Starting phenix.real_space_refine on Tue Mar 19 04:11:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbx_32409/03_2024/7wbx_32409.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbx_32409/03_2024/7wbx_32409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbx_32409/03_2024/7wbx_32409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbx_32409/03_2024/7wbx_32409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbx_32409/03_2024/7wbx_32409.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbx_32409/03_2024/7wbx_32409.pdb" } resolution = 4.0 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 310 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 28729 2.51 5 N 8372 2.21 5 O 9507 1.98 5 H 44620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A TYR 853": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 863": "OD1" <-> "OD2" Residue "A PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 134": "OD1" <-> "OD2" Residue "G PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 8": "OD1" <-> "OD2" 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 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 21": "OE1" <-> "OE2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "K ASP 14": "OD1" <-> "OD2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "W PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 91763 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: 4617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4617 Classifications: {'DNA': 145} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 144} Chain breaks: 1 Chain: "P" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 494 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 4738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 4738 Classifications: {'DNA': 150} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 149} 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 71.970 64.553 172.153 1.00101.38 S ATOM 1092 SG CYS A 70 75.435 64.011 173.566 1.00 99.35 S ATOM 1174 SG CYS A 77 74.206 67.573 172.803 1.00 98.48 S ATOM 1652 SG CYS A 107 76.469 73.302 125.030 1.00177.40 S ATOM 1694 SG CYS A 110 78.193 71.012 124.612 1.00194.27 S ATOM 2467 SG CYS A 168 75.464 73.432 122.703 1.00204.23 S ATOM 39789 SG CYS B1163 85.334 59.408 160.342 1.00105.14 S ATOM 39826 SG CYS B1166 83.824 62.407 158.463 1.00107.94 S ATOM 40079 SG CYS B1182 81.621 59.890 160.096 1.00108.01 S ATOM 40125 SG CYS B1185 83.626 58.927 156.966 1.00108.18 S ATOM 42038 SG CYS C 85 87.425 97.728 231.607 1.00133.89 S ATOM 42063 SG CYS C 87 84.049 96.545 230.862 1.00144.74 S ATOM 42122 SG CYS C 91 84.534 99.466 233.228 1.00120.81 S ATOM 42160 SG CYS C 94 85.064 99.917 229.428 1.00119.88 S ATOM 58328 SG CYS I 75 88.367 161.790 148.969 1.00314.03 S ATOM 58368 SG CYS I 78 86.001 163.898 147.795 1.00316.05 S ATOM 58789 SG CYS I 103 88.095 160.045 146.475 1.00280.62 S ATOM 57303 SG CYS I 10 62.579 135.862 115.292 1.00243.56 S ATOM 57624 SG CYS I 29 65.591 134.970 114.251 1.00255.07 S ATOM 57673 SG CYS I 32 63.779 136.694 112.643 1.00257.89 S ATOM 59084 SG CYS J 7 90.372 125.439 209.764 1.00 62.94 S ATOM 59126 SG CYS J 10 92.553 125.316 212.834 1.00 64.01 S ATOM 59680 SG CYS J 44 93.599 127.644 210.010 1.00 58.53 S ATOM 59691 SG CYS J 45 90.655 128.292 212.301 1.00 58.70 S ATOM 62038 SG CYS L 33 49.110 110.459 203.479 1.00119.52 S ATOM 62066 SG CYS L 36 47.406 111.073 206.842 1.00119.64 S ATOM 62281 SG CYS L 50 46.401 108.098 204.762 1.00110.10 S ATOM 62329 SG CYS L 53 45.378 111.445 203.663 1.00107.40 S ATOM 62859 SG CYS M 25 51.923 97.664 119.623 1.00258.92 S ATOM 62909 SG CYS M 28 51.795 94.083 120.442 1.00265.10 S ATOM 63224 SG CYS M 49 54.931 95.532 118.738 1.00254.10 S ATOM 63279 SG CYS M 52 51.904 95.205 116.673 1.00261.67 S ATOM 73583 SG CYS V 12 19.793 80.046 146.910 1.00354.36 S ATOM 73630 SG CYS V 15 21.053 82.067 143.852 1.00345.13 S ATOM 73838 SG CYS V 29 18.188 83.324 146.093 1.00377.12 S ATOM 73877 SG CYS V 32 17.770 80.271 143.736 1.00368.52 S Time building chain proxies: 28.99, per 1000 atoms: 0.32 Number of scatterers: 91763 At special positions: 0 Unit cell: (174.9, 175.96, 251.22, 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 310 15.00 Mg 1 11.99 O 9507 8.00 N 8372 7.00 C 28729 6.00 H 44620 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: 57.16 Conformation dependent library (CDL) restraints added in 6.8 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 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " 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 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " 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 28 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " 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 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: 194 helices and 61 sheets defined 43.1% alpha, 14.6% beta 124 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 31.00 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 128 removed outlier: 4.118A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.892A 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 234 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.968A pdb=" N GLU A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 306 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.824A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 506 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 526 through 536 removed outlier: 3.888A pdb=" N LYS A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.546A pdb=" N PHE A 552 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 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 660 removed outlier: 3.619A pdb=" N CYS A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.537A pdb=" N MET A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 810 through 846 removed outlier: 4.105A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.524A 