Starting phenix.real_space_refine on Mon Mar 25 07:52:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j50_0675/03_2024/6j50_0675.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j50_0675/03_2024/6j50_0675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j50_0675/03_2024/6j50_0675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j50_0675/03_2024/6j50_0675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j50_0675/03_2024/6j50_0675.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j50_0675/03_2024/6j50_0675.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 9 6.06 5 P 348 5.49 5 Mg 1 5.21 5 S 208 5.16 5 C 28785 2.51 5 N 8440 2.21 5 O 9631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1129": "OD1" <-> "OD2" Residue "A PHE 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1200": "OD1" <-> "OD2" Residue "A PHE 1335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1183": "NH1" <-> "NH2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 181": "OD1" <-> "OD2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 6": "NH1" <-> "NH2" Residue "K PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 777": "NH1" <-> "NH2" Residue "W PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47422 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 11139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1414, 11139 Classifications: {'peptide': 1414} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1345} Chain breaks: 5 Chain: "B" Number of atoms: 9228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9228 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 52, 'TRANS': 1104} Chain breaks: 5 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1314 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2610 Classifications: {'DNA': 128} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 127} Chain: "N" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2527 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain breaks: 1 Chain: "V" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 792 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "W" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2226 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 4 Chain: "a" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 797 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "0" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "1" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 835 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} 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: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 76.238 61.757 139.711 1.00103.22 S ATOM 549 SG CYS A 70 79.699 60.875 140.690 1.00 94.73 S ATOM 594 SG CYS A 77 78.587 64.473 141.120 1.00 74.48 S ATOM 829 SG CYS A 107 81.245 82.810 96.354 1.00142.68 S ATOM 851 SG CYS A 110 82.599 79.436 95.768 1.00152.38 S ATOM 1245 SG CYS A 168 79.368 82.750 93.315 1.00155.44 S ATOM 19899 SG CYS B1163 90.106 61.148 127.149 1.00 76.06 S ATOM 19917 SG CYS B1166 88.300 64.499 125.920 1.00 77.90 S ATOM 20040 SG CYS B1182 86.303 61.037 127.107 1.00108.37 S ATOM 20063 SG CYS B1185 88.540 61.189 123.779 1.00109.59 S ATOM 21008 SG CYS C 85 88.187 78.361 206.166 1.00126.06 S ATOM 21056 SG CYS C 91 83.919 79.309 207.844 1.00108.11 S ATOM 21079 SG CYS C 94 85.470 81.610 204.308 1.00108.09 S ATOM 29187 SG CYS I 78 85.261 167.468 141.945 1.00173.59 S ATOM 29403 SG CYS I 103 85.482 163.824 141.498 1.00166.64 S ATOM 28803 SG CYS I 29 67.381 145.914 101.592 1.00154.71 S ATOM 28828 SG CYS I 32 64.427 148.185 99.873 1.00153.57 S ATOM 29544 SG CYS J 7 90.149 111.568 192.642 1.00 34.60 S ATOM 29567 SG CYS J 10 92.589 111.039 195.322 1.00 33.65 S ATOM 29843 SG CYS J 44 93.574 113.857 193.335 1.00 40.97 S ATOM 29849 SG CYS J 45 90.754 113.906 196.233 1.00 40.49 S ATOM 31011 SG CYS L 33 49.236 96.578 181.722 1.00114.61 S ATOM 31026 SG CYS L 36 47.178 97.026 184.900 1.00124.33 S ATOM 31136 SG CYS L 50 46.595 94.188 181.928 1.00122.63 S ATOM 31160 SG CYS L 53 46.153 98.161 180.721 1.00130.70 S ATOM 36834 SG CYS V 12 24.020 81.316 116.261 1.00 34.75 S ATOM 36958 SG CYS V 29 22.052 84.700 115.787 1.00 18.00 S Time building chain proxies: 24.81, per 1000 atoms: 0.52 Number of scatterers: 47422 At special positions: 0 Unit cell: (177.31, 178.8, 230.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 208 16.00 P 348 15.00 Mg 1 11.99 O 9631 8.00 N 8440 7.00 C 28785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.85 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " 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 B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " Number of angles added : 21 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9466 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 60 sheets defined 43.3% alpha, 17.2% beta 150 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 18.16 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 removed outlier: 3.653A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.559A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.699A 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 244 through 248 Processing helix chain 'A' and resid 261 through 279 removed outlier: 3.511A pdb=" N GLN A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.621A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.587A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 removed outlier: 3.608A pdb=" N GLU A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) 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 475 through 480 removed outlier: 3.717A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.502A pdb=" N ALA A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.519A pdb=" N LYS A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.947A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.958A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.753A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.583A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 removed outlier: 3.683A pdb=" N LEU A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 removed outlier: 3.588A pdb=" N ILE A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.738A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.769A 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 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 904 through 908 