Starting phenix.real_space_refine on Tue Mar 19 06:37:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbv_32407/03_2024/7wbv_32407.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbv_32407/03_2024/7wbv_32407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbv_32407/03_2024/7wbv_32407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbv_32407/03_2024/7wbv_32407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbv_32407/03_2024/7wbv_32407.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbv_32407/03_2024/7wbv_32407.pdb" } resolution = 4.1 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 10 6.06 5 P 328 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 28903 2.51 5 N 8450 2.21 5 O 9611 1.98 5 H 44823 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ASP 87": "OD1" <-> "OD2" Residue "V TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 92340 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 22279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1412, 22279 Classifications: {'peptide': 1412} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1343} Chain breaks: 5 Chain: "B" Number of atoms: 18471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 18471 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 52, 'TRANS': 1104} Chain breaks: 5 Chain: "C" Number of atoms: 4160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 4160 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2631 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3495 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1371 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2666 Classifications: {'peptide': 171} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2104 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1790 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1109 Classifications: {'peptide': 66} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1876 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 722 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "M" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1005 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "N" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 4910 Classifications: {'DNA': 154} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 153} Chain breaks: 1 Chain: "P" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 504 Classifications: {'RNA': 16} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 5012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 5012 Classifications: {'DNA': 159} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 158} Chain: "V" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1554 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "W" Number of atoms: 4503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 4503 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 4 Chain: "a" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1632 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1315 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "c" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1645 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1518 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1629 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1279 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1677 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1472 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} 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 1051 SG CYS A 67 65.142 62.491 162.987 1.00104.46 S ATOM 1092 SG CYS A 70 67.992 60.857 164.972 1.00 99.81 S ATOM 1174 SG CYS A 77 67.701 64.597 164.582 1.00101.13 S ATOM 1652 SG CYS A 107 80.993 82.984 122.442 1.00203.84 S ATOM 1694 SG CYS A 110 82.570 80.963 121.579 1.00226.37 S ATOM 2467 SG CYS A 168 80.122 83.910 119.266 1.00236.80 S ATOM 39789 SG CYS B1163 81.246 59.932 153.608 1.00120.92 S ATOM 39826 SG CYS B1166 79.970 63.348 152.602 1.00127.27 S ATOM 40079 SG CYS B1182 77.514 60.490 152.868 1.00128.87 S ATOM 40125 SG CYS B1185 80.178 60.494 150.084 1.00130.63 S ATOM 42038 SG CYS C 85 63.912 78.588 230.681 1.00134.53 S ATOM 42063 SG CYS C 87 60.997 77.801 228.448 1.00168.76 S ATOM 42122 SG CYS C 91 60.392 79.796 231.573 1.00124.98 S ATOM 42160 SG CYS C 94 62.091 81.300 228.513 1.00122.75 S ATOM 58328 SG CYS I 75 83.850 162.359 170.095 1.00468.75 S ATOM 58368 SG CYS I 78 81.705 164.790 169.238 1.00475.39 S ATOM 58789 SG CYS I 103 83.739 161.732 166.933 1.00459.33 S ATOM 57303 SG CYS I 10 66.464 146.308 125.798 1.00314.66 S ATOM 57624 SG CYS I 29 70.792 145.572 125.646 1.00369.76 S ATOM 57673 SG CYS I 32 68.904 148.275 123.925 1.00365.23 S ATOM 59084 SG CYS J 7 71.136 110.955 218.061 1.00 56.69 S ATOM 59126 SG CYS J 10 72.432 110.204 221.357 1.00 53.74 S ATOM 59680 SG CYS J 44 74.162 113.052 219.626 1.00 51.95 S ATOM 59691 SG CYS J 45 70.699 113.319 221.125 1.00 56.19 S ATOM 62038 SG CYS L 33 33.398 99.483 198.669 1.00109.62 S ATOM 62066 SG CYS L 36 30.557 99.491 201.258 1.00109.90 S ATOM 62281 SG CYS L 50 30.566 96.985 198.324 1.00101.07 S ATOM 62329 SG CYS L 53 29.965 100.552 197.646 1.00107.34 S ATOM 62859 SG CYS M 25 57.164 108.766 117.264 1.00213.30 S ATOM 62909 SG CYS M 28 57.162 105.047 116.980 1.00223.36 S ATOM 63224 SG CYS M 49 60.409 107.127 116.575 1.00214.79 S ATOM 63279 SG CYS M 52 57.994 107.389 113.855 1.00217.38 S ATOM 74160 SG CYS V 12 20.231 85.837 130.148 1.00566.69 S ATOM 74207 SG CYS V 15 22.107 88.511 128.335 1.00504.67 S ATOM 74415 SG CYS V 29 18.727 89.373 129.830 1.00593.84 S ATOM 74454 SG CYS V 32 18.877 86.980 126.846 1.00559.57 S Time building chain proxies: 34.00, per 1000 atoms: 0.37 Number of scatterers: 92340 At special positions: 0 Unit cell: (164.3, 177.02, 259.