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 904 through 908 Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.609A pdb=" N LEU A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 948 Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 984 through 997 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: 3.666A 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 removed outlier: 3.617A pdb=" N LEU A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.886A pdb=" N SER A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.657A pdb=" N VAL A1214 " --> pdb=" O THR A1210 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A1222 " --> pdb=" O ILE A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1274 removed outlier: 3.805A pdb=" N ILE A1274 " --> pdb=" O MET A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1322 removed outlier: 3.601A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1342 removed outlier: 3.625A pdb=" N ILE A1338 " --> pdb=" O SER A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 4.037A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1394 Processing helix chain 'A' and resid 1398 through 1406 removed outlier: 3.820A pdb=" N PHE A1405 " --> pdb=" O MET A1401 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A1406 " --> pdb=" O ARG A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 4.105A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1452 through 1456 Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.574A pdb=" N ALA A1461 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 44 removed outlier: 3.560A pdb=" N LEU B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 removed outlier: 4.289A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.629A pdb=" N ALA B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.857A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.502A pdb=" N ILE B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 313 removed outlier: 3.746A pdb=" N LEU B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.988A pdb=" N ARG B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 351 removed outlier: 3.654A pdb=" N LYS B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 430 removed outlier: 3.541A pdb=" N LEU B 405 " --> pdb=" O LEU B 401 " (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 489 removed outlier: 3.555A pdb=" N ARG B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.216A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 585 through 599 removed outlier: 4.051A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.638A pdb=" N ILE B 698 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.857A pdb=" N LEU B 707 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B 708 " --> pdb=" O PRO B 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 703 through 708' Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.833A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.806A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.916A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.009A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.683A pdb=" N LEU B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 817 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.640A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.968A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1063 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.623A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 265 Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.915A pdb=" N ALA D 35 " --> pdb=" O PRO D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 73 Processing helix chain 'D' and resid 85 through 91 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: 3.652A 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 181 removed outlier: 3.940A pdb=" N ILE D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 30 through 35 removed outlier: 3.608A pdb=" N MET E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP E 35 " --> pdb=" O GLN E 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 30 through 35' Processing helix chain 'E' and resid 37 through 46 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: 3.999A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.595A pdb=" N VAL E 126 " --> pdb=" O ILE E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' 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 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.715A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.881A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.747A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 removed outlier: 3.590A pdb=" N LEU H 131 " --> pdb=" O GLY H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.550A pdb=" N ILE I 62 " --> pdb=" O VAL I 59 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY I 63 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.710A pdb=" N ALA J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.631A 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: 4.813A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.515A pdb=" N ARG J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.242A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR K 53 " --> pdb=" O GLU K 49 " (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 27 removed outlier: 3.564A pdb=" N PHE V 24 " --> pdb=" O PRO V 20 " (cutoff:3.500A) 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 Processing helix chain 'W' and resid 213 through 218 removed outlier: 3.507A pdb=" N LEU W 216 " --> pdb=" O PRO W 213 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 removed outlier: 3.660A pdb=" N ILE W 282 " --> pdb=" O LYS W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 310 removed outlier: 4.322A pdb=" N LYS W 307 " --> pdb=" O ILE W 303 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP W 308 " --> pdb=" O VAL W 304 