Starting phenix.real_space_refine on Tue Sep 24 18:45:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/09_2024/7ade_11725.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/09_2024/7ade_11725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/09_2024/7ade_11725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/09_2024/7ade_11725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/09_2024/7ade_11725.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ade_11725/09_2024/7ade_11725.cif" } resolution = 4.2 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= 0.003 sd= 0.018 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 102 5.49 5 Mg 6 5.21 5 S 223 5.16 5 Be 5 3.05 5 C 31985 2.51 5 N 9103 2.21 5 O 10112 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51553 Number of models: 1 Model: "" Number of chains: 26 Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3852 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 480} Chain: "U" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1825 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain: "V" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2504 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 303} Chain: "W" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "X" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "Y" Number of atoms: 10431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10431 Classifications: {'peptide': 1343} Link IDs: {'PTRANS': 54, 'TRANS': 1288} Chain breaks: 1 Chain: "L" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 741 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 474 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 674 Classifications: {'RNA': 32} Modifications used: {'rna2p_pyr': 4, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 4, 'rna3p': 27} Chain breaks: 1 Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" 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: "a" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39504 SG CYS Y 70 57.251 119.873 115.660 1.00255.29 S ATOM 39518 SG CYS Y 72 57.104 116.504 116.477 1.00254.09 S ATOM 39626 SG CYS Y 85 55.146 118.411 118.894 1.00259.98 S ATOM 45224 SG CYS Y 814 72.424 185.924 117.303 1.00120.89 S ATOM 45789 SG CYS Y 888 74.512 181.871 117.403 1.00111.12 S ATOM 45840 SG CYS Y 895 71.574 181.911 115.497 1.00113.71 S ATOM 45861 SG CYS Y 898 75.032 184.652 115.284 1.00 98.22 S Time building chain proxies: 22.38, per 1000 atoms: 0.43 Number of scatterers: 51553 At special positions: 0 Unit cell: (163.68, 228.16, 192.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 223 16.00 P 102 15.00 Mg 6 11.99 F 15 9.00 O 10112 8.00 N 9103 7.00 C 31985 6.00 Be 5 4.00 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 - 3.00 Amino acid : True - 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: 10.24 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 85 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " pdb=" ZN Y1503 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 888 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 898 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 895 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 814 " Number of angles added : 6 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11722 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 66 sheets defined 41.4% alpha, 16.8% beta 21 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 14.97 Creating SS restraints... Processing helix chain 'f' and resid 3 through 8 Processing helix chain 'f' and resid 10 through 21 removed outlier: 3.625A pdb=" N LEU f 14 " --> pdb=" O PRO f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 removed outlier: 4.034A pdb=" N ARG f 28 " --> pdb=" O ASN f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 45 Processing helix chain 'f' and resid 82 through 89 removed outlier: 3.808A pdb=" N ILE f 86 " --> pdb=" O SER f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 123 through 129 removed outlier: 4.290A pdb=" N ASN f 129 " --> pdb=" O GLU f 125 " (cutoff:3.500A) Processing helix chain 'f' and resid 155 through 166 removed outlier: 4.238A pdb=" N ALA f 159 " --> pdb=" O GLU f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 184 through 199 Processing helix chain 'f' and resid 212 through 220 Processing helix chain 'f' and resid 235 through 256 removed outlier: 3.728A pdb=" N HIS f 239 " --> pdb=" O PRO f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 278 Processing helix chain 'f' and resid 294 through 303 Processing helix chain 'f' and resid 326 through 335 Processing helix chain 'f' and resid 346 through 351 removed outlier: 3.611A pdb=" N ALA f 350 " --> pdb=" O SER f 346 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 371 Processing helix chain 'f' and resid 373 through 388 Processing helix chain 'f' and resid 392 through 406 removed outlier: 4.026A pdb=" N MET f 405 " --> pdb=" O ASN f 401 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR f 406 " --> pdb=" O LYS f 402 " (cutoff:3.500A) Processing helix chain 'f' and resid 408 through 417 Processing helix chain 'a' and resid 3 through 8 Processing helix chain 'a' and resid 10 through 21 removed outlier: 3.625A pdb=" N LEU a 14 " --> pdb=" O PRO a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 29 removed outlier: 4.034A pdb=" N ARG a 28 " --> pdb=" O ASN a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 45 Processing helix chain 'a' and resid 82 through 89 removed outlier: 3.808A pdb=" N ILE a 86 " --> pdb=" O SER a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 129 removed outlier: 4.290A pdb=" N ASN a 129 " --> pdb=" O GLU a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 155 through 166 removed outlier: 4.239A pdb=" N ALA a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 199 Processing helix chain 'a' and resid 212 through 220 Processing helix chain 'a' and resid 235 through 256 removed outlier: 3.728A pdb=" N HIS a 239 " --> pdb=" O PRO a 235 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 326 through 335 Processing helix chain 'a' and resid 346 through 351 removed outlier: 3.611A pdb=" N ALA a 350 " --> pdb=" O SER