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 10 29.99 S 214 16.00 P 328 15.00 Mg 1 11.99 O 9611 8.00 N 8450 7.00 C 28903 6.00 H 44823 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.48 Conformation dependent library (CDL) restraints added in 6.5 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 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " 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 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " Number of angles added : 39 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9592 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 63 sheets defined 42.6% alpha, 14.7% beta 129 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 35.68 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.870A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 279 Processing helix chain 'A' and resid 287 through 304 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 395 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.514A pdb=" N MET A 456 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.605A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 526 through 536 removed outlier: 3.920A pdb=" N LYS A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.620A pdb=" N ILE A 583 " --> pdb=" O LEU A 579 " (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: 3.737A pdb=" N CYS A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.650A pdb=" N HIS A 700 " --> pdb=" O TYR A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 removed outlier: 3.570A pdb=" N ILE A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.237A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.632A 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 910 through 914 Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.556A pdb=" N ILE A 920 " --> pdb=" O TYR A 916 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 916 through 921' Processing helix chain 'A' and resid 924 through 948 removed outlier: 3.726A pdb=" N GLU A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 984 through 997 removed outlier: 3.757A pdb=" N LYS A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1017 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 1080 Proline residue: A1077 - end of helix removed outlier: 3.986A pdb=" N GLN A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1109 Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1144 through 1148 removed outlier: 3.760A pdb=" N VAL A1148 " --> pdb=" O THR A1144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1144 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 1273 Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.605A pdb=" N VAL A1319 " --> pdb=" O ASN A1315 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A1320 " --> pdb=" O LEU A1316 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1315 through 1321' Processing helix chain 'A' and resid 1334 through 1361 removed outlier: 3.661A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N GLU A1345 " --> pdb=" O VAL A1341 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A1347 " --> pdb=" O GLY A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.900A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1395 Processing helix chain 'A' and resid 1398 through 1406 removed outlier: 3.518A pdb=" N ARG A1402 " --> pdb=" O GLY A1398 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A1404 " --> pdb=" O LEU A1400 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A1405 " --> pdb=" O MET A1401 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A1406 " --> pdb=" O ARG A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1434 removed outlier: 4.685A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1443 Processing helix chain 'A' and resid 1451 through 1456 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 53 removed outlier: 4.220A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 175 through 184 removed outlier: 4.010A pdb=" N LEU B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 313 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 Processing helix chain 'B' and resid 336 through 351 removed outlier: 4.092A pdb=" N ILE B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 3.791A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 430 removed outlier: 3.604A pdb=" N LEU B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 585 through 599 removed outlier: 4.305A 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 685 Processing helix chain 'B' and resid 692 through 696 Processing helix chain 'B' and resid 703 through 708 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.515A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.972A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.816A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.507A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.224A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.865A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.567A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1141 Processing helix chain 'B' and resid 1143 through 1151 removed outlier: 3.768A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.565A pdb=" N TRP C 170 " --> pdb=" O HIS C 167 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.791A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 4.110A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 73 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.579A pdb=" N LYS D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 113 