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 450 Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.937A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS a 79 " --> pdb=" O ALA a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 removed outlier: 3.602A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 76 removed outlier: 4.270A 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 21 Processing helix chain 'c' and resid 27 through 37 Processing helix chain 'c' and resid 46 through 74 Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.648A 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 81 Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.615A 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: 3.744A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 removed outlier: 3.533A pdb=" N ILE e 89 " --> pdb=" O GLN e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.713A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 77 removed outlier: 3.578A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.565A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) 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: 3.644A 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 46 Processing helix chain 'h' and resid 52 through 82 Processing helix chain 'h' and resid 87 through 99 removed outlier: 3.872A 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 91 removed outlier: 10.753A pdb=" N LYS A 88 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.275A 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 removed outlier: 3.702A pdb=" N TRP A 183 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 254 removed outlier: 5.334A pdb=" N ALA A 252 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 259 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 254 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 346 removed outlier: 3.670A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 469 through 471 removed outlier: 7.748A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER A 355 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 488 " --> pdb=" O THR A 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 469 through 471 removed outlier: 7.748A pdb=" N PHE A 469 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 353 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU A 471 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER A 355 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 364 through 368 removed outlier: 5.925A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.571A pdb=" N ARG A 435 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.576A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB3, first strand: chain 'A' and resid 566 through 568 removed outlier: 5.893A pdb=" N ILE A 566 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE H 97 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A 568 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL H 12 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 589 through 591 removed outlier: 7.188A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB6, first strand: chain 'A' and resid 850 through 851 removed outlier: 3.525A pdb=" N ARG A 858 " --> pdb=" O MET A 850 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 880 through 883 Processing sheet with id=AB8, first strand: chain 'A' and resid 1285 through 1295 Processing sheet with id=AB9, first strand: chain 'A' and resid 1143 through 1144 Processing sheet with id=AC1, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 4.311A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A1240 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A1194 " --> pdb=" O TYR A1155 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR A1155 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N SER A1150 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU I 47 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR A1152 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A1154 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.455A pdb=" N ILE D 49 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 2 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A1446 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AC4, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.882A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS B 157 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC7, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC8, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AC9, first strand: chain 'B' and resid 214 through 218 removed outlier: 4.244A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 229 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 247 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 262 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 537 through 540 removed outlier: 6.714A pdb=" N GLY B 537 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL B 626 " --> pdb=" O GLY B 537 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER B 539 " --> pdb=" O GLY B 624 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.148A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 572 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE B 574 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 633 through 634 removed outlier: 3.853A pdb=" N GLU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AD5, first strand: chain 'B' and resid 792 through 793 removed outlier: 3.509A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 947 " --> pdb=" O VAL B 905 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 792 through 793 removed outlier: 3.509A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS L 60 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL L 29 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU L 42 