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.627A pdb=" N VAL A 913 " --> pdb=" O LYS A 910 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 914' Processing helix chain 'A' and resid 923 through 947 removed outlier: 3.993A pdb=" N GLU A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 973 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.632A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1035 Processing helix chain 'A' and resid 1040 through 1058 removed outlier: 3.600A pdb=" N GLN A1056 " --> pdb=" O GLU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.594A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.546A pdb=" N ALA A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.773A 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 1223 removed outlier: 3.725A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1272 removed outlier: 3.897A pdb=" N LYS A1264 " --> pdb=" O ASP A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.629A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.565A pdb=" N SER A1340 " --> pdb=" O VAL A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1362 removed outlier: 3.582A pdb=" N SER A1349 " --> pdb=" O GLU A1345 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A1362 " --> pdb=" O VAL A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1380 removed outlier: 4.107A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.664A 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 1449 through 1454 removed outlier: 3.700A pdb=" N THR A1454 " --> pdb=" O GLU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1456 No H-bonds generated for 'chain 'A' and resid 1455 through 1456' Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.591A pdb=" N TYR A1460 " --> pdb=" O PRO A1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 44 removed outlier: 3.715A pdb=" N SER B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.603A pdb=" N LEU B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 312 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.642A pdb=" N ILE B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 4.262A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) 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 429 removed outlier: 3.908A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (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: 3.561A 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 544 through 554 Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.690A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 600 removed outlier: 3.851A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 683 removed outlier: 3.636A pdb=" N LEU B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 682 " --> pdb=" O TRP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.699A pdb=" N GLU B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.578A pdb=" N GLN B 708 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.910A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 768 " --> pdb=" O SER B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.918A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.508A pdb=" N LEU B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) 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 1141 Processing helix chain 'B' and resid 1143 through 1151 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 removed outlier: 3.742A pdb=" N LEU C 68 " --> pdb=" O HIS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.697A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.504A pdb=" N GLU C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 removed outlier: 3.577A pdb=" N LEU D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.522A pdb=" N VAL D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.507A pdb=" N ILE D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.773A pdb=" N THR D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.914A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 167' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 removed outlier: 3.506A pdb=" N ARG E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 127 removed outlier: 3.723A pdb=" N ILE E 123 " --> pdb=" O ASN E 120 " (cutoff:3.500A) Proline residue: E 124 - end of helix removed outlier: 4.165A pdb=" N SER E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.506A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.597A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.510A pdb=" N ILE G 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.622A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.931A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.938A pdb=" N ARG J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.955A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.616A pdb=" N ILE K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 27 removed outlier: 3.725A 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: 3.884A pdb=" N ILE W 218 " --> pdb=" O ARG W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 279 through 287 Processing helix chain 'W' and resid 302 through 304 No H-bonds generated for 'chain 'W' and resid 302 through 304' Processing helix chain 'W' and resid 305 through 310 removed outlier: 3.618A pdb=" N LEU W 309 " --> pdb=" O GLU W 305 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 305 through 310' 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 removed outlier: 3.818A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.977A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.736A pdb=" N ILE a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.855A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 50 through 77 Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.605A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 74 Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.726A pdb=" N LEU c 83 " --> pdb=" O ILE c 79 " (cutoff:3.500A) removed outlier: 3.767A 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 80 Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.668A pdb=" N ILE d 91 " --> pdb=" O THR d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.902A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 55 Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.826A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.653A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 77 Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 