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.532A pdb=" N ILE D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 170 through 182 removed outlier: 3.641A pdb=" N ILE D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 removed outlier: 3.708A pdb=" N GLY E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 35 removed outlier: 3.721A pdb=" N MET E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.637A pdb=" N SER E 58 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.527A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix 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: 3.705A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 187 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 21 through 35 removed outlier: 3.910A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 115 removed outlier: 3.939A pdb=" N ILE G 115 " --> pdb=" O THR G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.691A 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 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.770A pdb=" N GLU J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.981A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.727A pdb=" N LEU K 9 " --> pdb=" O ARG K 6 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.176A 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 32 through 37 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 removed outlier: 3.649A pdb=" N VAL V 95 " --> pdb=" O PRO V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 213 through 218 removed outlier: 3.553A pdb=" N LEU W 216 " --> pdb=" O PRO W 213 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE W 218 " --> pdb=" O ARG W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 250 Processing helix chain 'W' and resid 278 through 287 Processing helix chain 'W' and resid 302 through 309 removed outlier: 4.271A pdb=" N LYS W 307 " --> pdb=" O ILE W 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP W 308 " --> pdb=" O VAL W 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 395 through 403 removed outlier: 3.547A pdb=" N ALA W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) Processing helix chain 'W' and resid 443 through 450 Processing helix chain 'W' and resid 792 through 794 No H-bonds generated for 'chain 'W' and resid 792 through 794' Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 77 removed outlier: 3.817A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 removed outlier: 3.725A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 4.074A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 22 Processing helix chain 'c' and resid 26 through 37 removed outlier: 3.698A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 73 Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.530A pdb=" N LEU c 83 " --> pdb=" O ILE c 79 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 82 Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.699A pdb=" N ILE d 91 " --> pdb=" O THR d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 121 Processing helix chain 'e' and resid 44 through 55 Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.931A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.661A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 removed outlier: 3.775A pdb=" N GLY f 28 " --> pdb=" O ASN f 25 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE f 29 " --> pdb=" O ILE f 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 25 through 29' Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 46 through 73 removed outlier: 3.607A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 removed outlier: 3.505A pdb=" N ILE h 91 " --> pdb=" O THR h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 121 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 85 through 90 removed outlier: 10.866A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL A 239 " --> 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 254 removed outlier: 6.783A pdb=" N THR A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 442 through 443 removed outlier: 3.700A pdb=" N LYS A 462 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 470 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER A 355 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 350 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 442 through 443 removed outlier: 3.700A pdb=" N LYS A 462 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 470 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER A 355 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 351 " --> pdb=" O HIS B1104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 413 through 415 removed outlier: 4.556A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.586A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB1, first strand: chain 'A' and resid 607 through 609 removed outlier: 7.001A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 663 through 664 removed outlier: 3.846A pdb=" N PHE A 663 " --> pdb=" O CYS B 829 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 981 " --> pdb=" O GLN B1093 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B1085 " --> pdb=" O GLU B1070 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 663 through 664 removed outlier: 3.846A pdb=" N PHE A 663 " --> pdb=" O CYS B 829 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B1085 " --> pdb=" O GLU B1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB5, first strand: chain 'A' and resid 850 through 851 removed outlier: 3.542A pdb=" N GLN A 866 " --> pdb=" O THR A 857 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB7, first strand: chain 'A' and resid 1284 through 