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD8, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.646A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.586A pdb=" N GLU B 873 " --> pdb=" O THR B 915 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AE2, first strand: chain 'B' and resid 1159 through 1163 Processing sheet with id=AE3, first strand: chain 'C' and resid 6 through 12 removed outlier: 5.609A pdb=" N VAL C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER C 22 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE C 9 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET C 20 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 6 through 12 removed outlier: 5.609A pdb=" N VAL C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER C 22 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE C 9 " --> pdb=" O MET C 20 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N MET C 20 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 42 through 53 removed outlier: 6.420A pdb=" N ILE C 158 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL C 48 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG C 156 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE C 50 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN C 154 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.473A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.506A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE9, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.638A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AF2, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.584A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 85 through 90 removed outlier: 4.482A pdb=" N GLU G 85 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL G 147 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL G 87 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL G 148 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR G 150 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY G 161 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.080A pdb=" N VAL G 120 " --> pdb=" O MET G 131 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET G 131 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN G 122 " --> pdb=" O ALA G 129 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 137 " --> pdb=" O TYR G 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF6, first strand: chain 'I' and resid 84 through 86 removed outlier: 3.686A pdb=" N PHE I 86 " --> pdb=" O PHE I 100 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 20 through 23 Processing sheet with id=AF8, first strand: chain 'M' and resid 23 through 24 removed outlier: 4.551A pdb=" N PHE M 23 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL M 34 " --> pdb=" O PHE M 23 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU M 46 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP M 39 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AG1, first strand: chain 'V' and resid 82 through 85 removed outlier: 6.869A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER W 261 " --> pdb=" O GLU W 275 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL W 272 " --> pdb=" O VAL W 229 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE W 274 " --> pdb=" O TRP W 227 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP W 227 " --> pdb=" O ILE W 274 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 407 through 408 removed outlier: 4.109A pdb=" N ARG W 407 " --> pdb=" O THR W 415 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR W 415 " --> pdb=" O ARG W 407 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS W 428 " --> pdb=" O LEU W 352 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU W 342 " --> pdb=" O ARG W 351 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS W 353 " --> pdb=" O VAL W 340 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL W 340 " --> pdb=" O LYS W 353 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE W 436 " --> pdb=" O ARG W 327 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 756 through 758 Processing sheet with id=AG4, first strand: chain 'W' and resid 768 through 772 removed outlier: 6.226A pdb=" N VAL W 770 " --> pdb=" O GLU W 781 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU W 781 " --> pdb=" O VAL W 770 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU W 772 " --> pdb=" O ARG W 779 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS W 787 " --> pdb=" O LEU W 782 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG6, first strand: chain 'e' and resid 83 through 84 removed outlier: 7.399A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.045A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 1774 hydrogen bonds defined for protein. 4968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 306 hydrogen bonds 600 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 40.64 Time building geometry restraints manager: 60.26 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: 44536 1.03 - 1.23: 885 1.23 - 1.43: 20023 1.43 - 1.63: 27458 1.63 - 1.82: 342 Bond restraints: 93244 Sorted by residual: bond pdb=" N GLY L 28 " pdb=" CA GLY L 28 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.30e+00 bond pdb=" C LEU B 354 " pdb=" O LEU B 354 " ideal model delta sigma weight residual 1.233 1.245 -0.012 4.80e-03 4.34e+04 6.13e+00 bond pdb=" N SER I 3 " pdb=" CA SER I 3 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N GLU F 71 " pdb=" CA GLU F 71 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N ARG b 23 " pdb=" CA ARG b 23 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 93239 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.14: 1527 104.14 - 111.62: 104662 111.62 - 119.11: 23274 119.11 - 126.59: 37986 126.59 - 134.07: 1342 Bond angle restraints: 168791 Sorted by residual: angle pdb=" C GLN A 526 " pdb=" CA GLN A 526 " pdb=" CB GLN A 526 " ideal model delta sigma weight residual 116.63 111.00 5.63 1.16e+00 