 Evaluate side-chains 326 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 5.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 669 optimal weight: 5.9990 chunk 601 optimal weight: 0.7980 chunk 333 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 405 optimal weight: 20.0000 chunk 321 optimal weight: 5.9990 chunk 621 optimal weight: 50.0000 chunk 240 optimal weight: 0.9990 chunk 377 optimal weight: 5.9990 chunk 462 optimal weight: 30.0000 chunk 720 optimal weight: 50.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 GLN C 8 ASN C 25 ASN G 93 ASN ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 784 ASN n 166 GLN q 132 ASN q 319 ASN ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 67526 Z= 0.233 Angle : 0.511 9.027 91655 Z= 0.272 Chirality : 0.041 0.165 10203 Planarity : 0.004 0.047 11489 Dihedral : 12.226 176.947 10017 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.30 % Favored : 97.69 % Rotamer: Outliers : 0.31 % Allowed : 3.92 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.10), residues: 7841 helix: 2.16 (0.09), residues: 3431 sheet: 0.31 (0.15), residues: 1136 loop : 0.26 (0.11), residues: 3274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP q 64 HIS 0.007 0.001 HIS u 97 PHE 0.026 0.001 PHE G 42 TYR 0.025 0.001 TYR q 871 ARG 0.007 0.000 ARG B 423 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 336 time to evaluate : 5.936 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: A 64 ASN cc_start: 0.9145 (p0) cc_final: 0.8806 (p0) REVERT: A 65 PHE cc_start: 0.8428 (m-10) cc_final: 0.8162 (m-80) REVERT: A 74 MET cc_start: 0.8809 (ttt) cc_final: 0.8382 (ttp) REVERT: A 108 MET cc_start: 0.9191 (mmm) cc_final: 0.8684 (mmm) REVERT: A 146 MET cc_start: 0.8988 (tpp) cc_final: 0.8745 (tpp) REVERT: A 176 ARG cc_start: 0.7093 (mmt180) cc_final: 0.6855 (mmt180) REVERT: A 294 GLU cc_start: 0.8648 (pt0) cc_final: 0.8410 (pt0) REVERT: A 308 ASP cc_start: 0.9019 (m-30) cc_final: 0.8365 (p0) REVERT: A 488 MET cc_start: 0.9314 (mtp) cc_final: 0.8877 (mtt) REVERT: A 1270 MET cc_start: 0.8662 (mmp) cc_final: 0.8267 (mmp) REVERT: B 237 LYS cc_start: 0.9036 (tppp) cc_final: 0.8713 (pptt) REVERT: B 302 MET cc_start: 0.8589 (ptm) cc_final: 0.7851 (ptp) REVERT: B 305 MET cc_start: 0.9076 (mtp) cc_final: 0.8674 (mtp) REVERT: B 792 MET cc_start: 0.9148 (mtt) cc_final: 0.8827 (mtt) REVERT: B 839 MET cc_start: 0.9478 (ptp) cc_final: 0.9262 (ptp) REVERT: B 968 MET cc_start: 0.8705 (tmm) cc_final: 0.8391 (tmm) REVERT: B 1082 MET cc_start: 0.9170 (tpp) cc_final: 0.8647 (tpt) REVERT: B 1152 MET cc_start: 0.9230 (mmm) cc_final: 0.8969 (mmm) REVERT: D 167 LYS cc_start: 0.8267 (mmmt) cc_final: 0.8046 (mmmt) REVERT: E 21 MET cc_start: 0.9451 (ttm) cc_final: 0.9174 (ttm) REVERT: E 92 MET cc_start: 0.9629 (tpp) cc_final: 0.9237 (tpp) REVERT: E 136 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8525 (mt-10) REVERT: G 55 ASP cc_start: 0.8555 (t0) cc_final: 0.8292 (t0) REVERT: H 46 MET cc_start: 0.9343 (mmm) cc_final: 0.9055 (mmm) REVERT: H 104 GLU cc_start: 0.8781 (mt-10) cc_final: 0.7989 (tm-30) REVERT: H 105 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8374 (tp30) REVERT: J 26 GLU cc_start: 0.8996 (tp30) cc_final: 0.8553 (tm-30) REVERT: L 48 VAL cc_start: 0.9403 (t) cc_final: 0.9197 (t) REVERT: V 113 ILE cc_start: 0.7726 (tt) cc_final: 0.7472 (mt) REVERT: m 511 MET cc_start: 0.2420 (tmm) cc_final: 0.0884 (tpt) REVERT: m 570 MET cc_start: -0.1405 (ttm) cc_final: -0.2114 (mmp) REVERT: m 659 MET cc_start: 0.8086 (mtt) cc_final: 0.7763 (mtt) REVERT: n 180 GLN cc_start: 0.8817 (mt0) cc_final: 0.8146 (pt0) REVERT: n 270 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6410 (mm-30) REVERT: q 1 MET cc_start: 0.5750 (mtt) cc_final: 0.5164 (tpt) REVERT: r 336 ASN cc_start: 0.9057 (m-40) cc_final: 0.8666 (t0) outliers start: 22 outliers final: 11 residues processed: 342 average time/residue: 0.6404 time to fit residues: 377.4502 Evaluate side-chains 322 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 311 time to evaluate : 5.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 566 GLN Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain m residue 925 MET Chi-restraints excluded: chain n residue 289 MET Chi-restraints excluded: chain q residue 172 LEU Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain v residue 204 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 400 optimal weight: 40.0000 chunk 223 optimal weight: 6.9990 chunk 599 optimal weight: 8.9990 chunk 490 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 721 optimal weight: 40.0000 chunk 779 optimal weight: 20.0000 chunk 642 optimal weight: 50.0000 chunk 715 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 578 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN I 11 ASN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 710 GLN m 816 ASN ** n 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN q 483 ASN ** q 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 67526 Z= 0.432 Angle : 0.564 9.308 91655 Z= 0.296 Chirality : 