1286 removed outlier: 3.966A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A1292 " --> pdb=" O GLU A1304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1284 through 1286 removed outlier: 3.966A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1229 through 1230 removed outlier: 4.660A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR I 44 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR A1156 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LYS I 42 " --> pdb=" O TYR A1156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.708A pdb=" N VAL A1446 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE G 61 " --> pdb=" O VAL A1446 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AC3, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AC4, first strand: chain 'B' and resid 82 through 84 removed outlier: 5.612A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC6, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC7, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AC8, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.010A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU B 235 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 241 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 248 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AD1, first strand: chain 'B' and resid 644 through 645 removed outlier: 3.822A pdb=" N GLU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 741 " --> pdb=" O PHE B 631 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 578 through 583 removed outlier: 6.467A pdb=" N ILE B 573 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE B 582 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR B 571 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.605A pdb=" N ASP B 861 " --> pdb=" O VAL B 964 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.564A pdb=" N GLU B 873 " --> pdb=" O THR B 915 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 915 " --> pdb=" O GLU B 873 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1111 through 1112 removed outlier: 3.640A pdb=" N GLN B1117 " --> pdb=" O GLN B1112 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 8 through 11 removed outlier: 5.140A pdb=" N ILE C 9 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N MET C 20 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 8 through 11 removed outlier: 5.140A pdb=" N ILE C 9 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N MET C 20 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.710A pdb=" N GLY C 162 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 44 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 98 " --> pdb=" O CYS C 157 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.710A pdb=" N GLY C 162 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA C 44 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 51 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.370A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.000A pdb=" N PHE G 2 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TRP G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE G 45 " --> pdb=" O TRP G 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.152A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE E 59 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR E 111 " --> pdb=" O PHE E 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.606A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 85 through 89 removed outlier: 3.978A pdb=" N GLU G 85 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL G 87 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G 143 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 85 through 89 removed outlier: 3.978A pdb=" N GLU G 85 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL G 87 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL G 143 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.424A pdb=" N VAL G 120 " --> pdb=" O MET G 131 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET G 131 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 94 through 96 removed outlier: 3.823A pdb=" N LEU H 59 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE H 6 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP H 41 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE H 111 " --> pdb=" O GLY H 126 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 18 through 19 removed outlier: 3.622A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU I 36 " --> pdb=" O TYR I 27 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 84 through 86 removed outlier: 3.755A pdb=" N VAL I 84 " --> pdb=" O VAL I 102 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 20 through 23 Processing sheet with id=AF7, first strand: chain 'L' and resid 39 through 41 removed outlier: 3.711A pdb=" N PHE L 40 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 34 through 35 Processing sheet with id=AF9, first strand: chain 'M' and resid 38 through 39 removed outlier: 3.624A pdb=" N ASP M 39 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 18 through 19 removed outlier: 3.748A pdb=" N LEU V 19 " --> pdb=" O ARG V 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER V 51 " --> pdb=" O ALA V 11 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'V' and resid 81 through 82 removed outlier: 3.532A pdb=" N VAL V 58 " --> pdb=" O TYR V 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU V 57 " --> pdb=" O GLN W 264 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER W 261 " --> pdb=" O GLU W 275 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 407 through 410 removed outlier: 3.517A