7.43e-01 2.36e+01 angle pdb=" C ALA D 10 " pdb=" CA ALA D 10 " pdb=" CB ALA D 10 " ideal model delta sigma weight residual 117.23 110.97 6.26 1.36e+00 5.41e-01 2.12e+01 angle pdb=" N ILE A 61 " pdb=" CA ILE A 61 " pdb=" C ILE A 61 " ideal model delta sigma weight residual 113.47 109.54 3.93 1.01e+00 9.80e-01 1.51e+01 angle pdb=" CB MET A 736 " pdb=" CG MET A 736 " pdb=" SD MET A 736 " ideal model delta sigma weight residual 112.70 124.19 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C ASP C 89 " pdb=" CA ASP C 89 " pdb=" CB ASP C 89 " ideal model delta sigma weight residual 115.89 111.41 4.48 1.32e+00 5.74e-01 1.15e+01 ... (remaining 168786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 40139 35.72 - 71.44: 2221 71.44 - 107.16: 100 107.16 - 142.88: 2 142.88 - 178.60: 6 Dihedral angle restraints: 42468 sinusoidal: 25456 harmonic: 17012 Sorted by residual: dihedral pdb=" CA ARG e 63 " pdb=" C ARG e 63 " pdb=" N LYS e 64 " pdb=" CA LYS e 64 " ideal model delta harmonic sigma weight residual -180.00 -156.24 -23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" C4' DT N -64 " pdb=" C3' DT N -64 " pdb=" O3' DT N -64 " pdb=" P DT N -63 " ideal model delta sinusoidal sigma weight residual 220.00 41.40 178.60 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG N -45 " pdb=" C3' DG N -45 " pdb=" O3' DG N -45 " pdb=" P DG N -44 " ideal model delta sinusoidal sigma weight residual 220.00 50.67 169.33 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 42465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6416 0.055 - 0.111: 971 0.111 - 0.166: 125 0.166 - 0.221: 1 0.221 - 0.276: 1 Chirality restraints: 7514 Sorted by residual: chirality pdb=" P DC T 55 " pdb=" OP1 DC T 55 " pdb=" OP2 DC T 55 " pdb=" O5' DC T 55 " both_signs ideal model delta sigma weight residual True 2.35 -2.62 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ARG B 337 " pdb=" N ARG B 337 " pdb=" C ARG B 337 " pdb=" CB ARG B 337 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA ILE M 15 " pdb=" N ILE M 15 " pdb=" C ILE M 15 " pdb=" CB ILE M 15 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 7511 not shown) Planarity restraints: 12665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG a 42 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO a 43 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO a 43 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO a 43 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN W 784 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO W 785 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO W 785 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO W 785 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 999 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO B1000 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B1000 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B1000 " -0.023 5.00e-02 4.00e+02 ... (remaining 12662 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 1309 2.03 - 2.67: 135102 2.67 - 3.32: 266537 3.32 - 3.96: 341658 3.96 - 4.60: 533678 Nonbonded interactions: 1278284 Sorted by model distance: nonbonded pdb=" HB3 CYS A 168 " pdb="ZN ZN A1802 " model vdw 1.388 1.544 nonbonded pdb=" HB3 CYS I 103 " pdb="ZN ZN I 201 " model vdw 1.411 1.544 nonbonded pdb=" OD1 ASN A1040 " pdb=" H ALA A1043 " model vdw 1.506 1.850 nonbonded pdb=" OD1 ASP A 130 " pdb=" H LYS A 133 " model vdw 1.507 1.850 nonbonded pdb=" OE1 GLU A 796 " pdb=" H GLU A 796 " model vdw 1.515 1.850 ... (remaining 1278279 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.990 Extract box with map and model: 11.400 Check model and map are aligned: 1.050 Set scattering table: 0.670 Process input model: 266.280 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 287.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 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 0.050 48624 Z= 0.273 Angle : 0.581 11.492 66980 Z= 0.340 Chirality : 0.040 0.276 7514 Planarity : 0.004 0.061 7566 Dihedral : 18.617 178.603 19319 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % 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: -0.13 (0.12), residues: 5045 helix: 1.12 (0.12), residues: 1897 sheet: -0.89 (0.21), residues: 662 loop : -0.77 (0.13), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 459 HIS 0.008 0.001 HIS A 300 PHE 0.019 0.001 PHE A1222 TYR 0.019 0.001 TYR B 797 ARG 0.006 0.000 ARG B 904 *********************** 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 152 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 5.166 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: A 84 MET cc_start: 0.7336 (tmm) cc_final: 0.6631 (tmm) REVERT: A 305 MET cc_start: 0.8638 (mmm) cc_final: 0.8265 (mmm) REVERT: A 709 MET cc_start: 0.8367 (mtp) cc_final: 0.7697 (mtp) REVERT: A 850 MET cc_start: 0.8699 (ttp) cc_final: 0.8049 (ttt) REVERT: B 702 MET cc_start: 0.8858 (tpp) cc_final: 0.8506 (tpp) REVERT: F 103 MET cc_start: 0.8169 (ppp) cc_final: 0.7537 (ppp) REVERT: J 48 MET cc_start: 0.8284 (mtt) cc_final: 0.8081 (mtp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 1.1840 time to fit residues: 304.3314 Evaluate side-chains 143 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 5.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 450 optimal weight: 10.0000 chunk 403 optimal weight: 40.0000 chunk 224 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 417 optimal weight: 30.0000 chunk 161 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 310 optimal weight: 0.0470 chunk 484 optimal weight: 8.