removed outlier: 3.565A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.466A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.735A 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 91 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: 3.711A 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 82 through 91 removed outlier: 6.893A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.763A pdb=" N GLY A 184 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 201 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TRP A 186 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU A 199 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.588A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.760A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.559A pdb=" N SER A 349 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.833A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 406 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.757A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.467A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 589 through 591 removed outlier: 7.037A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB4, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.837A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB6, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 4.195A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 7.229A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 3.581A pdb=" N ARG A1243 " --> pdb=" O PHE A1227 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N SER A1150 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU I 47 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A1152 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE A1154 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.189A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N HIS B 157 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC3, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC4, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.514A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.038A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC8, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.766A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.882A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.882A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE L 40 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.046A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.555A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.823A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.870A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.927A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.779A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.553A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.643A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE G 45 " --> pdb=" O TRP G 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.522A pdb=" N PHE G 2 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE7, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.228A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.637A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 152 through 154 Processing sheet with id=AF1, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.865A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY G 161 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU G 106 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL G 143 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.485A pdb=" N VAL G 120 " --> pdb=" O MET G 131 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET G 131 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.525A pdb=" N SER I 71 " --> pdb=" O CYS I 83 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF7, first strand: chain 'V' and resid 54 through 60 removed outlier: 6.900A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 259 through 263 removed outlier: 3.757A pdb=" N SER W 261 " --> pdb=" O GLU W 275 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 407 through 410 removed outlier: 6.541A pdb=" N PHE W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS W 353 " --> pdb=" O VAL W 340 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL W 340 " --> pdb=" O LYS W 353 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 788 through 792 removed outlier: 6.691A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.674A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG4, first strand: chain 'e' and resid 83 through 84 removed outlier: 7.459A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.670A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'g' and resid 77 through 78 1830 hydrogen bonds defined for protein. 5070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 29.56 Time building geometry restraints manager: 21.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11154 1.33 - 1.45: 11744 1.45 - 1.57: 25065 1.57 - 1.70: 692 1.70 - 1.82: 336 Bond restraints: 48991 Sorted by residual: bond pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 1.335 1.431 -0.097 1.19e-02 7.06e+03 6.59e+01 bond pdb=" C1' G P -1 " pdb=" N9 G P -1 " ideal model delta sigma weight residual 1.475 1.362 0.113 1.50e-02 4.44e+03 5.66e+01 bond pdb=" C1' C P 4 " pdb=" N1 C P 4 " ideal model delta sigma weight residual 1.480 1.592 -0.112 1.50e-02 4.44e+03 5.56e+01 bond pdb=" C1' G P 2 " pdb=" N9 G P 2 " ideal model delta sigma weight residual 1.475 1.363 0.112 1.50e-02 4.44e+03 5.56e+01 bond pdb=" CA ILE W 440 " pdb=" C ILE W 440 " ideal model delta sigma weight residual 1.521 1.431 0.090 1.21e-02 6.83e+03 5.52e+01 ... (remaining 48986 not shown) Histogram of bond angle deviations from ideal: 92.30 - 100.71: 309 100.71 - 109.13: 8236 109.13 - 117.54: 29151 117.54 - 125.95: 28372 125.95 - 134.36: 1575 Bond angle restraints: 67643 Sorted by residual: angle pdb=" N GLN B 63 " pdb=" CA GLN B 63 " pdb=" C GLN B 63 " ideal model delta sigma weight residual 108.26 92.30 15.96 1.66e+00 3.63e-01 9.24e+01 angle pdb=" CA PRO W 389 " pdb=" N PRO W 389 " pdb=" CD PRO W 389 " ideal model delta sigma weight residual 112.00 99.54 12.46 1.40e+00 5.10e-01 7.92e+01 angle pdb=" N GLN B 63 " pdb=" CA GLN B 63 " pdb=" CB GLN B 63 " ideal model delta sigma weight residual 110.77 96.81 13.96 1.63e+00 3.76e-01 7.33e+01 angle pdb=" O