0.042 0.178 10203 Planarity : 0.004 0.047 11489 Dihedral : 12.270 177.739 10017 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.67 % Favored : 97.32 % Rotamer: Outliers : 0.48 % Allowed : 6.04 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.10), residues: 7841 helix: 2.11 (0.09), residues: 3433 sheet: 0.15 (0.15), residues: 1167 loop : 0.21 (0.11), residues: 3241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 554 HIS 0.009 0.001 HIS m1287 PHE 0.028 0.002 PHE G 3 TYR 0.026 0.001 TYR q 871 ARG 0.008 0.000 ARG A 591 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 315 time to evaluate : 6.055 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: A 64 ASN cc_start: 0.9194 (p0) cc_final: 0.8939 (p0) REVERT: A 74 MET cc_start: 0.8943 (ttt) cc_final: 0.8578 (ttp) REVERT: A 146 MET cc_start: 0.8961 (tpp) cc_final: 0.8744 (mmm) REVERT: A 294 GLU cc_start: 0.8655 (pt0) cc_final: 0.8426 (pt0) REVERT: A 308 ASP cc_start: 0.9090 (m-30) cc_final: 0.8430 (p0) REVERT: A 488 MET cc_start: 0.9383 (mtp) cc_final: 0.9069 (mtm) REVERT: A 1204 MET cc_start: 0.9211 (tmm) cc_final: 0.8888 (tmm) REVERT: B 119 MET cc_start: 0.9235 (mtt) cc_final: 0.9017 (mtt) REVERT: B 237 LYS cc_start: 0.8916 (tppp) cc_final: 0.8607 (pptt) REVERT: B 302 MET cc_start: 0.8572 (ptm) cc_final: 0.7796 (ptp) REVERT: B 305 MET cc_start: 0.9121 (mtp) cc_final: 0.8659 (mtp) REVERT: B 792 MET cc_start: 0.9162 (mtm) cc_final: 0.8885 (mtt) REVERT: B 929 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 968 MET cc_start: 0.8775 (tmm) cc_final: 0.8441 (tmm) REVERT: B 1082 MET cc_start: 0.9179 (tpp) cc_final: 0.8686 (tpt) REVERT: D 167 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7695 (mmmt) REVERT: E 21 MET cc_start: 0.9469 (ttm) cc_final: 0.9168 (ttm) REVERT: E 92 MET cc_start: 0.9627 (tpp) cc_final: 0.9170 (tpp) REVERT: G 158 TYR cc_start: 0.7302 (m-80) cc_final: 0.7063 (m-80) REVERT: H 105 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8369 (tp30) REVERT: I 61 ASP cc_start: 0.8353 (t0) cc_final: 0.8129 (t0) REVERT: J 26 GLU cc_start: 0.9032 (tp30) cc_final: 0.8658 (tm-30) REVERT: V 113 ILE cc_start: 0.7602 (tt) cc_final: 0.7346 (mt) REVERT: W 578 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8359 (p0) REVERT: m 511 MET cc_start: 0.1422 (tmm) cc_final: 0.0081 (tpt) REVERT: m 563 MET cc_start: 0.5355 (OUTLIER) cc_final: 0.3858 (tpt) REVERT: m 570 MET cc_start: -0.1441 (ttm) cc_final: -0.1814 (tpp) REVERT: m 659 MET cc_start: 0.8171 (mtt) cc_final: 0.7765 (mtt) REVERT: n 180 GLN cc_start: 0.8961 (mt0) cc_final: 0.8246 (pt0) REVERT: q 1 MET cc_start: 0.6020 (mtt) cc_final: 0.5166 (tpt) REVERT: q 114 MET cc_start: 0.2654 (mtt) cc_final: 0.2214 (mtt) REVERT: q 547 MET cc_start: 0.1357 (mmm) cc_final: 0.1004 (tpt) REVERT: r 336 ASN cc_start: 0.9067 (m-40) cc_final: 0.8691 (t0) REVERT: u 128 MET cc_start: 0.6107 (mmp) cc_final: 0.5641 (ptp) REVERT: v 167 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7466 (pp20) outliers start: 34 outliers final: 19 residues processed: 331 average time/residue: 0.6611 time to fit residues: 380.4731 Evaluate side-chains 327 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 304 time to evaluate : 5.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain q residue 72 VAL Chi-restraints excluded: chain q residue 172 LEU Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 204 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 712 optimal weight: 20.0000 chunk 542 optimal weight: 50.0000 chunk 374 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 344 optimal weight: 5.9990 chunk 484 optimal weight: 10.0000 chunk 724 optimal weight: 50.0000 chunk 766 optimal weight: 20.0000 chunk 378 optimal weight: 4.9990 chunk 686 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 438 ASN q 578 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 67526 Z= 0.319 Angle : 0.505 9.404 91655 Z= 0.267 Chirality : 0.041 0.160 10203 Planarity : 0.003 0.045 11489 Dihedral : 12.263 179.270 10017 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.53 % Favored : 97.46 % Rotamer: Outliers : 0.68 % Allowed : 7.34 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 7841 helix: 2.15 (0.09), residues: 3430 sheet: 0.16 (0.15), residues: 1141 loop : 0.23 (0.11), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.006 0.001 HIS A 660 PHE 0.020 0.001 PHE K 35 TYR 0.024 0.001 TYR q 871 ARG 0.007 0.000 ARG m 728 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 310 time to evaluate : 5.994 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: A 65 PHE cc_start: 0.8368 (m-80) cc_final: 0.7905 (m-80) REVERT: A 74 MET cc_start: 0.8912 (ttt) cc_final: 0.8513 (ttp) REVERT: A 282 MET cc_start: 0.8474 (ppp) cc_final: 0.8263 (ppp) REVERT: A 294 GLU cc_start: 0.8658 (pt0) cc_final: 0.8409 (pt0) REVERT: A 488 MET cc_start: 0.9376 (mtp) cc_final: 0.9081 (mtm) REVERT: B 237 LYS cc_start: 0.8935 (tppp) cc_final: 0.8608 (pptt) REVERT: B 302 MET cc_start: 0.8636 (ptm) cc_final: 0.8337 (ptp) REVERT: B 305 MET cc_start: 0.9116 (mtp) cc_final: 