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 802 HIS c 38 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 48624 Z= 0.254 Angle : 0.565 6.361 66980 Z= 0.323 Chirality : 0.041 0.188 7514 Planarity : 0.004 0.054 7566 Dihedral : 21.625 178.719 9092 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 0.13 % Allowed : 1.72 % Favored : 98.14 % 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: 0.00 (0.12), residues: 5045 helix: 1.23 (0.12), residues: 1929 sheet: -0.79 (0.20), residues: 688 loop : -0.72 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 956 HIS 0.004 0.001 HIS b 75 PHE 0.012 0.001 PHE E 28 TYR 0.014 0.001 TYR B 295 ARG 0.005 0.000 ARG B 904 *********************** 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 149 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 5.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7291 (tmm) cc_final: 0.6571 (tmm) REVERT: A 850 MET cc_start: 0.8711 (ttp) cc_final: 0.7985 (ttt) REVERT: B 593 MET cc_start: 0.7864 (mmp) cc_final: 0.7645 (mmp) REVERT: B 702 MET cc_start: 0.8886 (tpp) cc_final: 0.8549 (tpp) REVERT: F 103 MET cc_start: 0.8272 (ppp) cc_final: 0.7933 (ppp) outliers start: 6 outliers final: 3 residues processed: 145 average time/residue: 1.1202 time to fit residues: 275.9592 Evaluate side-chains 147 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 5.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain h residue 56 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 268 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 402 optimal weight: 30.0000 chunk 329 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 484 optimal weight: 6.9990 chunk 523 optimal weight: 6.9990 chunk 431 optimal weight: 30.0000 chunk 480 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 389 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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** D 99 ASN W 802 HIS ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 48624 Z= 0.311 Angle : 0.572 8.442 66980 Z= 0.324 Chirality : 0.040 0.160 7514 Planarity : 0.004 0.051 7566 Dihedral : 21.745 178.108 9092 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.69 % Favored : 94.27 % Rotamer: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.15 % 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: -0.16 (0.12), residues: 5045 helix: 1.18 (0.12), residues: 1936 sheet: -0.98 (0.20), residues: 686 loop : -0.86 (0.13), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 71 HIS 0.005 0.001 HIS A 400 PHE 0.014 0.001 PHE E 28 TYR 0.015 0.001 TYR B 295 ARG 0.005 0.000 ARG B 995 *********************** 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 152 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 5.360 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 84 MET cc_start: 0.7305 (tmm) cc_final: 0.6560 (tmm) REVERT: A 548 MET cc_start: 0.8791 (mtm) cc_final: 0.8577 (mtm) REVERT: A 635 MET cc_start: 0.8568 (tpt) cc_final: 0.8326 (tpt) REVERT: A 850 MET cc_start: 0.8610 (ttp) cc_final: 0.7901 (ttt) REVERT: B 245 MET cc_start: 0.9095 (ppp) cc_final: 0.8804 (ptm) REVERT: B 593 MET cc_start: 0.8000 (mmp) cc_final: 0.7694 (mmp) REVERT: B 1169 MET cc_start: 0.7336 (pmm) cc_final: 0.7121 (pmm) REVERT: V 13 MET cc_start: 0.1021 (tpt) cc_final: 0.0593 (tpt) outliers start: 6 outliers final: 4 residues processed: 150 average time/residue: 1.0877 time to fit residues: 275.9980 Evaluate side-chains 150 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 5.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain h residue 56 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 479 optimal weight: 40.0000 chunk 364 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 325 optimal weight: 10.0000 chunk 486 optimal weight: 30.0000 chunk 515 optimal weight: 30.0000 chunk 254 optimal weight: 5.9990 chunk 461 optimal weight: 30.0000 chunk 138 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** A 291 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** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 48624 Z= 0.226 Angle : 0.532 8.667 66980 Z= 0.301 Chirality : 0.040 0.158 7514 Planarity : 0.004 0.048 7566 Dihedral : 21.715 177.413 9092 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 0.20 % Allowed : 4.50 % Favored : 95.30 % 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: 0.05 (0.12), residues: 5045 helix: 1.40 (0.12), residues: 1939 sheet: -0.99 (0.20), residues: 676 loop : -0.76 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1307 HIS 0.005 0.001 HIS W 802 PHE 0.012 0.001 PHE B 963 TYR 0.013 0.001 TYR B 295 ARG 0.005 0.000 ARG E 25 *********************** 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 157 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 5.150 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 84 MET cc_start: 0.7256 (tmm) cc_final: 0.6495 (tmm) REVERT: A 548 MET cc_start: 0.8695 (mtm) cc_final: 0.8448 (mtm) REVERT: A 635 MET cc_start: 0.8621 (tpt) cc_final: 0.8385 (tpt) REVERT: A 850 MET cc_start: 0.8691 (ttp) cc_final: 0.7919 (ttt) REVERT: B 593 MET cc_start: 0.8021 (mmp) cc_final: 0.7778 (mmp) REVERT: B 1169 MET cc_start: 0.7523 (pmm) cc_final: 0.7289 (pmm) REVERT: V 13 MET cc_start: 0.0978 (tpt) cc_final: 0.0545 (tpt) outliers start: 9 outliers final: 6 residues processed: 154 average time/residue: 1.1482 time to fit residues: 294.4545 Evaluate side-chains 154 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 5.