CYS V 29 " pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 121.31 114.26 7.05 8.50e-01 1.38e+00 6.88e+01 angle pdb=" C ARG W 388 " pdb=" N PRO W 389 " pdb=" CA PRO W 389 " ideal model delta sigma weight residual 119.84 128.72 -8.88 1.25e+00 6.40e-01 5.05e+01 ... (remaining 67638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 26981 34.96 - 69.93: 1943 69.93 - 104.89: 73 104.89 - 139.85: 9 139.85 - 174.81: 2 Dihedral angle restraints: 29008 sinusoidal: 14349 harmonic: 14659 Sorted by residual: dihedral pdb=" N GLN B 63 " pdb=" C GLN B 63 " pdb=" CA GLN B 63 " pdb=" CB GLN B 63 " ideal model delta harmonic sigma weight residual 122.80 98.12 24.68 0 2.50e+00 1.60e-01 9.75e+01 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 -142.24 -37.76 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA ARG a 63 " pdb=" C ARG a 63 " pdb=" N LYS a 64 " pdb=" CA LYS a 64 " ideal model delta harmonic sigma weight residual -180.00 -143.74 -36.26 0 5.00e+00 4.00e-02 5.26e+01 ... (remaining 29005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 7150 0.130 - 0.261: 420 0.261 - 0.391: 12 0.391 - 0.521: 2 0.521 - 0.651: 2 Chirality restraints: 7586 Sorted by residual: chirality pdb=" CA GLN B 63 " pdb=" N GLN B 63 " pdb=" C GLN B 63 " pdb=" CB GLN B 63 " both_signs ideal model delta sigma weight residual False 2.51 3.16 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.58 2.00e-01 2.50e+01 8.49e+00 chirality pdb=" CA TYR B 811 " pdb=" N TYR B 811 " pdb=" C TYR B 811 " pdb=" CB TYR B 811 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 7583 not shown) Planarity restraints: 7515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 336 " -0.030 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C ILE B 336 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE B 336 " -0.039 2.00e-02 2.50e+03 pdb=" N ARG B 337 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 88 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU C 88 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP C 89 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 89 " -0.019 2.00e-02 2.50e+03 3.67e-02 1.34e+01 pdb=" C ASP C 89 " 0.063 2.00e-02 2.50e+03 pdb=" O ASP C 89 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR C 90 " -0.022 2.00e-02 2.50e+03 ... (remaining 7512 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 184 2.45 - 3.06: 28843 3.06 - 3.67: 72720 3.67 - 4.29: 107904 4.29 - 4.90: 169970 Nonbonded interactions: 379621 Sorted by model distance: nonbonded pdb=" N1 DA T 23 " pdb=" C2 DG N -22 " model vdw 1.832 3.340 nonbonded pdb=" O ALA V 59 " pdb=" CA SER W 261 " model vdw 1.836 3.470 nonbonded pdb=" NH2 ARG V 106 " pdb=" OE1 GLN W 214 " model vdw 1.928 2.520 nonbonded pdb=" OE1 GLU V 9 " pdb=" NH2 ARG W 241 " model vdw 1.959 2.520 nonbonded pdb=" N VAL V 68 " pdb=" OE2 GLU W 275 " model vdw 1.981 2.520 ... (remaining 379616 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 31 through 121) selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.700 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: 0.040 Extract box with map and model: 6.190 Check model and map are aligned: 0.780 Set scattering table: 0.470 Process input model: 152.670 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 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 : 0.009 0.113 48991 Z= 0.586 Angle : 1.212 19.935 67643 Z= 0.701 Chirality : 0.068 0.651 7586 Planarity : 0.007 0.064 7515 Dihedral : 19.466 174.814 19542 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.66 % Allowed : 4.29 % Favored : 95.04 % Rotamer: Outliers : 0.77 % Allowed : 3.13 % Favored : 96.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.11), residues: 4983 helix: -1.27 (0.10), residues: 1842 sheet: -0.71 (0.18), residues: 685 loop : -0.96 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP G 79 HIS 0.014 0.003 HIS f 75 PHE 0.053 0.005 PHE A1176 TYR 0.049 0.004 TYR d 80 ARG 0.016 0.001 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 603 time to evaluate : 5.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ILE cc_start: 0.9262 (mt) cc_final: 0.8931 (tp) REVERT: A 306 ASP cc_start: 0.8234 (t0) cc_final: 0.7981 (t0) REVERT: A 326 ILE cc_start: 0.9390 (mt) cc_final: 0.9033 (tt) REVERT: A 473 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.6946 (mp) REVERT: A 476 THR cc_start: 0.9125 (p) cc_final: 0.8853 (p) REVERT: A 502 LEU cc_start: 0.8827 (mt) cc_final: 0.8518 (mm) REVERT: A 535 MET cc_start: 0.8896 (ttp) cc_final: 0.8464 (tmm) REVERT: A 548 MET cc_start: 0.8934 (mtm) cc_final: 0.8528 (mtm) REVERT: A 658 LEU cc_start: 0.8640 (tp) cc_final: 0.8315 (pp) REVERT: A 747 MET cc_start: 0.8720 (mtm) cc_final: 0.8465 (mtp) REVERT: A 825 LEU cc_start: 0.8878 (mt) cc_final: 0.8519 (tp) REVERT: A 958 LEU cc_start: 0.8613 (mt) cc_final: 0.8228 (mt) REVERT: A 995 LEU cc_start: 0.8919 (tp) cc_final: 0.8516 (tt) REVERT: A 1384 LEU cc_start: 0.9329 (mt) cc_final: 0.9045 (mt) REVERT: A 1409 VAL cc_start: 0.9159 (t) cc_final: 0.8645 (m) REVERT: B 406 LEU cc_start: 0.8698 (mt) cc_final: 0.8432 (mt) REVERT: B 500 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6420 (mtpt) REVERT: B 1138 MET cc_start: 0.7510 (mmm) cc_final: 0.7211 (tpp) REVERT: B 1202 LEU cc_start: 0.9346 (tp) cc_final: 0.8772 (tt) REVERT: D 174 ILE cc_start: 0.7999 (mt) cc_final: 0.7533 (mt) REVERT: D 181 LEU cc_start: 0.7351 (mt) cc_final: 0.7005 (tt) REVERT: K 87 LEU cc_start: 0.8935 (tp) cc_final: 0.8706 (tp) REVERT: W 790 PRO cc_start: 0.6836 (Cg_exo) cc_final: 0.6621 (Cg_endo) REVERT: c 89 ASN cc_start: 0.7929 (m-40) cc_final: 0.7233 (t0) REVERT: e 84 PHE cc_start: 0.4137 (OUTLIER) cc_final: 0.3816 (m-10) outliers start: 34 outliers final: 6 residues processed: 634 average time/residue: 0.6665 time to fit residues: 670.9400 Evaluate side-chains 314 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 305 time to evaluate : 4.