pdb=" N ARG W 407 " --> pdb=" O THR W 415 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR W 415 " --> pdb=" O ARG W 407 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS W 428 " --> pdb=" O LEU W 352 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU W 342 " --> pdb=" O ARG W 351 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS W 353 " --> pdb=" O VAL W 340 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL W 340 " --> pdb=" O LYS W 353 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 788 through 791 removed outlier: 7.253A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU W 799 " --> pdb=" O THR W 755 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.444A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.765A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG8, first strand: chain 'c' and resid 101 through 102 removed outlier: 7.648A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'g' and resid 42 through 43 removed outlier: 6.969A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 1786 hydrogen bonds defined for protein. 4983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 318 hydrogen bonds 608 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 49.81 Time building geometry restraints manager: 64.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 44739 1.03 - 1.23: 183 1.23 - 1.42: 20485 1.42 - 1.62: 28118 1.62 - 1.81: 343 Bond restraints: 93868 Sorted by residual: bond pdb=" CG PRO W 213 " pdb=" CD PRO W 213 " ideal model delta sigma weight residual 1.503 1.241 0.262 3.40e-02 8.65e+02 5.92e+01 bond pdb=" CB PRO W 213 " pdb=" CG PRO W 213 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.60e+00 bond pdb=" N GLY L 28 " pdb=" CA GLY L 28 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.53e+00 bond pdb=" N ILE M 15 " pdb=" CA ILE M 15 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.44e+00 bond pdb=" N GLU C 4 " pdb=" CA GLU C 4 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.32e+00 ... (remaining 93863 not shown) Histogram of bond angle deviations from ideal: 88.29 - 97.44: 2 97.44 - 106.59: 3232 106.59 - 115.74: 117780 115.74 - 124.89: 44817 124.89 - 134.04: 4086 Bond angle restraints: 169917 Sorted by residual: angle pdb=" N PRO W 213 " pdb=" CD PRO W 213 " pdb=" CG PRO W 213 " ideal model delta sigma weight residual 103.20 88.29 14.91 1.50e+00 4.44e-01 9.88e+01 angle pdb=" CA PRO W 213 " pdb=" N PRO W 213 " pdb=" CD PRO W 213 " ideal model delta sigma weight residual 112.00 102.63 9.37 1.40e+00 5.10e-01 4.48e+01 angle pdb=" CA PRO W 213 " pdb=" CB PRO W 213 " pdb=" CG PRO W 213 " ideal model delta sigma weight residual 104.50 95.12 9.38 1.90e+00 2.77e-01 2.44e+01 angle pdb=" C GLN A 526 " pdb=" CA GLN A 526 " pdb=" CB GLN A 526 " ideal model delta sigma weight residual 117.23 110.94 6.29 1.36e+00 5.41e-01 2.14e+01 angle pdb=" N VAL C 195 " pdb=" CA VAL C 195 " pdb=" C VAL C 195 " ideal model delta sigma weight residual 111.62 108.32 3.30 7.90e-01 1.60e+00 1.74e+01 ... (remaining 169912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 40144 34.71 - 69.41: 2419 69.41 - 104.12: 113 104.12 - 138.82: 2 138.82 - 173.53: 6 Dihedral angle restraints: 42684 sinusoidal: 25672 harmonic: 17012 Sorted by residual: dihedral pdb=" CA PHE B1086 " pdb=" C PHE B1086 " pdb=" N PHE B1087 " pdb=" CA PHE B1087 " ideal model delta harmonic sigma weight residual -180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ARG A 231 " pdb=" C ARG A 231 " pdb=" N PRO A 232 " pdb=" CA PRO A 232 " ideal model delta harmonic sigma weight residual -180.00 -159.24 -20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LYS B 319 " pdb=" C LYS B 319 " pdb=" N GLU B 320 " pdb=" CA GLU B 320 " ideal model delta harmonic sigma weight residual 180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 42681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 6971 0.074 - 0.148: 614 0.148 - 0.223: 0 0.223 - 0.297: 0 0.297 - 0.371: 1 Chirality restraints: 7586 Sorted by residual: chirality pdb=" P DC T 64 " pdb=" OP1 DC T 64 " pdb=" OP2 DC T 64 " pdb=" O5' DC T 64 " both_signs ideal model delta sigma weight residual True 2.35 -2.72 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA ILE E 29 " pdb=" N ILE E 29 " pdb=" C ILE E 29 " pdb=" CB ILE E 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE b 29 " pdb=" N ILE b 29 " pdb=" C ILE b 29 " pdb=" CB ILE b 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.26e-01 ... (remaining 7583 not shown) Planarity restraints: 12703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B1213 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO B1214 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B1214 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B1214 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 568 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 569 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 569 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 569 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 321 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO A 322 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.026 5.00e-02 4.00e+02 ... (remaining 12700 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 1216 2.01 - 2.66: 129254 2.66 - 3.30: 271448 3.30 - 3.95: 346125 3.95 - 4.60: 541615 Nonbonded interactions: 1289658 Sorted by model distance: nonbonded pdb=" HB3 CYS I 103 " pdb="ZN ZN I 201 " model vdw 1.361 1.544 nonbonded pdb=" HB3 CYS A 168 " pdb="ZN ZN A1802 " model vdw 1.398 1.544 nonbonded pdb=" O ASN A1147 " pdb="HH11 ARG A1203 " model vdw 1.460 1.850 nonbonded pdb=" H ASP A 891 " pdb=" O SER A1298 " model vdw 1.477 1.850 nonbonded pdb=" O SER A1328 " pdb=" H GLU E 147 " model vdw 1.483 1.850 ... (remaining 1289653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a' and resid 39 through 134) selection = (chain 'e' and resid 39 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 16 through 118) } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = (chain 'h' and (resid 29 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 80 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.980 Extract box with map and model: 11.770 Check model and map are aligned: 1.050 Set scattering table: 0.640 Process input model: 303.480 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.320 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 325.