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain h residue 56 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 429 optimal weight: 50.0000 chunk 292 optimal weight: 20.0000 chunk 7 optimal weight: 0.1980 chunk 383 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 439 optimal weight: 7.9990 chunk 356 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 462 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 48624 Z= 0.302 Angle : 0.562 7.429 66980 Z= 0.316 Chirality : 0.040 0.149 7514 Planarity : 0.004 0.046 7566 Dihedral : 21.723 176.779 9092 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.34 % Favored : 93.62 % Rotamer: Outliers : 0.40 % Allowed : 5.68 % Favored : 93.91 % 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: -0.11 (0.12), residues: 5045 helix: 1.29 (0.12), residues: 1943 sheet: -1.10 (0.20), residues: 668 loop : -0.87 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.007 0.001 HIS A 787 PHE 0.013 0.001 PHE B 617 TYR 0.015 0.001 TYR B 295 ARG 0.005 0.000 ARG C 33 *********************** 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 164 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 5.214 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 635 MET cc_start: 0.8715 (tpt) cc_final: 0.8416 (tpt) REVERT: A 850 MET cc_start: 0.8618 (ttp) cc_final: 0.7807 (ttt) REVERT: B 245 MET cc_start: 0.9071 (ppp) cc_final: 0.8818 (ptm) REVERT: E 122 MET cc_start: 0.8207 (tmm) cc_final: 0.7991 (tmm) REVERT: J 48 MET cc_start: 0.8297 (mtt) cc_final: 0.8057 (mtt) REVERT: V 13 MET cc_start: 0.1081 (tpt) cc_final: 0.0617 (tpt) outliers start: 18 outliers final: 12 residues processed: 161 average time/residue: 1.1116 time to fit residues: 299.6018 Evaluate side-chains 158 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 5.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain h residue 56 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 173 optimal weight: 8.9990 chunk 463 optimal weight: 40.0000 chunk 101 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 515 optimal weight: 0.0030 chunk 428 optimal weight: 30.0000 chunk 238 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 170 optimal weight: 30.0000 chunk 270 optimal weight: 9.9990 overall best weight: 5.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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** C 64 HIS W 802 HIS ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 48624 Z= 0.255 Angle : 0.537 7.416 66980 Z= 0.303 Chirality : 0.040 0.150 7514 Planarity : 0.004 0.045 7566 Dihedral : 21.689 175.942 9092 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 0.38 % Allowed : 6.44 % Favored : 93.18 % 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: -0.01 (0.12), residues: 5045 helix: 1.43 (0.12), residues: 1943 sheet: -1.07 (0.20), residues: 673 loop : -0.85 (0.13), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1307 HIS 0.006 0.001 HIS A 787 PHE 0.014 0.001 PHE B 963 TYR 0.014 0.001 TYR B 295 ARG 0.004 0.000 ARG B 904 *********************** 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 164 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 5.184 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: A 84 MET cc_start: 0.7259 (tmm) cc_final: 0.6529 (tmm) REVERT: A 635 MET cc_start: 0.8724 (tpt) cc_final: 0.8425 (tpt) REVERT: A 850 MET cc_start: 0.8791 (ttp) cc_final: 0.8022 (ttt) REVERT: E 122 MET cc_start: 0.8210 (tmm) cc_final: 0.7988 (tmm) outliers start: 17 outliers final: 13 residues processed: 161 average time/residue: 1.1364 time to fit residues: 310.4526 Evaluate side-chains 160 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 5.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain h residue 56 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 497 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 293 optimal weight: 40.0000 chunk 376 optimal weight: 0.7980 chunk 291 optimal weight: 30.0000 chunk 434 optimal weight: 30.0000 chunk 287 optimal weight: 30.0000 chunk 513 optimal weight: 20.0000 chunk 321 optimal weight: 8.9990 chunk 313 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 overall best weight: 5.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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** B 776 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 48624 Z= 0.267 Angle : 0.542 8.541 66980 Z= 0.304 Chirality : 0.040 0.148 7514 Planarity : 0.004 0.043 7566 Dihedral : 21.648 175.552 9092 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.09 % Rotamer: Outliers : 0.38 % Allowed : 7.00 % Favored : 92.62 % 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: -0.02 (0.12), residues: 5045 helix: 1.44 (0.12), residues: 1945 sheet: -1.10 (0.20), residues: 681 loop : -0.86 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.005 0.001 HIS A 787 PHE 0.011 0.001 PHE C 178 TYR 0.014 0.001 TYR B 295 ARG 0.004 0.000 ARG A 964 *********************** 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 164 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 5.285 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 635 MET cc_start: 0.8731 (tpt) cc_final: 0.8403 (tpt) REVERT: A 850 MET cc_start: 0.8774 (ttp) cc_final: 0.8015 (ttt) REVERT: B 245 MET cc_start: 0.9109 (ppp) cc_final: 0.8811 (ptm) REVERT: J 48 MET cc_start: 0.8311 (mtt) cc_final: 0.7963 (mtt) outliers start: 17 outliers final: 13 residues processed: 160 average time/residue: 1.1105 time to fit residues: 299.6734 Evaluate side-chains 160 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 5.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain h residue 56 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 317 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 326 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 403 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48624 Z= 0.210 Angle : 0.522 10.071 66980 Z= 0.292 Chirality : 0.040 0.147 7514 Planarity : 0.004 0.044 7566 Dihedral : 21.604 174.959 9092 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 0.31 % Allowed : 7.41 % Favored : 92.28 % 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: 0.18 (0.12), residues: 5045 helix: 1.65 (0.12), residues: 1945 sheet: -1.05 (0.20), residues: 680 loop : -0.77 (0.13), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.005 0.001 HIS B 984 PHE 0.012 0.001 PHE B 963 TYR 0.012 0.001 TYR B 295 ARG 0.004 0.000 ARG A 964 *********************** 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 160 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 5.186 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: A 84 MET cc_start: 0.7231 (tmm) cc_final: 0.6494 (tmm) REVERT: A 635 MET cc_start: 0.8741 (tpt) cc_final: 0.8416 (tpt) REVERT: A 850 MET cc_start: 0.8778 (ttp) cc_final: 0.7999 (ttt) REVERT: A 1439 MET cc_start: 0.9084 (ppp) cc_final: 0.8758 (ppp) outliers start: 14 outliers final: 12 residues processed: 156 average time/residue: 1.1143 time to fit residues: 293.6880 Evaluate side-chains 158 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 5.