0.8818 (mmm) REVERT: B 363 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: B 792 MET cc_start: 0.9174 (mtm) cc_final: 0.8867 (mtt) REVERT: B 929 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 968 MET cc_start: 0.8750 (tmm) cc_final: 0.8430 (tmm) REVERT: B 1082 MET cc_start: 0.9174 (tpp) cc_final: 0.8685 (tpt) REVERT: D 167 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7695 (mmmt) REVERT: E 21 MET cc_start: 0.9481 (ttm) cc_final: 0.9160 (ttm) REVERT: E 92 MET cc_start: 0.9640 (tpp) cc_final: 0.9202 (tpp) REVERT: G 80 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8696 (pttt) REVERT: G 158 TYR cc_start: 0.7179 (m-80) cc_final: 0.6966 (m-80) REVERT: H 104 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8034 (tm-30) REVERT: H 105 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8242 (tp30) REVERT: I 61 ASP cc_start: 0.8479 (t0) cc_final: 0.8075 (t0) REVERT: J 26 GLU cc_start: 0.9050 (tp30) cc_final: 0.8666 (tm-30) REVERT: V 113 ILE cc_start: 0.7437 (tt) cc_final: 0.7174 (mt) REVERT: m 511 MET cc_start: 0.1324 (tmm) cc_final: 0.0056 (tpt) REVERT: m 563 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.4221 (tpt) REVERT: m 570 MET cc_start: -0.1433 (ttm) cc_final: -0.1890 (mmp) REVERT: m 659 MET cc_start: 0.8106 (mtt) cc_final: 0.7722 (mtt) REVERT: m 1384 MET cc_start: 0.3510 (ppp) cc_final: 0.2983 (ptt) REVERT: n 180 GLN cc_start: 0.8939 (mt0) cc_final: 0.8230 (pt0) REVERT: q 1 MET cc_start: 0.6254 (mtt) cc_final: 0.5258 (tpt) REVERT: q 466 MET cc_start: 0.5891 (mmm) cc_final: 0.5539 (mpp) REVERT: q 547 MET cc_start: 0.1463 (mmm) cc_final: 0.1145 (tpt) REVERT: r 336 ASN cc_start: 0.9258 (m-40) cc_final: 0.8840 (t0) REVERT: u 128 MET cc_start: 0.6357 (mmp) cc_final: 0.5962 (ptp) outliers start: 48 outliers final: 21 residues processed: 335 average time/residue: 0.6369 time to fit residues: 370.4174 Evaluate side-chains 322 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 298 time to evaluate : 6.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain m residue 565 MET Chi-restraints excluded: chain m residue 925 MET Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain q residue 172 LEU Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain v residue 204 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 638 optimal weight: 10.0000 chunk 435 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 570 optimal weight: 40.0000 chunk 316 optimal weight: 5.9990 chunk 654 optimal weight: 50.0000 chunk 529 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 391 optimal weight: 40.0000 chunk 688 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS C 126 ASN G 93 ASN H 44 ASN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 970 HIS m 998 ASN m1449 ASN ** n 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 232 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 67526 Z= 0.488 Angle : 0.594 12.670 91655 Z= 0.308 Chirality : 0.043 0.167 10203 Planarity : 0.004 0.049 11489 Dihedral : 12.304 179.803 10017 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 0.80 % Allowed : 8.36 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 7841 helix: 2.07 (0.09), residues: 3412 sheet: 0.02 (0.15), residues: 1151 loop : 0.14 (0.11), residues: 3278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.009 0.001 HIS A 660 PHE 0.024 0.002 PHE M 23 TYR 0.026 0.002 TYR B 479 ARG 0.014 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 308 time to evaluate : 6.060 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: A 74 MET cc_start: 0.8983 (ttt) cc_final: 0.8579 (ttp) REVERT: A 146 MET cc_start: 0.9030 (tpp) cc_final: 0.8767 (tpp) REVERT: A 294 GLU cc_start: 0.8712 (pt0) cc_final: 0.8448 (pt0) REVERT: A 308 ASP cc_start: 0.8983 (m-30) cc_final: 0.8412 (p0) REVERT: A 488 MET cc_start: 0.9415 (mtp) cc_final: 0.9155 (mtm) REVERT: A 912 ASP cc_start: 0.9329 (OUTLIER) cc_final: 0.8846 (p0) REVERT: B 119 MET cc_start: 0.9177 (mtt) cc_final: 0.8976 (mtt) REVERT: B 237 LYS cc_start: 0.9010 (tppp) cc_final: 0.8673 (pptt) REVERT: B 363 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: B 929 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8373 (p) REVERT: B 968 MET cc_start: 0.8752 (tmm) cc_final: 0.8409 (tmm) REVERT: B 1082 MET cc_start: 0.9098 (tpp) cc_final: 0.8440 (tpt) REVERT: C 36 MET cc_start: 0.9441 (mtp) cc_final: 0.9106 (mtm) REVERT: C 137 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6957 (p0) REVERT: C 138 TYR cc_start: 0.7609 (m-80) cc_final: 0.7197 (m-10) REVERT: D 167 LYS cc_start: 0.8005 (mmmt) cc_final: 0.7688 (mmmt) REVERT: E 21 MET cc_start: 0.9442 (ttm) cc_final: 0.9216 (ttm) REVERT: E 92 MET cc_start: 0.9622 (tpp) cc_final: 0.9065 (tpp) REVERT: E 136 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: H 105 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8359 (tp30) REVERT: I 61 ASP cc_start: 0.8539 (t0) cc_final: 0.8093 (t0) REVERT: J 26 GLU cc_start: 0.9066 (tp30) cc_final: 0.8704 (tm-30) REVERT: V 113 ILE cc_start: 0.7540 (tt) cc_final: 0.7275 (mt) REVERT: W 578 