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 0.262 49045 Z= 0.263 Angle : 0.618 14.911 67631 Z= 0.366 Chirality : 0.041 0.371 7586 Planarity : 0.004 0.065 7584 Dihedral : 18.954 173.528 19511 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 5045 helix: 0.86 (0.12), residues: 1866 sheet: -1.38 (0.20), residues: 681 loop : -1.08 (0.13), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 657 HIS 0.014 0.001 HIS A 700 PHE 0.022 0.002 PHE D 115 TYR 0.022 0.001 TYR B1092 ARG 0.011 0.001 ARG A 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 5.412 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: B 1021 MET cc_start: 0.9204 (mpp) cc_final: 0.8760 (mpp) REVERT: B 1082 MET cc_start: 0.7393 (tpp) cc_final: 0.6786 (tpp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 1.1339 time to fit residues: 333.3397 Evaluate side-chains 155 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 5.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 450 optimal weight: 30.0000 chunk 404 optimal weight: 50.0000 chunk 224 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 418 optimal weight: 30.0000 chunk 161 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 311 optimal weight: 9.9990 chunk 484 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS ** W 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 49045 Z= 0.330 Angle : 0.639 8.587 67631 Z= 0.365 Chirality : 0.042 0.161 7586 Planarity : 0.005 0.059 7584 Dihedral : 22.239 172.817 9284 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.86 % Favored : 93.04 % Rotamer: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.12), residues: 5045 helix: 0.62 (0.12), residues: 1910 sheet: -1.42 (0.20), residues: 647 loop : -1.22 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 300 HIS 0.009 0.001 HIS A 92 PHE 0.027 0.002 PHE B 963 TYR 0.018 0.001 TYR K 61 ARG 0.005 0.000 ARG K 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 5.539 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: B 1021 MET cc_start: 0.9172 (mpp) cc_final: 0.8872 (mpp) REVERT: W 408 ARG cc_start: 0.2067 (mtt180) cc_final: 0.1311 (ttm170) REVERT: f 84 MET cc_start: 0.6879 (ppp) cc_final: 0.6615 (ppp) outliers start: 3 outliers final: 0 residues processed: 169 average time/residue: 1.0840 time to fit residues: 312.1294 Evaluate side-chains 151 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 5.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 269 optimal weight: 0.2980 chunk 150 optimal weight: 10.0000 chunk 403 optimal weight: 30.0000 chunk 330 optimal weight: 50.0000 chunk 133 optimal weight: 9.9990 chunk 485 optimal weight: 30.0000 chunk 524 optimal weight: 20.0000 chunk 432 optimal weight: 20.0000 chunk 481 optimal weight: 20.0000 chunk 165 optimal weight: 0.0570 chunk 389 optimal weight: 20.0000 overall best weight: 8.0708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN B 60 GLN G 107 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 HIS ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 49045 Z= 0.307 Angle : 0.611 8.630 67631 Z= 0.347 Chirality : 0.041 0.156 7586 Planarity : 0.005 0.066 7584 Dihedral : 22.362 172.169 9284 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.23 % Favored : 92.67 % Rotamer: Outliers : 0.02 % Allowed : 2.57 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 5045 helix: 0.55 (0.12), residues: 1917 sheet: -1.58 (0.20), residues: 655 loop : -1.30 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 300 HIS 0.009 0.001 HIS A 92 PHE 0.029 0.002 PHE B 963 TYR 0.022 0.002 TYR B1092 ARG 0.007 0.000 ARG h 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 5.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.0507 (tpt) cc_final: -0.0199 (tpt) REVERT: B 1021 MET cc_start: 0.9205 (mpp) cc_final: 0.8903 (mpp) REVERT: W 408 ARG cc_start: 0.2060 (mtt180) cc_final: 0.1343 (ttm-80) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 1.0863 time to fit residues: 311.7447 Evaluate side-chains 154 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 5.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 479 optimal weight: 40.0000 chunk 365 optimal weight: 40.0000 chunk 252 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 487 optimal weight: 50.0000 chunk 516 optimal weight: 50.0000 chunk 254 optimal weight: 8.9990 chunk 462 optimal weight: 30.0000 chunk 139 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 HIS A 491 HIS ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** B 761 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN c 24 GLN e 113 HIS g 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 49045 Z= 0.304 Angle : 0.606 7.463 67631 Z= 0.344 Chirality : 0.041 0.154 7586 Planarity : 0.005 0.069 7584 Dihedral : 22.356 174.600 9284 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.55 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 5045 helix: 0.53 (0.12), residues: 1921 sheet: -1.67 (0.20), residues: 659 loop : -1.36 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 300 HIS 0.012 0.001 HIS A 92 PHE 0.029 0.002 PHE B 963 TYR 0.022 0.002 TYR B1092 ARG 0.005 0.000 ARG B 848 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 5.