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 447 optimal weight: 20.0000 chunk 401 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 270 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 415 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 481 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN A 651 GLN A 737 ASN A 967 GLN A1072 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 359 GLN B 438 ASN B 763 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B 975 GLN B 996 HIS C 13 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 HIS G 21 GLN H 13 GLN I 23 GLN I 90 GLN W 330 ASN W 339 GLN W 434 ASN ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN c 73 ASN c 84 GLN c 89 ASN d 64 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN g 31 HIS g 112 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 48991 Z= 0.309 Angle : 0.744 9.747 67643 Z= 0.405 Chirality : 0.044 0.252 7586 Planarity : 0.005 0.103 7515 Dihedral : 24.218 179.174 9441 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.89 % Favored : 96.81 % Rotamer: Outliers : 0.16 % Allowed : 2.34 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 4983 helix: 0.49 (0.11), residues: 1899 sheet: -0.38 (0.19), residues: 691 loop : -0.44 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP V 67 HIS 0.010 0.002 HIS D 41 PHE 0.042 0.002 PHE A 445 TYR 0.025 0.002 TYR B 811 ARG 0.027 0.001 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 357 time to evaluate : 5.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.7182 (mm110) cc_final: 0.6928 (mp10) REVERT: A 278 GLN cc_start: 0.8838 (mt0) cc_final: 0.8531 (tm-30) REVERT: A 326 ILE cc_start: 0.9062 (mt) cc_final: 0.8772 (tt) REVERT: A 337 LEU cc_start: 0.8456 (mm) cc_final: 0.8239 (mm) REVERT: A 502 LEU cc_start: 0.9016 (mt) cc_final: 0.8553 (mm) REVERT: A 658 LEU cc_start: 0.8610 (tp) cc_final: 0.8249 (pp) REVERT: A 958 LEU cc_start: 0.9073 (mt) cc_final: 0.8764 (mt) REVERT: A 995 LEU cc_start: 0.8643 (tp) cc_final: 0.8346 (tt) REVERT: A 1068 VAL cc_start: 0.9223 (p) cc_final: 0.8618 (p) REVERT: A 1114 LYS cc_start: 0.8346 (tmtt) cc_final: 0.8080 (tptp) REVERT: A 1439 MET cc_start: 0.7879 (tmm) cc_final: 0.7459 (tmm) REVERT: B 305 MET cc_start: 0.8693 (mmp) cc_final: 0.8165 (mmm) REVERT: B 401 LEU cc_start: 0.8728 (mt) cc_final: 0.8363 (mp) REVERT: B 778 MET cc_start: 0.6662 (mtp) cc_final: 0.6141 (mtp) REVERT: B 1100 ASP cc_start: 0.8391 (p0) cc_final: 0.7988 (p0) REVERT: B 1207 LEU cc_start: 0.9105 (mt) cc_final: 0.8540 (tp) REVERT: B 1208 MET cc_start: 0.8224 (mpp) cc_final: 0.8006 (mpp) REVERT: E 92 MET cc_start: 0.8722 (tmm) cc_final: 0.8155 (ttp) REVERT: J 56 ILE cc_start: 0.8996 (tt) cc_final: 0.8787 (tp) REVERT: K 87 LEU cc_start: 0.9199 (tp) cc_final: 0.8912 (tp) REVERT: V 13 MET cc_start: 0.7793 (mmp) cc_final: 0.7204 (mmm) REVERT: c 89 ASN cc_start: 0.8162 (m110) cc_final: 0.7478 (t0) REVERT: h 56 MET cc_start: 0.2531 (mtm) cc_final: 0.2075 (mtp) outliers start: 7 outliers final: 2 residues processed: 362 average time/residue: 0.6120 time to fit residues: 366.0763 Evaluate side-chains 250 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 5.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 267 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 400 optimal weight: 10.0000 chunk 327 optimal weight: 50.0000 chunk 132 optimal weight: 1.9990 chunk 482 optimal weight: 50.0000 chunk 520 optimal weight: 9.9990 chunk 429 optimal weight: 30.0000 chunk 478 optimal weight: 40.0000 chunk 164 optimal weight: 1.9990 chunk 386 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN A 359 ASN A 511 GLN A 590 GLN A 737 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN H 44 ASN I 12 ASN I 31 ASN W 339 GLN ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN g 112 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 48991 Z= 0.265 Angle : 0.643 10.531 67643 Z= 0.354 Chirality : 0.042 0.224 7586 Planarity : 0.004 0.093 7515 Dihedral : 24.136 176.427 9441 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.23 % Favored : 96.53 % Rotamer: Outliers : 0.09 % Allowed : 2.25 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.12), residues: 4983 helix: 1.00 (0.12), residues: 1931 sheet: -0.35 (0.19), residues: 682 loop : -0.25 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP V 67 HIS 0.010 0.001 HIS B1015 PHE 0.034 0.002 PHE B 278 TYR 0.018 0.002 TYR a 41 ARG 0.029 0.001 ARG H 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 306 time to evaluate : 5.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.1416 (mtp) cc_final: 0.1185 (mmt) REVERT: A 146 MET cc_start: 0.4392 (pmm) cc_final: 0.3822 (ptp) REVERT: A 326 ILE cc_start: 0.9122 (mt) cc_final: 0.8891 (tt) REVERT: A 502 LEU cc_start: 0.8993 (mt) cc_final: 0.7978 (mt) REVERT: A 658 LEU cc_start: 0.8739 (tp) cc_final: 0.8244 (pp) REVERT: A 995 LEU cc_start: 0.8755 (tp) cc_final: 0.8471 (tt) REVERT: A 1065 MET cc_start: 0.8959 (tpt) cc_final: 0.7952 (tpp) REVERT: A 1068 VAL cc_start: 0.9459 (p) cc_final: 0.9255 (p) REVERT: A 1114 LYS cc_start: 0.8220 (tmtt) cc_final: 0.8001 (tptp) REVERT: A 1385 MET cc_start: 0.8590 (mpp) cc_final: 0.8248 (mpp) REVERT: B 274 ILE cc_start: 0.9041 (mm) cc_final: 0.8455 (mm) REVERT: B 305 MET cc_start: 0.8562 (mmp) cc_final: 0.8215 (mmm) REVERT: B 778 MET cc_start: 0.7004 (mtp) cc_final: 0.6417 (mtp) REVERT: B 980 PHE cc_start: 0.7785 (m-80) cc_final: 0.7530 (m-80) REVERT: B 1100 ASP cc_start: 0.8251 (p0) cc_final: 0.8041 (p0) REVERT: B 1152 MET cc_start: 0.6848 (tpp) cc_final: 0.5629 (tpt) REVERT: B 1202 LEU cc_start: 0.8860 (mt) cc_final: 0.8609 (mt) REVERT: C 230 MET cc_start: 0.8144 (mtm) cc_final: 0.7572 (mtp) REVERT: E 92 MET cc_start: 0.8393 (tmm) cc_final: 0.7986 (ttp) REVERT: E 125 THR cc_start: 0.6935 (p) cc_final: 0.6539 (p) REVERT: K 87 LEU cc_start: 0.9299 (tp) cc_final: 0.9082 (tp) REVERT: V 13 MET cc_start: 0.7754 (mmp) cc_final: 0.7284 (mmm) REVERT: c 89 ASN cc_start: 0.8216 (m110) cc_final: 0.7655 (t0) REVERT: d 59 MET cc_start: 0.8602 (tpt) cc_final: 0.8094 (tpp) REVERT: e 73 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.5656 (mp0) REVERT: h 56 MET cc_start: 0.2646 (mtm) cc_final: 0.2136 (mtp) outliers start: 4 outliers final: 1 residues processed: 309 average time/residue: 0.6320 time to fit residues: 326.4226 Evaluate side-chains 243 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 476 optimal weight: 4.9990 chunk 362 optimal weight: 40.0000 chunk 250 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 230 optimal weight: 0.1980 chunk 323 optimal weight: 5.9990 chunk 483 optimal weight: 30.0000 chunk 512 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 458 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 737 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS B 763 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 252 GLN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G 41 GLN ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 79 HIS ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 48991 Z= 0.211 Angle : 0.592 9.444 67643 Z= 0.324 Chirality : 0.041 0.183 7586 Planarity : 0.004 0.060 7515 Dihedral : 24.061 175.569 9441 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.99 % Favored : 96.77 % Rotamer: Outliers : 0.05 % Allowed : 2.02 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.59 (0.12), residues: 4983 helix: 1.38 (0.12), residues: 1930 sheet: -0.37 (0.19), residues: 711 loop : -0.10 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP V 67 HIS 0.006 0.001 HIS b 75 PHE 0.024 0.001 PHE B1204 TYR 0.022 0.001 TYR A 805 ARG 0.009 0.000 ARG H 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 297 time to evaluate : 5.203 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 146 MET cc_start: 0.4582 (pmm) cc_final: 0.4067 (ptp) REVERT: A 253 MET cc_start: -0.0697 (tpt) cc_final: -0.1061 (tpt) REVERT: A 326 ILE cc_start: 0.9158 (mt) cc_final: 0.8849 (tt) REVERT: A 464 MET cc_start: 0.7205 (ptt) cc_final: 0.6390 (ptt) REVERT: A 505 LEU cc_start: 0.8519 (mt) cc_final: 0.8140 (mt) REVERT: A 506 CYS cc_start: 0.7863 (m) cc_final: 0.5451 (t) REVERT: A 658 LEU cc_start: 0.8751 (tp) cc_final: 0.8441 (tp) REVERT: A 747 MET cc_start: 0.8498 (mmt) cc_final: 0.8240 (mmt) REVERT: A 995 LEU cc_start: 0.8861 (tp) cc_final: 0.8571 (tt) REVERT: A 1065 MET cc_start: 0.8845 (tpt) cc_final: 0.7915 (tpp) REVERT: A 1114 LYS cc_start: 0.8342 (tmtt) cc_final: 0.8063 (tptp) REVERT: A 1374 LEU cc_start: 0.9190 (pp) cc_final: 0.8926 (pp) REVERT: A 1377 VAL cc_start: 0.9408 (t) cc_final: 0.9206 (p) REVERT: A 1385 MET cc_start: 0.8281 (mpp) cc_final: 0.7803 (mpp) REVERT: B 305 MET cc_start: 0.8463 (mmp) cc_final: 0.8153 (mmm) REVERT: B 699 MET cc_start: 0.7440 (ptm) cc_final: 0.7037 (ptm) REVERT: B 778 MET cc_start: 0.6679 (mtp) cc_final: 0.5999 (mtp) REVERT: B 980 PHE cc_start: 0.7976 (m-80) cc_final: 0.7383 (m-80) REVERT: B 1202 LEU cc_start: 0.8865 (mt) cc_final: 0.8552 (mt) REVERT: V 13 MET cc_start: 0.7710 (mmp) cc_final: 0.7432 (mmm) REVERT: c 89 ASN cc_start: 0.8296 (m110) cc_final: 0.7994 (t0) REVERT: h 56 MET cc_start: 0.2709 (mtm) cc_final: 0.2291 (mtp) outliers start: 2 outliers final: 1 residues processed: 299 average time/residue: 0.5892 time to fit residues: 297.6627 Evaluate side-chains 234 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 4.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 426 optimal weight: 10.0000 chunk 290 optimal weight: 0.7980 chunk 7 optimal weight: 0.0040 chunk 381 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 437 optimal weight: 40.0000 chunk 354 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 459 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 overall best weight: 4.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 HIS ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 48991 Z= 0.235 Angle : 0.599 10.794 67643 Z= 0.328 Chirality : 0.040 0.254 7586 Planarity : 0.004 0.107 7515 Dihedral : 24.064 175.631 9441 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.66 (0.12), residues: 4983 helix: 1.51 (0.12), residues: 1927 sheet: -0.47 (0.19), residues: 694 loop : -0.08 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 67 HIS 0.007 0.001 HIS b 75 PHE 0.035 0.002 PHE B 278 TYR 0.025 0.001 TYR e 54 ARG 0.012 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 5.209 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 122 MET cc_start: -0.0255 (mtt) cc_final: -0.0621 (mtp) REVERT: A 146 MET cc_start: 0.4742 (pmm) cc_final: 0.4221 (ptp) REVERT: A 253 MET cc_start: -0.0733 (tpt) cc_final: -0.1106 (tpt) REVERT: A 326 ILE cc_start: 0.9174 (mt) cc_final: 0.8884 (tt) REVERT: A 506 CYS cc_start: 0.7551 (m) cc_final: 0.6120 (t) REVERT: A 658 LEU cc_start: 0.8779 (tp) cc_final: 0.8508 (tp) REVERT: A 995 LEU cc_start: 0.8976 (tp) cc_final: 0.8718 (tt) REVERT: A 1065 MET cc_start: 0.8920 (tpt) cc_final: 0.7827 (tpp) REVERT: A 1114 LYS cc_start: 0.8332 (tmtt) cc_final: 0.8098 (tptp) REVERT: A 1371 MET cc_start: 0.8537 (mpp) cc_final: 0.8294 (mpp) REVERT: B 42 MET cc_start: 0.8602 (mmp) cc_final: 0.8395 (mmm) REVERT: B 305 MET cc_start: 0.8485 (mmp) cc_final: 0.8156 (mmm) REVERT: B 778 MET cc_start: 0.6074 (mtp) cc_final: 0.5658 (mtp) REVERT: B 980 PHE cc_start: 0.7941 (m-80) cc_final: 0.7533 (m-80) REVERT: B 1152 MET cc_start: 0.6107 (tpt) cc_final: 0.5692 (tpt) REVERT: B 1202 LEU cc_start: 0.8899 (mt) cc_final: 0.8608 (mt) REVERT: B 1205 GLN cc_start: 0.8282 (mp10) cc_final: 0.7903 (mp10) REVERT: C 32 LEU cc_start: 0.8584 (tp) cc_final: 0.8251 (tp) REVERT: H 46 MET cc_start: 0.7458 (tpp) cc_final: 0.7175 (tpp) REVERT: V 13 MET cc_start: 0.7688 (mmp) cc_final: 0.7467 (mmm) REVERT: c 89 ASN cc_start: 0.8442 (m110) cc_final: 0.8034 (t0) REVERT: h 56 MET cc_start: 0.2957 (mtm) cc_final: 0.2522 (mtp) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.5810 time to fit residues: 285.3695 Evaluate side-chains 232 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 5.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 172 optimal weight: 5.9990 chunk 461 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 300 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 512 optimal weight: 9.9990 chunk 425 optimal weight: 30.0000 chunk 237 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS A 737 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 GLN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 48991 Z= 0.283 Angle : 0.654 13.913 67643 Z= 0.352 Chirality : 0.041 0.229 7586 Planarity : 0.005 0.075 7515 Dihedral : 24.199 176.002 9441 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.83 % Favored : 96.05 % Rotamer: Outliers : 0.02 % Allowed : 2.04 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.58 (0.12), residues: 4983 helix: 1.43 (0.12), residues: 1928 sheet: -0.49 (0.19), residues: 699 loop : -0.11 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 956 HIS 0.007 0.002 HIS b 75 PHE 0.050 0.002 PHE G 42 TYR 0.023 0.002 TYR A 466 ARG 0.012 0.001 ARG B 852 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 5.543 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 122 MET cc_start: -0.1259 (mtt) cc_final: -0.1763 (mtp) REVERT: A 253 MET cc_start: -0.0267 (tpt) cc_final: -0.0693 (tpt) REVERT: A 282 MET cc_start: 0.8677 (pmm) cc_final: 0.7430 (pmm) REVERT: A 326 ILE cc_start: 0.9221 (mt) cc_final: 0.8957 (tt) REVERT: A 535 MET cc_start: 0.8068 (tmm) cc_final: 0.7256 (tmm) REVERT: A 614 MET cc_start: 0.8243 (mpp) cc_final: 0.7844 (mpp) REVERT: A 819 MET cc_start: 0.8248 (mmt) cc_final: 0.8030 (mmt) REVERT: A 995 LEU cc_start: 0.9168 (tp) cc_final: 0.8872 (tt) REVERT: A 1114 LYS cc_start: 0.8377 (tmtt) cc_final: 0.8145 (tptp) REVERT: A 1385 MET cc_start: 0.8198 (mpp) cc_final: 0.7801 (mpp) REVERT: A 1447 MET cc_start: 0.7285 (mmp) cc_final: 0.6986 (mmp) REVERT: B 42 MET cc_start: 0.8648 (mmp) cc_final: 0.8424 (mmm) REVERT: B 305 MET cc_start: 0.8499 (mmp) cc_final: 0.8121 (mmm) REVERT: B 778 MET cc_start: 0.6352 (mtp) cc_final: 0.6080 (mtp) REVERT: B 860 MET cc_start: 0.8069 (tmm) cc_final: 0.7047 (tmm) REVERT: B 1152 MET cc_start: 0.6855 (tpt) cc_final: 0.6273 (tpt) REVERT: B 1202 LEU cc_start: 0.8994 (mt) cc_final: 0.8700 (mt) REVERT: H 46 MET cc_start: 0.7803 (tpp) cc_final: 0.7465 (tpp) REVERT: K 87 LEU cc_start: 0.9522 (tp) cc_final: 0.9320 (tp) REVERT: V 13 MET cc_start: 0.7674 (mmp) cc_final: 0.7410 (mmm) REVERT: c 89 ASN cc_start: 0.8448 (m110) cc_final: 0.8007 (t0) REVERT: h 56 MET cc_start: 0.3193 (mtm) cc_final: 0.2740 (mtp) outliers start: 1 outliers final: 1 residues processed: 281 average time/residue: 0.5644 time to fit residues: 269.8944 Evaluate side-chains 221 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 4.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 494 optimal weight: 40.0000 chunk 57 optimal weight: 6.9990 chunk 292 optimal weight: 30.0000 chunk 374 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 chunk 431 optimal weight: 50.0000 chunk 286 optimal weight: 50.0000 chunk 510 optimal weight: 30.0000 chunk 319 optimal weight: 9.9990 chunk 311 optimal weight: 0.0370 chunk 235 optimal weight: 0.9980 overall best weight: 4.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 438 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 48991 Z= 0.209 Angle : 0.591 13.079 67643 Z= 0.321 Chirality : 0.041 0.183 7586 Planarity : 0.004 0.040 7515 Dihedral : 24.134 175.942 9441 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.74 (0.12), residues: 4983 helix: 1.61 (0.12), residues: 1921 sheet: -0.55 (0.19), residues: 694 loop : -0.02 (0.13), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 657 HIS 0.007 0.001 HIS f 75 PHE 0.027 0.001 PHE A 445 TYR 0.020 0.001 TYR A1352 ARG 0.007 0.000 ARG H 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 5.179 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 122 MET cc_start: -0.0682 (mtt) cc_final: -0.1284 (mtp) REVERT: A 282 MET cc_start: 0.8643 (pmm) cc_final: 0.8401 (pmm) REVERT: A 326 ILE cc_start: 0.9203 (mt) cc_final: 0.8950 (tt) REVERT: A 819 MET cc_start: 0.8283 (mmt) cc_final: 0.8052 (mmt) REVERT: A 995 LEU cc_start: 0.9125 (tp) cc_final: 0.8815 (tt) REVERT: A 1065 MET cc_start: 0.8858 (tpp) cc_final: 0.8421 (tpp) REVERT: A 1114 LYS cc_start: 0.8389 (tmtt) cc_final: 0.8140 (tptp) REVERT: A 1447 MET cc_start: 0.7385 (mmp) cc_final: 0.7046 (mmp) REVERT: B 305 MET cc_start: 0.8551 (mmp) cc_final: 0.8187 (mmm) REVERT: B 702 MET cc_start: 0.7002 (tpp) cc_final: 0.6786 (mmm) REVERT: B 860 MET cc_start: 0.8032 (tmm) cc_final: 0.7068 (tmm) REVERT: B 1152 MET cc_start: 0.6561 (tpt) cc_final: 0.6062 (tpt) REVERT: B 1202 LEU cc_start: 0.9049 (mt) cc_final: 0.8685 (mt) REVERT: B 1204 PHE cc_start: 0.6197 (t80) cc_final: 0.5953 (t80) REVERT: C 230 MET cc_start: 0.7467 (mtp) cc_final: 0.6243 (ttm) REVERT: H 46 MET cc_start: 0.7871 (tpp) cc_final: 0.7503 (tpp) REVERT: V 13 MET cc_start: 0.7619 (mmp) cc_final: 0.7416 (mmm) REVERT: c 89 ASN cc_start: 0.8400 (m110) cc_final: 0.7976 (t0) REVERT: h 56 MET cc_start: 0.3218 (mtm) cc_final: 0.2782 (mtp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.5617 time to fit residues: 274.5971 Evaluate side-chains 221 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 4.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 316 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 305 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 100 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 324 optimal weight: 9.9990 chunk 348 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 401 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN A 737 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN I 22 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 48991 Z= 0.213 Angle : 0.588 13.858 67643 Z= 0.319 Chirality : 0.040 0.263 7586 Planarity : 0.004 0.100 7515 Dihedral : 24.047 175.828 9441 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.82 (0.12), residues: 4983 helix: 1.67 (0.12), residues: 1927 sheet: -0.54 (0.19), residues: 708 loop : 0.04 (0.14), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 657 HIS 0.007 0.001 HIS f 75 PHE 0.038 0.001 PHE A 445 TYR 0.024 0.001 TYR e 54 ARG 0.007 0.000 ARG H 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 4.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: -0.0655 (mtt) cc_final: -0.0960 (mtp) REVERT: A 282 MET cc_start: 0.8712 (pmm) cc_final: 0.8493 (pmm) REVERT: A 326 ILE cc_start: 0.9198 (mt) cc_final: 0.8978 (tt) REVERT: A 614 MET cc_start: 0.8290 (mpp) cc_final: 0.7841 (mpp) REVERT: A 819 MET cc_start: 0.8253 (mmt) cc_final: 0.7989 (mmt) REVERT: A 995 LEU cc_start: 0.9127 (tp) cc_final: 0.8794 (tt) REVERT: A 1065 MET cc_start: 0.8961 (tpp) cc_final: 0.8439 (tpp) REVERT: B 42 MET cc_start: 0.8615 (mmp) cc_final: 0.8388 (mmm) REVERT: B 254 ASP cc_start: 0.7060 (t0) cc_final: 0.6795 (t0) REVERT: B 305 MET cc_start: 0.8594 (mmp) cc_final: 0.8217 (mmm) REVERT: B 860 MET cc_start: 0.8026 (tmm) cc_final: 0.7031 (tmm) REVERT: B 1152 MET cc_start: 0.6707 (tpt) cc_final: 0.5948 (tpt) REVERT: B 1202 LEU cc_start: 0.9030 (mt) cc_final: 0.8761 (mt) REVERT: B 1205 GLN cc_start: 0.8423 (mp10) cc_final: 0.8152 (mp10) REVERT: C 36 MET cc_start: 0.7898 (ptt) cc_final: 0.7530 (ptt) REVERT: C 230 MET cc_start: 0.7268 (mtp) cc_final: 0.6028 (ttm) REVERT: H 46 MET cc_start: 0.7881 (tpp) cc_final: 0.7526 (tpp) REVERT: K 87 LEU cc_start: 0.9515 (tp) cc_final: 0.9269 (tp) REVERT: c 89 ASN cc_start: 0.8385 (m110) cc_final: 0.7985 (t0) REVERT: h 56 MET cc_start: 0.3258 (mtm) cc_final: 0.2807 (mtp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.5698 time to fit residues: 268.5192 Evaluate side-chains 219 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 4.