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8105 (p0) REVERT: m 511 MET cc_start: 0.1231 (tmm) cc_final: -0.0011 (tpt) REVERT: m 563 MET cc_start: 0.5720 (OUTLIER) cc_final: 0.4152 (tpt) REVERT: m 570 MET cc_start: -0.1306 (ttm) cc_final: -0.1776 (mmp) REVERT: m 659 MET cc_start: 0.8208 (mtt) cc_final: 0.7726 (mtt) REVERT: m 1286 PHE cc_start: 0.0519 (t80) cc_final: 0.0004 (t80) REVERT: n 180 GLN cc_start: 0.8942 (mt0) cc_final: 0.8252 (pt0) REVERT: q 1 MET cc_start: 0.6176 (mtt) cc_final: 0.4896 (tpt) REVERT: q 114 MET cc_start: 0.2331 (mtt) cc_final: 0.2088 (mtt) REVERT: q 385 ASP cc_start: 0.5094 (OUTLIER) cc_final: 0.4865 (t0) REVERT: q 466 MET cc_start: 0.5833 (mmm) cc_final: 0.5510 (mpp) REVERT: q 547 MET cc_start: 0.1618 (mmm) cc_final: 0.1207 (tpp) REVERT: r 336 ASN cc_start: 0.9264 (m-40) cc_final: 0.8854 (t0) REVERT: u 128 MET cc_start: 0.6386 (mmp) cc_final: 0.6018 (ptp) REVERT: x 246 ASN cc_start: 0.8161 (p0) cc_final: 0.7921 (p0) outliers start: 57 outliers final: 33 residues processed: 349 average time/residue: 0.6258 time to fit residues: 384.1258 Evaluate side-chains 338 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 297 time to evaluate : 5.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain m residue 575 ASP Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain q residue 172 LEU Chi-restraints excluded: chain q residue 385 ASP Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain v residue 204 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 257 optimal weight: 3.9990 chunk 690 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 450 optimal weight: 20.0000 chunk 189 optimal weight: 0.8980 chunk 767 optimal weight: 5.9990 chunk 636 optimal weight: 50.0000 chunk 355 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 402 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN B1141 HIS E 112 GLN G 93 ASN H 44 ASN V 100 GLN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 172 GLN ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 67526 Z= 0.171 Angle : 0.468 9.273 91655 Z= 0.247 Chirality : 0.040 0.148 10203 Planarity : 0.003 0.044 11489 Dihedral : 12.160 179.928 10017 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.13 % Favored : 97.86 % Rotamer: Outliers : 0.54 % Allowed : 9.09 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.10), residues: 7841 helix: 2.23 (0.09), residues: 3429 sheet: 0.14 (0.15), residues: 1142 loop : 0.26 (0.11), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.004 0.001 HIS A 660 PHE 0.024 0.001 PHE M 23 TYR 0.023 0.001 TYR q 871 ARG 0.004 0.000 ARG m1056 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 317 time to evaluate : 6.124 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: A 74 MET cc_start: 0.8906 (ttt) cc_final: 0.8504 (ttp) REVERT: A 146 MET cc_start: 0.9030 (tpp) cc_final: 0.8769 (tpp) REVERT: A 294 GLU cc_start: 0.8687 (pt0) cc_final: 0.8418 (pt0) REVERT: A 488 MET cc_start: 0.9378 (mtp) cc_final: 0.9054 (mtm) REVERT: A 1112 ASN cc_start: 0.9402 (p0) cc_final: 0.9068 (p0) REVERT: A 1270 MET cc_start: 0.8455 (mmp) cc_final: 0.8040 (mmp) REVERT: A 1318 GLU cc_start: 0.8972 (mp0) cc_final: 0.8617 (mp0) REVERT: B 119 MET cc_start: 0.9136 (mtt) cc_final: 0.8880 (mtt) REVERT: B 164 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8967 (ttp) REVERT: B 237 LYS cc_start: 0.9011 (tppp) cc_final: 0.8699 (pptt) REVERT: B 302 MET cc_start: 0.8193 (ptp) cc_final: 0.7846 (ptp) REVERT: B 363 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: B 792 MET cc_start: 0.9094 (mtt) cc_final: 0.8871 (mtt) REVERT: B 929 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 968 MET cc_start: 0.8673 (tmm) cc_final: 0.8372 (tmm) REVERT: B 1082 MET cc_start: 0.9194 (tpp) cc_final: 0.8706 (tpt) REVERT: B 1152 MET cc_start: 0.9237 (mmm) cc_final: 0.8983 (mmm) REVERT: B 1194 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9208 (mt) REVERT: C 137 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6724 (p0) REVERT: D 167 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7669 (mmmt) REVERT: E 21 MET cc_start: 0.9484 (ttm) cc_final: 0.9144 (ttm) REVERT: E 92 MET cc_start: 0.9598 (tpp) cc_final: 0.9140 (tpp) REVERT: H 104 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8030 (tm-30) REVERT: H 105 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8211 (tp30) REVERT: I 61 ASP cc_start: 0.8507 (t0) cc_final: 0.8002 (t0) REVERT: J 26 GLU cc_start: 0.8972 (tp30) cc_final: 0.8747 (tm-30) REVERT: J 41 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8778 (mmtm) REVERT: V 42 ASP cc_start: 0.8470 (p0) cc_final: 0.8219 (p0) REVERT: V 113 ILE cc_start: 0.7559 (tt) cc_final: 0.7292 (mt) REVERT: W 578 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.7988 (p0) REVERT: m 511 MET cc_start: 0.1890 (tmm) cc_final: 0.0754 (tpt) REVERT: m 563 MET cc_start: 0.5634 (OUTLIER) cc_final: 0.4442 (tpt) REVERT: m 570 MET cc_start: -0.1284 (ttm) cc_final: -0.1760 (mmp) REVERT: m 659 MET cc_start: 0.8172 (mtt) cc_final: 0.7697 (mtt) REVERT: m 1019 MET cc_start: 