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1287 MET cc_start: 0.7157 (ppp) cc_final: 0.6876 (ppp) REVERT: B 190 MET cc_start: 0.8418 (mmm) cc_final: 0.8022 (tpp) REVERT: B 302 MET cc_start: 0.8329 (mtt) cc_final: 0.7865 (mtp) REVERT: B 1021 MET cc_start: 0.9195 (mpp) cc_final: 0.8927 (mpp) REVERT: W 408 ARG cc_start: 0.1945 (mtt180) cc_final: 0.1226 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 1.1228 time to fit residues: 324.0707 Evaluate side-chains 153 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 429 optimal weight: 50.0000 chunk 293 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 384 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 440 optimal weight: 30.0000 chunk 356 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 463 optimal weight: 50.0000 chunk 130 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN C 25 ASN E 113 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN g 84 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 49045 Z= 0.320 Angle : 0.619 7.528 67631 Z= 0.351 Chirality : 0.042 0.189 7586 Planarity : 0.005 0.061 7584 Dihedral : 22.392 173.164 9284 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.93 % Favored : 91.97 % Rotamer: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.12), residues: 5045 helix: 0.44 (0.12), residues: 1918 sheet: -1.82 (0.20), residues: 668 loop : -1.47 (0.12), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 657 HIS 0.009 0.001 HIS A 700 PHE 0.031 0.002 PHE B 963 TYR 0.028 0.002 TYR B1092 ARG 0.009 0.001 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 159 time to evaluate : 5.542 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: B 190 MET cc_start: 0.8481 (mmm) cc_final: 0.8075 (tpp) REVERT: B 1021 MET cc_start: 0.9202 (mpp) cc_final: 0.8864 (mpp) REVERT: E 122 MET cc_start: 0.7407 (ppp) cc_final: 0.7165 (ppp) REVERT: W 408 ARG cc_start: 0.1739 (mtt180) cc_final: 0.1057 (ttm-80) outliers start: 3 outliers final: 1 residues processed: 162 average time/residue: 1.0763 time to fit residues: 300.1767 Evaluate side-chains 149 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 5.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 9.9990 chunk 464 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 303 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 516 optimal weight: 50.0000 chunk 428 optimal weight: 30.0000 chunk 239 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 170 optimal weight: 40.0000 chunk 271 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 49045 Z= 0.305 Angle : 0.606 7.149 67631 Z= 0.345 Chirality : 0.041 0.151 7586 Planarity : 0.005 0.064 7584 Dihedral : 22.404 176.325 9284 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.33 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.12), residues: 5045 helix: 0.46 (0.12), residues: 1921 sheet: -1.90 (0.19), residues: 671 loop : -1.49 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 657 HIS 0.010 0.001 HIS A 288 PHE 0.030 0.002 PHE B 963 TYR 0.032 0.002 TYR B1092 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 5.829 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: B 190 MET cc_start: 0.8430 (mmm) cc_final: 0.8002 (tpp) REVERT: B 1021 MET cc_start: 0.9197 (mpp) cc_final: 0.8866 (mpp) REVERT: W 408 ARG cc_start: 0.1746 (mtt180) cc_final: 0.1080 (ttm-80) REVERT: f 84 MET cc_start: 0.6691 (ppp) cc_final: 0.6266 (ptt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.0999 time to fit residues: 305.3245 Evaluate side-chains 149 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 5.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 498 optimal weight: 50.0000 chunk 58 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 377 optimal weight: 0.8980 chunk 292 optimal weight: 40.0000 chunk 434 optimal weight: 20.0000 chunk 288 optimal weight: 30.0000 chunk 514 optimal weight: 40.0000 chunk 322 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 overall best weight: 6.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 49045 Z= 0.275 Angle : 0.588 7.154 67631 Z= 0.333 Chirality : 0.041 0.150 7586 Planarity : 0.005 0.080 7584 Dihedral : 22.422 174.201 9284 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.85 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 5045 helix: 0.59 (0.12), residues: 1924 sheet: -1.91 (0.20), residues: 663 loop : -1.46 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 657 HIS 0.008 0.001 HIS A 700 PHE 0.030 0.002 PHE B 963 TYR 0.024 0.001 TYR B1092 ARG 0.005 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 5.492 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: A 850 MET cc_start: 0.7971 (ppp) cc_final: 0.7516 (ppp) REVERT: B 190 MET cc_start: 0.8465 (mmm) cc_final: 0.8038 (tpp) REVERT: B 1021 MET cc_start: 0.9169 (mpp) cc_final: 0.8840 (mpp) REVERT: W 408 ARG cc_start: 0.1701 (mtt180) cc_final: 0.1030 (ttm-80) REVERT: f 84 MET cc_start: 0.6685 (ppp) cc_final: 0.6264 (ptt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.0847 time to fit residues: 302.6538 Evaluate side-chains 151 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 5.