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 464 optimal weight: 9.9990 chunk 489 optimal weight: 10.0000 chunk 446 optimal weight: 40.0000 chunk 476 optimal weight: 7.9990 chunk 286 optimal weight: 50.0000 chunk 207 optimal weight: 10.0000 chunk 373 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 430 optimal weight: 10.0000 chunk 450 optimal weight: 50.0000 chunk 474 optimal weight: 10.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN A 511 GLN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN C 64 HIS D 72 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN I 12 ASN I 22 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 GLN h 46 HIS ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 48991 Z= 0.392 Angle : 0.787 19.166 67643 Z= 0.418 Chirality : 0.044 0.327 7586 Planarity : 0.006 0.088 7515 Dihedral : 24.402 176.648 9441 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 4983 helix: 0.91 (0.12), residues: 1937 sheet: -0.77 (0.19), residues: 717 loop : -0.25 (0.13), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP J 18 HIS 0.011 0.002 HIS B 157 PHE 0.039 0.003 PHE A 445 TYR 0.026 0.003 TYR A1365 ARG 0.015 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 5.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8121 (ppp) cc_final: 0.7691 (ptm) REVERT: A 464 MET cc_start: 0.8504 (pmm) cc_final: 0.8050 (pmm) REVERT: A 488 MET cc_start: 0.8020 (ttt) cc_final: 0.7412 (ttt) REVERT: A 614 MET cc_start: 0.8379 (mpp) cc_final: 0.8023 (mpp) REVERT: A 819 MET cc_start: 0.8290 (mmt) cc_final: 0.8038 (mmt) REVERT: A 1114 LYS cc_start: 0.8551 (tmtt) cc_final: 0.8309 (tptp) REVERT: A 1262 MET cc_start: 0.7951 (tpt) cc_final: 0.7744 (tpt) REVERT: A 1447 MET cc_start: 0.7422 (mmp) cc_final: 0.6987 (mmp) REVERT: B 42 MET cc_start: 0.8704 (mmp) cc_final: 0.8401 (mmm) REVERT: B 305 MET cc_start: 0.8553 (mmp) cc_final: 0.8159 (mmm) REVERT: B 778 MET cc_start: 0.7133 (ptp) cc_final: 0.6919 (ptp) REVERT: B 860 MET cc_start: 0.8077 (tmm) cc_final: 0.7278 (tmm) REVERT: B 1133 MET cc_start: 0.8481 (pmm) cc_final: 0.8246 (pmm) REVERT: B 1152 MET cc_start: 0.7132 (tpt) cc_final: 0.6894 (tpt) REVERT: B 1202 LEU cc_start: 0.8941 (mt) cc_final: 0.8697 (mt) REVERT: C 36 MET cc_start: 0.8072 (ptt) cc_final: 0.7715 (ptt) REVERT: E 122 MET cc_start: 0.4691 (tmm) cc_final: 0.4268 (tpt) REVERT: H 46 MET cc_start: 0.7810 (tpp) cc_final: 0.7296 (tpp) REVERT: J 65 LEU cc_start: 0.6094 (mm) cc_final: 0.5796 (mm) REVERT: c 89 ASN cc_start: 0.8370 (m110) cc_final: 0.7958 (t0) REVERT: h 56 MET cc_start: 0.3736 (mtm) cc_final: 0.3173 (mtp) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.5894 time to fit residues: 259.5366 Evaluate side-chains 205 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 312 optimal weight: 3.9990 chunk 503 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 349 optimal weight: 30.0000 chunk 528 optimal weight: 30.0000 chunk 485 optimal weight: 7.9990 chunk 420 optimal weight: 0.0070 chunk 43 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN H 44 ASN I 22 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 783 HIS ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 786 ASN d 64 ASN ** d 81 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 48991 Z= 0.195 Angle : 0.606 15.713 67643 Z= 0.327 Chirality : 0.041 0.280 7586 Planarity : 0.004 0.044 7515 Dihedral : 24.206 175.512 9441 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 0.05 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.58 (0.12), residues: 4983 helix: 1.46 (0.12), residues: 1936 sheet: -0.67 (0.19), residues: 696 loop : -0.09 (0.14), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1230 HIS 0.013 0.001 HIS W 783 PHE 0.038 0.001 PHE A 445 TYR 0.024 0.001 TYR e 54 ARG 0.008 0.000 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 266 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: A 108 MET cc_start: 0.7315 (ppp) cc_final: 0.6916 (ptm) REVERT: A 506 CYS cc_start: 0.8063 (m) cc_final: 0.6257 (t) REVERT: A 819 MET cc_start: 0.8205 (mmt) cc_final: 0.7943 (mmt) REVERT: A 995 LEU cc_start: 0.9117 (tp) cc_final: 0.8785 (tt) REVERT: A 1065 MET cc_start: 0.8776 (tpp) cc_final: 0.8509 (tpp) REVERT: A 1114 LYS cc_start: 0.8491 (tmtt) cc_final: 0.8140 (tptp) REVERT: A 1447 MET cc_start: 0.7128 (mmp) cc_final: 0.6797 (mmp) REVERT: B 42 MET cc_start: 0.8514 (mmp) cc_final: 0.8309 (mmm) REVERT: B 254 ASP cc_start: 0.7584 (t0) cc_final: 0.7318 (t0) REVERT: B 305 MET cc_start: 0.8460 (mmp) cc_final: 0.8093 (mmm) REVERT: B 860 MET cc_start: 0.8161 (tmm) cc_final: 0.7184 (tmm) REVERT: B 1204 PHE cc_start: 0.6794 (t80) cc_final: 0.6518 (t80) REVERT: C 36 MET cc_start: 0.8077 (ptt) cc_final: 0.7763 (ptt) REVERT: C 230 MET cc_start: 0.7173 (mtp) cc_final: 0.5944 (ttm) REVERT: H 46 MET cc_start: 0.7705 (tpp) cc_final: 0.7190 (tpp) REVERT: K 87 LEU cc_start: 0.9568 (tp) cc_final: 0.9348 (tp) REVERT: c 89 ASN cc_start: 0.8307 (m110) cc_final: 0.7907 (t0) REVERT: h 56 MET cc_start: 0.3624 (mtm) cc_final: 0.3068 (mtp) outliers start: 2 outliers final: 0 residues processed: 268 average time/residue: 0.5565 time to fit residues: 257.2197 Evaluate side-chains 216 residues out of total 4408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 5.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 333 optimal weight: 7.9990 chunk 447 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 421 optimal weight: 0.9980 chunk 176 optimal weight: 30.0000 chunk 432 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN I 22 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 783 HIS ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.054351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.036970 restraints weight = 555015.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.038017 restraints weight = 324092.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.038686 restraints weight = 227070.954| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48991 Z= 0.211 Angle : 0.593 15.145 67643 Z= 0.321 Chirality : 0.040 0.306 7586 Planarity : 0.004 0.042 7515 Dihedral : 24.068 175.442 9441 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.69 (0.12), residues: 4983 helix: 1.56 (0.12), residues: 1939 sheet: -0.64 (0.19), residues: 716 loop : -0.02 (0.14), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1230 HIS 0.007 0.001 HIS B1015 PHE 0.025 0.001 PHE A 445 TYR 0.024 0.001 TYR e 54 ARG 0.006 0.000 ARG B 904 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8150.13 seconds wall clock time: 149 minutes 47.03 seconds (8987.03 seconds total)