0.8066 (ptt) cc_final: 0.7707 (mtm) REVERT: m 1465 MET cc_start: 0.2470 (tmm) cc_final: 0.1682 (ptm) REVERT: n 180 GLN cc_start: 0.8919 (mt0) cc_final: 0.8240 (pt0) REVERT: q 1 MET cc_start: 0.5973 (mtt) cc_final: 0.4651 (tpt) REVERT: q 405 MET cc_start: 0.5823 (ttt) cc_final: 0.5614 (ttt) REVERT: q 466 MET cc_start: 0.6161 (mmm) cc_final: 0.5896 (mpp) REVERT: q 547 MET cc_start: 0.1612 (mmm) cc_final: 0.1222 (tpp) REVERT: r 336 ASN cc_start: 0.9263 (m-40) cc_final: 0.8866 (t0) REVERT: x 246 ASN cc_start: 0.8289 (p0) cc_final: 0.8060 (p0) outliers start: 38 outliers final: 15 residues processed: 343 average time/residue: 0.6280 time to fit residues: 375.9430 Evaluate side-chains 322 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 300 time to evaluate : 6.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain q residue 172 LEU Chi-restraints excluded: chain v residue 204 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 739 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 437 optimal weight: 50.0000 chunk 560 optimal weight: 40.0000 chunk 434 optimal weight: 30.0000 chunk 645 optimal weight: 0.8980 chunk 428 optimal weight: 8.9990 chunk 764 optimal weight: 50.0000 chunk 478 optimal weight: 30.0000 chunk 465 optimal weight: 20.0000 chunk 352 optimal weight: 8.9990 overall best weight: 8.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN B1141 HIS E 100 GLN I 46 HIS ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 100 GLN W 283 ASN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 187 GLN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.111 67526 Z= 0.601 Angle : 0.653 11.089 91655 Z= 0.337 Chirality : 0.045 0.193 10203 Planarity : 0.004 0.067 11489 Dihedral : 12.338 178.968 10017 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.41 % Favored : 96.58 % Rotamer: Outliers : 0.90 % Allowed : 9.47 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.10), residues: 7841 helix: 1.96 (0.09), residues: 3419 sheet: -0.05 (0.15), residues: 1155 loop : 0.10 (0.11), residues: 3267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP n 219 HIS 0.010 0.001 HIS A 660 PHE 0.025 0.002 PHE M 23 TYR 0.028 0.002 TYR B 479 ARG 0.007 0.001 ARG B1094 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 299 time to evaluate : 6.064 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: A 54 ASN cc_start: 0.9538 (OUTLIER) cc_final: 0.9211 (m-40) REVERT: A 74 MET cc_start: 0.9013 (ttt) cc_final: 0.8619 (ttp) REVERT: A 146 MET cc_start: 0.8916 (tpp) cc_final: 0.8665 (mmm) REVERT: A 282 MET cc_start: 0.8485 (ppp) cc_final: 0.8249 (ppp) REVERT: A 308 ASP cc_start: 0.8971 (m-30) cc_final: 0.8567 (p0) REVERT: A 488 MET cc_start: 0.9439 (mtp) cc_final: 0.9170 (mtm) REVERT: A 912 ASP cc_start: 0.9348 (OUTLIER) cc_final: 0.8879 (p0) REVERT: B 237 LYS cc_start: 0.9021 (tppp) cc_final: 0.8626 (pptt) REVERT: B 363 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: B 929 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 968 MET cc_start: 0.8751 (tmm) cc_final: 0.8403 (tmm) REVERT: B 1082 MET cc_start: 0.9078 (tpp) cc_final: 0.8460 (tpt) REVERT: B 1194 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9187 (mt) REVERT: C 137 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6912 (p0) REVERT: C 138 TYR cc_start: 0.7653 (m-80) cc_final: 0.7225 (m-10) REVERT: D 167 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7660 (mmmt) REVERT: E 21 MET cc_start: 0.9437 (ttm) cc_final: 0.9200 (ttm) REVERT: E 92 MET cc_start: 0.9577 (tpp) cc_final: 0.9021 (tpp) REVERT: E 136 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: I 61 ASP cc_start: 0.8510 (t0) cc_final: 0.8046 (t0) REVERT: I 108 LYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6354 (pttp) REVERT: J 26 GLU cc_start: 0.9041 (tp30) cc_final: 0.8781 (tm-30) REVERT: V 42 ASP cc_start: 0.8462 (p0) cc_final: 0.8245 (p0) REVERT: W 578 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8212 (p0) REVERT: m 511 MET cc_start: 0.2578 (tmm) cc_final: 0.1413 (tpt) REVERT: m 563 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.4482 (tpt) REVERT: m 570 MET cc_start: -0.1210 (ttm) cc_final: -0.1659 (mmp) REVERT: m 659 MET cc_start: 0.8201 (mtt) cc_final: 0.7645 (mtt) REVERT: m 1019 MET cc_start: 0.7630 (ptt) cc_final: 0.7374 (ptt) REVERT: m 1058 MET cc_start: 0.5869 (mpp) cc_final: 0.5074 (mpp) REVERT: m 1465 MET cc_start: 0.2450 (tmm) cc_final: 0.1658 (ptm) REVERT: n 180 GLN cc_start: 0.8937 (mt0) cc_final: 0.8248 (pt0) REVERT: q 1 MET cc_start: 0.6047 (mtt) cc_final: 0.5439 (ptp) REVERT: q 385 ASP cc_start: 0.5139 (OUTLIER) cc_final: 0.4880 (t0) REVERT: q 466 MET cc_start: 0.5714 (mmm) cc_final: 0.5495 (mpp) REVERT: q 547 MET cc_start: 0.2299 (mmm) cc_final: 0.1954 (tpp) REVERT: r 336 ASN cc_start: 0.9265 (m-40) cc_final: 0.8878 (t0) REVERT: u 128 MET cc_start: 0.6704 (ptt) cc_final: 0.6341 (mmp) REVERT: x 246 ASN cc_start: 0.8329 (p0) cc_final: 0.8121 (p0) outliers start: 64 outliers final: 34 residues processed: 345 average time/residue: 0.6318 time to fit residues: 380.0451 Evaluate side-chains 339 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 294 time to evaluate : 5.