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 318 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 327 optimal weight: 50.0000 chunk 350 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 404 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 49045 Z= 0.204 Angle : 0.551 6.810 67631 Z= 0.313 Chirality : 0.040 0.174 7586 Planarity : 0.004 0.077 7584 Dihedral : 22.387 175.612 9284 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 5045 helix: 0.88 (0.12), residues: 1929 sheet: -1.84 (0.20), residues: 668 loop : -1.30 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 12 HIS 0.006 0.001 HIS b 75 PHE 0.020 0.001 PHE B 963 TYR 0.028 0.001 TYR B1092 ARG 0.007 0.000 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 5.550 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: A 614 MET cc_start: 0.9174 (mmm) cc_final: 0.8945 (mmm) REVERT: B 190 MET cc_start: 0.8383 (mmm) cc_final: 0.7944 (tpp) REVERT: B 1021 MET cc_start: 0.9178 (mpp) cc_final: 0.8870 (mpp) REVERT: W 408 ARG cc_start: 0.1713 (mtt180) cc_final: 0.1013 (ttm-80) REVERT: f 84 MET cc_start: 0.6701 (ppp) cc_final: 0.6270 (ptt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 1.0907 time to fit residues: 310.4176 Evaluate side-chains 155 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 5.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 468 optimal weight: 50.0000 chunk 493 optimal weight: 30.0000 chunk 449 optimal weight: 30.0000 chunk 479 optimal weight: 50.0000 chunk 492 optimal weight: 20.0000 chunk 288 optimal weight: 30.0000 chunk 208 optimal weight: 30.0000 chunk 376 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 433 optimal weight: 50.0000 chunk 453 optimal weight: 6.9990 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN B 197 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN c 89 ASN h 92 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 49045 Z= 0.523 Angle : 0.754 9.102 67631 Z= 0.426 Chirality : 0.046 0.184 7586 Planarity : 0.006 0.062 7584 Dihedral : 22.612 174.309 9284 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.96 % Favored : 88.86 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.11), residues: 5045 helix: -0.11 (0.12), residues: 1926 sheet: -2.09 (0.19), residues: 638 loop : -1.95 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP F 146 HIS 0.017 0.002 HIS A 700 PHE 0.046 0.003 PHE B 963 TYR 0.037 0.003 TYR B1092 ARG 0.008 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 5.494 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: A 614 MET cc_start: 0.9365 (mmm) cc_final: 0.9118 (mmm) REVERT: B 1021 MET cc_start: 0.9185 (mpp) cc_final: 0.8838 (mpp) REVERT: W 408 ARG cc_start: 0.1666 (mtt180) cc_final: 0.0972 (ttm-80) REVERT: f 84 MET cc_start: 0.6662 (ppp) cc_final: 0.6256 (ptt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 1.0751 time to fit residues: 297.2567 Evaluate side-chains 149 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 5.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 477 optimal weight: 30.0000 chunk 314 optimal weight: 2.9990 chunk 507 optimal weight: 30.0000 chunk 309 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 352 optimal weight: 7.9990 chunk 532 optimal weight: 40.0000 chunk 489 optimal weight: 40.0000 chunk 423 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 327 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 49045 Z= 0.235 Angle : 0.585 7.129 67631 Z= 0.332 Chirality : 0.041 0.152 7586 Planarity : 0.005 0.079 7584 Dihedral : 22.554 175.021 9284 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.68 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 5045 helix: 0.47 (0.12), residues: 1924 sheet: -1.97 (0.20), residues: 638 loop : -1.62 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 79 HIS 0.016 0.001 HIS G 14 PHE 0.029 0.002 PHE D 112 TYR 0.020 0.001 TYR B 424 ARG 0.008 0.000 ARG B1183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10090 Ramachandran restraints generated. 5045 Oldfield, 0 Emsley, 5045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 5.477 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: B 190 MET cc_start: 0.8511 (mmm) cc_final: 0.8070 (tpp) REVERT: B 1021 MET cc_start: 0.9159 (mpp) cc_final: 0.8804 (mpp) REVERT: D 39 TYR cc_start: 0.6409 (m-80) cc_final: 0.6187 (m-80) REVERT: E 122 MET cc_start: 0.7393 (ppp) cc_final: 0.7088 (ppp) REVERT: W 408 ARG cc_start: 0.1667 (mtt180) cc_final: 0.0989 (ttm-80) REVERT: f 84 MET cc_start: 0.6750 (ppp) cc_final: 0.6399 (ptt) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.1062 time to fit residues: 306.1304 Evaluate side-chains 154 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 5.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 259 optimal weight: 6.9990 chunk 336 optimal weight: 40.0000 chunk 451 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 390 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 435 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.066469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.051570 restraints weight = 1294035.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.052350 restraints weight = 649895.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.052290 restraints weight = 422945.399| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 49045 Z= 0.264 Angle : 0.582 6.621 67631 Z= 0.330 Chirality : 0.041 0.151 7586 Planarity : 0.005 0.059 7584 Dihedral : 22.545 174.708 9284 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.62 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.12), residues: 5045 helix: 0.56 (0.12), residues: 1939 sheet: -1.98 (0.20), residues: 641 loop : -1.59 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 573 HIS 0.008 0.001 HIS A 700 PHE 0.026 0.002 PHE B 963 TYR 0.023 0.001 TYR B1092 ARG 0.007 0.000 ARG B1183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11498.04 seconds wall clock time: 203 minutes 25.17 seconds (12205.17 seconds total)