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain h residue 56 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 467 optimal weight: 50.0000 chunk 492 optimal weight: 50.0000 chunk 449 optimal weight: 50.0000 chunk 478 optimal weight: 50.0000 chunk 288 optimal weight: 50.0000 chunk 208 optimal weight: 40.0000 chunk 375 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 432 optimal weight: 40.0000 chunk 452 optimal weight: 10.0000 chunk 477 optimal weight: 6.9990 overall best weight: 13.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 48624 Z= 0.570 Angle : 0.710 9.794 66980 Z= 0.397 Chirality : 0.045 0.188 7514 Planarity : 0.005 0.051 7566 Dihedral : 21.789 174.219 9092 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.60 % Favored : 91.34 % Rotamer: Outliers : 0.43 % Allowed : 7.92 % Favored : 91.65 % 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: -0.95 (0.12), residues: 5045 helix: 0.64 (0.12), residues: 1937 sheet: -1.42 (0.19), residues: 696 loop : -1.43 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 18 HIS 0.008 0.002 HIS A 660 PHE 0.029 0.002 PHE B 617 TYR 0.023 0.002 TYR B 295 ARG 0.009 0.001 ARG C 33 *********************** 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 164 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 5.197 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: A 548 MET cc_start: 0.8778 (mtm) cc_final: 0.8379 (mtm) REVERT: A 635 MET cc_start: 0.8825 (tpt) cc_final: 0.8471 (tpt) REVERT: A 850 MET cc_start: 0.8679 (ttp) cc_final: 0.7870 (ttt) REVERT: A 1204 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6999 (ppp) REVERT: B 245 MET cc_start: 0.9194 (ppp) cc_final: 0.8840 (ptm) outliers start: 19 outliers final: 15 residues processed: 159 average time/residue: 1.1080 time to fit residues: 298.5966 Evaluate side-chains 160 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain V residue 25 MET Chi-restraints excluded: chain h residue 56 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 314 optimal weight: 0.9990 chunk 506 optimal weight: 30.0000 chunk 308 optimal weight: 0.0000 chunk 240 optimal weight: 1.9990 chunk 351 optimal weight: 5.9990 chunk 531 optimal weight: 20.0000 chunk 488 optimal weight: 7.9990 chunk 422 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 326 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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** W 271 HIS ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 48624 Z= 0.159 Angle : 0.539 11.323 66980 Z= 0.297 Chirality : 0.040 0.152 7514 Planarity : 0.004 0.045 7566 Dihedral : 21.665 173.103 9092 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 0.25 % Allowed : 8.17 % Favored : 91.59 % 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: 0.04 (0.12), residues: 5045 helix: 1.58 (0.12), residues: 1931 sheet: -1.19 (0.19), residues: 695 loop : -0.86 (0.13), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 183 HIS 0.005 0.001 HIS B 984 PHE 0.011 0.001 PHE G 3 TYR 0.014 0.001 TYR J 62 ARG 0.005 0.000 ARG A 470 ********************** 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 157 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 5.194 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: A 84 MET cc_start: 0.7259 (tmm) cc_final: 0.6523 (tmm) REVERT: A 548 MET cc_start: 0.9022 (mtm) cc_final: 0.8712 (mtm) REVERT: A 635 MET cc_start: 0.8711 (tpt) cc_final: 0.8456 (tpt) REVERT: A 850 MET cc_start: 0.8668 (ttp) cc_final: 0.7894 (ttt) REVERT: A 1204 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6863 (ppp) REVERT: A 1439 MET cc_start: 0.9064 (ppp) cc_final: 0.8791 (ppp) REVERT: B 245 MET cc_start: 0.9139 (ppp) cc_final: 0.8761 (ptm) outliers start: 11 outliers final: 10 residues processed: 152 average time/residue: 1.1111 time to fit residues: 283.8224 Evaluate side-chains 156 residues out of total 4469 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 5.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 1204 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain h residue 56 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 335 optimal weight: 40.0000 chunk 450 optimal weight: 30.0000 chunk 129 optimal weight: 7.9990 chunk 389 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 423 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 434 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 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** ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 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 = 0.4146 r_free = 0.4146 target = 0.070826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.051758 restraints weight = 1067558.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.052686 restraints weight = 503227.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.052252 restraints weight = 317848.159| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 48624 Z= 0.317 Angle : 0.572 10.260 66980 Z= 0.318 Chirality : 0.040 0.149 7514 Planarity : 0.004 0.044 7566 Dihedral : 21.651 173.559 9092 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.68 % Favored : 93.28 % Rotamer: Outliers : 0.27 % Allowed : 8.26 % Favored : 91.47 % 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: -0.17 (0.12), residues: 5045 helix: 1.39 (0.12), residues: 1941 sheet: -1.27 (0.19), residues: 706 loop : -0.98 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 HIS 0.005 0.001 HIS B 736 PHE 0.015 0.001 PHE B 617 TYR 0.016 0.001 TYR B 295 ARG 0.006 0.000 ARG A 964 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10580.54 seconds wall clock time: 187 minutes 25.60 seconds (11245.60 seconds total)