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1320 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain n residue 216 VAL Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain q residue 385 ASP Chi-restraints excluded: chain v residue 204 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 472 optimal weight: 7.9990 chunk 305 optimal weight: 0.0060 chunk 456 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 485 optimal weight: 50.0000 chunk 520 optimal weight: 50.0000 chunk 377 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 600 optimal weight: 40.0000 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN B 63 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN H 44 ASN ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 100 GLN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 67526 Z= 0.255 Angle : 0.500 10.011 91655 Z= 0.263 Chirality : 0.040 0.168 10203 Planarity : 0.003 0.045 11489 Dihedral : 12.248 179.135 10017 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.46 % Favored : 97.53 % Rotamer: Outliers : 0.59 % Allowed : 10.18 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.10), residues: 7841 helix: 2.14 (0.09), residues: 3420 sheet: 0.04 (0.15), residues: 1139 loop : 0.20 (0.11), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.005 0.001 HIS A 660 PHE 0.020 0.001 PHE K 35 TYR 0.024 0.001 TYR q 871 ARG 0.003 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 300 time to evaluate : 6.087 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: A 54 ASN cc_start: 0.9517 (OUTLIER) cc_final: 0.9149 (m-40) REVERT: A 74 MET cc_start: 0.8951 (ttt) cc_final: 0.8547 (ttp) REVERT: A 282 MET cc_start: 0.8380 (ppp) cc_final: 0.8132 (ppp) REVERT: A 308 ASP cc_start: 0.8968 (m-30) cc_final: 0.8394 (p0) REVERT: A 488 MET cc_start: 0.9395 (mtp) cc_final: 0.9122 (mtm) REVERT: A 1112 ASN cc_start: 0.9421 (p0) cc_final: 0.9059 (p0) REVERT: B 237 LYS cc_start: 0.9018 (tppp) cc_final: 0.8674 (pptt) REVERT: B 305 MET cc_start: 0.9363 (mmm) cc_final: 0.8853 (mpp) REVERT: B 363 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: B 792 MET cc_start: 0.9121 (mtt) cc_final: 0.8872 (mtt) REVERT: B 929 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 968 MET cc_start: 0.8708 (tmm) cc_final: 0.8402 (tmm) REVERT: B 1082 MET cc_start: 0.9144 (tpp) cc_final: 0.8466 (tpt) REVERT: B 1152 MET cc_start: 0.9196 (mmm) cc_final: 0.8920 (mmm) REVERT: B 1194 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9214 (mt) REVERT: C 137 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6799 (p0) REVERT: D 167 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7699 (mmmt) REVERT: E 21 MET cc_start: 0.9491 (ttm) cc_final: 0.9267 (ttm) REVERT: E 92 MET cc_start: 0.9556 (tpp) cc_final: 0.9248 (tpp) REVERT: H 104 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8071 (tm-30) REVERT: I 61 ASP cc_start: 0.8515 (t0) cc_final: 0.8022 (t0) REVERT: I 108 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7066 (pttp) REVERT: J 26 GLU cc_start: 0.8977 (tp30) cc_final: 0.8756 (tm-30) REVERT: J 41 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8793 (mmtm) REVERT: V 42 ASP cc_start: 0.8468 (p0) cc_final: 0.8248 (p0) REVERT: W 578 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8209 (p0) REVERT: m 511 MET cc_start: 0.2654 (tmm) cc_final: 0.1446 (tpt) REVERT: m 563 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.4315 (tpp) REVERT: m 570 MET cc_start: -0.1207 (ttm) cc_final: -0.1662 (mmp) REVERT: m 659 MET cc_start: 0.8172 (mtt) cc_final: 0.7615 (mtt) REVERT: m 1019 MET cc_start: 0.7544 (ptt) cc_final: 0.7328 (ptp) REVERT: m 1058 MET cc_start: 0.5661 (mpp) cc_final: 0.5373 (mpp) REVERT: m 1465 MET cc_start: 0.2429 (tmm) cc_final: 0.1669 (ptm) REVERT: n 180 GLN cc_start: 0.8874 (mt0) cc_final: 0.8205 (pt0) REVERT: q 1 MET cc_start: 0.5851 (mtt) cc_final: 0.4410 (tpt) REVERT: q 466 MET cc_start: 0.6256 (mmm) cc_final: 0.6038 (mpp) REVERT: q 547 MET cc_start: 0.1899 (mmm) cc_final: 0.1550 (tpp) REVERT: r 227 MET cc_start: 0.6243 (tpt) cc_final: 0.6001 (tpt) REVERT: r 336 ASN cc_start: 0.9266 (m-40) cc_final: 0.8892 (t0) REVERT: u 128 MET cc_start: 0.7137 (ptt) cc_final: 0.6795 (mmp) REVERT: x 246 ASN cc_start: 0.8321 (p0) cc_final: 0.8103 (p0) outliers start: 42 outliers final: 27 residues processed: 326 average time/residue: 0.6339 time to fit residues: 361.8781 Evaluate side-chains 330 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 295 time to evaluate : 5.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain n residue 216 VAL Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain v residue 204 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 695 optimal weight: 6.9990 chunk 732 optimal weight: 40.0000 chunk 668 optimal weight: 50.0000 chunk 712 optimal weight: 30.0000 chunk 428 optimal weight: 7.9990 chunk 310 optimal weight: 0.0170 chunk 559 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 643 optimal weight: 5.9990 chunk 673 optimal weight: 20.0000 chunk 709 optimal weight: 20.0000 overall best weight: 2.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 67526 Z= 0.232 Angle : 0.489 11.932 91655 Z= 0.255 Chirality : 0.040 0.158 10203 Planarity : 0.003 0.043 11489 Dihedral : 12.173 179.153 10017 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.64 % Favored : 97.35 % Rotamer: Outliers : 0.64 % Allowed : 10.35 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.10), residues: 7841 helix: 2.22 (0.09), residues: 3427 sheet: 0.09 (0.15), residues: 1144 loop : 0.25 (0.11), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.004 0.001 HIS A 660 PHE 0.018 0.001 PHE K 35 TYR 0.026 0.001 TYR q 871 ARG 0.003 0.000 ARG m 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 297 time to evaluate : 5.914 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: A 54 ASN cc_start: 0.9513 (OUTLIER) cc_final: 0.9160 (m-40) REVERT: A 74 MET cc_start: 0.8927 (ttt) cc_final: 0.8529 (ttp) REVERT: A 108 MET cc_start: 0.9171 (mmm) cc_final: 0.8688 (mmm) REVERT: A 282 MET cc_start: 0.8320 (ppp) cc_final: 0.8062 (ppp) REVERT: A 488 MET cc_start: 0.9371 (mtp) cc_final: 0.9097 (mtm) REVERT: A 1112 ASN cc_start: 0.9421 (p0) cc_final: 0.9069 (p0) REVERT: A 1204 MET cc_start: 0.9148 (tmm) cc_final: 0.8888 (tmm) REVERT: B 237 LYS cc_start: 0.9020 (tppp) cc_final: 0.8650 (pptt) REVERT: B 363 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: B 792 MET cc_start: 0.9119 (mtt) cc_final: 0.8845 (mtt) REVERT: B 929 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8315 (p) REVERT: B 968 MET cc_start: 0.8686 (tmm) cc_final: 0.8379 (tmm) REVERT: B 1082 MET cc_start: 0.9152 (tpp) cc_final: 0.8439 (tpt) REVERT: B 1152 MET cc_start: 0.9237 (mmm) cc_final: 0.8961 (mmm) REVERT: B 1194 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9202 (mt) REVERT: C 137 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6802 (p0) REVERT: D 167 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7744 (mmmt) REVERT: E 21 MET cc_start: 0.9496 (ttm) cc_final: 0.9276 (ttm) REVERT: E 92 MET cc_start: 0.9541 (tpp) cc_final: 0.9263 (tpp) REVERT: E 136 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: H 104 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8023 (tm-30) REVERT: I 61 ASP cc_start: 0.8500 (t0) cc_final: 0.7993 (t0) REVERT: I 108 LYS cc_start: 0.7531 (ptmm) cc_final: 0.7152 (pttp) REVERT: J 26 GLU cc_start: 0.8963 (tp30) cc_final: 0.8745 (tm-30) REVERT: J 41 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8792 (mmtm) REVERT: W 578 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8191 (p0) REVERT: m 511 MET cc_start: 0.2897 (tmm) cc_final: 0.1742 (tpt) REVERT: m 563 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.4535 (tpp) REVERT: m 570 MET cc_start: -0.1203 (ttm) cc_final: -0.1690 (mmp) REVERT: m 659 MET cc_start: 0.8173 (mtt) cc_final: 0.7614 (mtt) REVERT: m 1019 MET cc_start: 0.7547 (ptt) cc_final: 0.7347 (ptp) REVERT: n 167 MET cc_start: 0.8499 (ppp) cc_final: 0.7908 (ppp) REVERT: n 180 GLN cc_start: 0.8882 (mt0) cc_final: 0.8170 (pt0) REVERT: q 1 MET cc_start: 0.5925 (mtt) cc_final: 0.4419 (tpt) REVERT: q 114 MET cc_start: 0.2459 (mtt) cc_final: 0.2240 (mtt) REVERT: q 547 MET cc_start: 0.1848 (mmm) cc_final: 0.1487 (tpp) REVERT: r 227 MET cc_start: 0.6395 (tpt) cc_final: 0.6116 (tpt) REVERT: r 336 ASN cc_start: 0.9270 (m-40) cc_final: 0.8894 (t0) REVERT: u 128 MET cc_start: 0.6980 (ptt) cc_final: 0.6669 (mmp) REVERT: x 246 ASN cc_start: 0.8342 (p0) cc_final: 0.8112 (p0) outliers start: 45 outliers final: 27 residues processed: 329 average time/residue: 0.6206 time to fit residues: 356.4562 Evaluate side-chains 327 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 292 time to evaluate : 5.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain v residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 467 optimal weight: 9.9990 chunk 753 optimal weight: 7.9990 chunk 459 optimal weight: 2.9990 chunk 357 optimal weight: 4.9990 chunk 523 optimal weight: 0.9980 chunk 790 optimal weight: 10.0000 chunk 727 optimal weight: 0.0570 chunk 629 optimal weight: 50.0000 chunk 65 optimal weight: 7.9990 chunk 485 optimal weight: 50.0000 chunk 385 optimal weight: 0.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS H 44 ASN ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 100 GLN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 359 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 67526 Z= 0.176 Angle : 0.487 11.910 91655 Z= 0.254 Chirality : 0.040 0.213 10203 Planarity : 0.003 0.044 11489 Dihedral : 12.113 179.190 10017 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.41 % Favored : 97.58 % Rotamer: Outliers : 0.59 % Allowed : 10.39 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.10), residues: 7841 helix: 2.26 (0.09), residues: 3433 sheet: 0.12 (0.15), residues: 1156 loop : 0.30 (0.11), residues: 3252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP n 219 HIS 0.005 0.001 HIS A 459 PHE 0.023 0.001 PHE M 23 TYR 0.022 0.001 TYR q 871 ARG 0.003 0.000 ARG B 469 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15682 Ramachandran restraints generated. 7841 Oldfield, 0 Emsley, 7841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 300 time to evaluate : 6.124 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: A 54 ASN cc_start: 0.9503 (OUTLIER) cc_final: 0.9136 (m-40) REVERT: A 74 MET cc_start: 0.8903 (ttt) cc_final: 0.8512 (ttp) REVERT: A 108 MET cc_start: 0.9196 (mmm) cc_final: 0.8698 (mmm) REVERT: A 282 MET cc_start: 0.8265 (ppp) cc_final: 0.8010 (ppp) REVERT: A 488 MET cc_start: 0.9361 (mtp) cc_final: 0.9097 (mtm) REVERT: A 1112 ASN cc_start: 0.9397 (p0) cc_final: 0.9068 (p0) REVERT: A 1204 MET cc_start: 0.9158 (tmm) cc_final: 0.8933 (tmm) REVERT: A 1287 MET cc_start: 0.8639 (ttp) cc_final: 0.8422 (tmm) REVERT: B 237 LYS cc_start: 0.9021 (tppp) cc_final: 0.8663 (pptt) REVERT: B 302 MET cc_start: 0.8186 (ptp) cc_final: 0.7960 (ptp) REVERT: B 305 MET cc_start: 0.9241 (mmm) cc_final: 0.8410 (mtp) REVERT: B 363 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: B 792 MET cc_start: 0.9089 (mtt) cc_final: 0.8806 (mtt) REVERT: B 929 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8287 (p) REVERT: B 968 MET cc_start: 0.8631 (tmm) cc_final: 0.8324 (tmm) REVERT: B 1082 MET cc_start: 0.9168 (tpp) cc_final: 0.8460 (tpt) REVERT: B 1152 MET cc_start: 0.9231 (mmm) cc_final: 0.8976 (mmm) REVERT: B 1194 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9197 (mt) REVERT: C 137 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6800 (p0) REVERT: D 167 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7897 (mmmt) REVERT: E 21 MET cc_start: 0.9490 (ttm) cc_final: 0.9273 (ttm) REVERT: E 92 MET cc_start: 0.9532 (tpp) cc_final: 0.9269 (tpp) REVERT: E 136 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: H 104 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8060 (tm-30) REVERT: I 61 ASP cc_start: 0.8487 (t0) cc_final: 0.7969 (t0) REVERT: I 108 LYS cc_start: 0.7722 (ptmm) cc_final: 0.7353 (pttp) REVERT: J 26 GLU cc_start: 0.8955 (tp30) cc_final: 0.8730 (tm-30) REVERT: J 41 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8775 (mmtm) REVERT: W 578 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8021 (p0) REVERT: m 511 MET cc_start: 0.2841 (tmm) cc_final: 0.1709 (tpt) REVERT: m 563 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.4527 (tpp) REVERT: m 570 MET cc_start: -0.1211 (ttm) cc_final: -0.1692 (mmp) REVERT: m 659 MET cc_start: 0.8166 (mtt) cc_final: 0.7610 (mtt) REVERT: m 1465 MET cc_start: 0.2508 (tmm) cc_final: 0.1693 (ptm) REVERT: n 167 MET cc_start: 0.8614 (ppp) cc_final: 0.7890 (ppp) REVERT: n 180 GLN cc_start: 0.8855 (mt0) cc_final: 0.8160 (pt0) REVERT: q 1 MET cc_start: 0.6092 (mtt) cc_final: 0.4408 (tpt) REVERT: q 114 MET cc_start: 0.2637 (mtt) cc_final: 0.2324 (mtt) REVERT: q 547 MET cc_start: 0.1848 (mmm) cc_final: 0.1478 (tpp) REVERT: r 227 MET cc_start: 0.6417 (tpt) cc_final: 0.6130 (tpt) REVERT: r 270 MET cc_start: 0.7838 (mmm) cc_final: 0.7356 (mmp) REVERT: r 336 ASN cc_start: 0.9272 (m-40) cc_final: 0.8894 (t0) REVERT: u 128 MET cc_start: 0.6982 (ptt) cc_final: 0.6682 (mmp) REVERT: x 246 ASN cc_start: 0.8345 (p0) cc_final: 0.8119 (p0) outliers start: 42 outliers final: 28 residues processed: 326 average time/residue: 0.6490 time to fit residues: 370.9324 Evaluate side-chains 329 residues out of total 7083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 293 time to evaluate : 5.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 563 ASP Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 563 MET Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain v residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 793 random chunks: chunk 499 optimal weight: 30.0000 chunk 670 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 580 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 630 optimal weight: 50.0000 chunk 263 optimal weight: 10.0000 chunk 647 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1141 HIS ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.121785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070225 restraints weight = 217170.016| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.74 r_work: 0.2745 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 67526 Z= 0.518 Angle : 0.614 11.241 91655 Z= 0.317 Chirality : 0.043 0.192 10203 Planarity : 0.004 0.045 11489 Dihedral : 12.270 178.402 10017 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.23 % Favored : 96.76 % Rotamer: Outliers : 0.56 % Allowed : 10.41 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.10), residues: 7841 helix: 2.07 (0.09), residues: 3417 sheet: -0.03 (0.15), residues: 1190 loop : 0.20 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP n 219 HIS 0.009 0.001 HIS A 660 PHE 0.024 0.002 PHE M 23 TYR 0.026 0.002 TYR B 479 ARG 0.007 0.001 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12155.18 seconds wall clock time: 216 minutes 51.34 seconds (13011.34 seconds total)