a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 367 through 371 Processing helix chain 'a' and resid 373 through 388 Processing helix chain 'a' and resid 392 through 406 removed outlier: 4.025A pdb=" N MET a 405 " --> pdb=" O ASN a 401 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR a 406 " --> pdb=" O LYS a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 408 through 417 Processing helix chain 'b' and resid 3 through 8 Processing helix chain 'b' and resid 10 through 21 removed outlier: 3.625A pdb=" N LEU b 14 " --> pdb=" O PRO b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 29 removed outlier: 4.034A pdb=" N ARG b 28 " --> pdb=" O ASN b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 45 Processing helix chain 'b' and resid 82 through 89 removed outlier: 3.808A pdb=" N ILE b 86 " --> pdb=" O SER b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 129 removed outlier: 4.290A pdb=" N ASN b 129 " --> pdb=" O GLU b 125 " (cutoff:3.500A) Processing helix chain 'b' and resid 155 through 166 removed outlier: 4.239A pdb=" N ALA b 159 " --> pdb=" O GLU b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 184 through 199 Processing helix chain 'b' and resid 212 through 220 Processing helix chain 'b' and resid 235 through 256 removed outlier: 3.729A pdb=" N HIS b 239 " --> pdb=" O PRO b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 278 Processing helix chain 'b' and resid 294 through 303 Processing helix chain 'b' and resid 326 through 335 Processing helix chain 'b' and resid 346 through 351 removed outlier: 3.611A pdb=" N ALA b 350 " --> pdb=" O SER b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 367 through 371 Processing helix chain 'b' and resid 373 through 388 Processing helix chain 'b' and resid 392 through 406 removed outlier: 4.026A pdb=" N MET b 405 " --> pdb=" O ASN b 401 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR b 406 " --> pdb=" O LYS b 402 " (cutoff:3.500A) Processing helix chain 'b' and resid 408 through 417 Processing helix chain 'c' and resid 3 through 8 Processing helix chain 'c' and resid 10 through 21 removed outlier: 3.624A pdb=" N LEU c 14 " --> pdb=" O PRO c 10 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 29 removed outlier: 4.033A pdb=" N ARG c 28 " --> pdb=" O ASN c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 45 Processing helix chain 'c' and resid 82 through 89 removed outlier: 3.807A pdb=" N ILE c 86 " --> pdb=" O SER c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 129 removed outlier: 4.290A pdb=" N ASN c 129 " --> pdb=" O GLU c 125 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 166 removed outlier: 4.239A pdb=" N ALA c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 199 Processing helix chain 'c' and resid 212 through 220 Processing helix chain 'c' and resid 235 through 256 removed outlier: 3.727A pdb=" N HIS c 239 " --> pdb=" O PRO c 235 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 Processing helix chain 'c' and resid 294 through 303 Processing helix chain 'c' and resid 326 through 335 Processing helix chain 'c' and resid 346 through 351 removed outlier: 3.611A pdb=" N ALA c 350 " --> pdb=" O SER c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 367 through 371 Processing helix chain 'c' and resid 373 through 388 Processing helix chain 'c' and resid 392 through 406 removed outlier: 4.026A pdb=" N MET c 405 " --> pdb=" O ASN c 401 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR c 406 " --> pdb=" O LYS c 402 " (cutoff:3.500A) Processing helix chain 'c' and resid 408 through 417 Processing helix chain 'd' and resid 3 through 8 Processing helix chain 'd' and resid 10 through 21 removed outlier: 3.625A pdb=" N LEU d 14 " --> pdb=" O PRO d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 29 removed outlier: 4.034A pdb=" N ARG d 28 " --> pdb=" O ASN d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 45 Processing helix chain 'd' and resid 82 through 89 removed outlier: 3.808A pdb=" N ILE d 86 " --> pdb=" O SER d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 129 removed outlier: 4.290A pdb=" N ASN d 129 " --> pdb=" O GLU d 125 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 166 removed outlier: 4.238A pdb=" N ALA d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 199 Processing helix chain 'd' and resid 212 through 220 Processing helix chain 'd' and resid 235 through 256 removed outlier: 3.727A pdb=" N HIS d 239 " --> pdb=" O PRO d 235 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 278 Processing helix chain 'd' and resid 294 through 303 Processing helix chain 'd' and resid 326 through 335 Processing helix chain 'd' and resid 346 through 351 removed outlier: 3.611A pdb=" N ALA d 350 " --> pdb=" O SER d 346 " (cutoff:3.500A) Processing helix chain 'd' and resid 367 through 371 Processing helix chain 'd' and resid 373 through 388 Processing helix chain 'd' and resid 392 through 406 removed outlier: 4.026A pdb=" N MET d 405 " --> pdb=" O ASN d 401 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR d 406 " --> pdb=" O LYS d 402 " (cutoff:3.500A) Processing helix chain 'd' and resid 408 through 417 Processing helix chain 'e' and resid 3 through 8 Processing helix chain 'e' and resid 10 through 21 removed outlier: 3.625A pdb=" N LEU e 14 " --> pdb=" O PRO e 10 " (cutoff:3.500A) Processing helix chain 'e' and resid 25 through 29 removed outlier: 4.033A pdb=" N ARG e 28 " --> pdb=" O ASN e 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 45 Processing helix chain 'e' and resid 82 through 89 removed outlier: 3.809A pdb=" N ILE e 86 " --> pdb=" O SER e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 129 removed outlier: 4.290A pdb=" N ASN e 129 " --> pdb=" O GLU e 125 " (cutoff:3.500A) Processing helix chain 'e' and resid 155 through 166 removed outlier: 4.238A pdb=" N ALA e 159 " --> pdb=" O GLU e 155 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 199 Processing helix chain 'e' and resid 212 through 220 Processing helix chain 'e' and resid 235 through 256 removed outlier: 3.728A pdb=" N HIS e 239 " --> pdb=" O PRO e 235 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 278 Processing helix chain 'e' and resid 294 through 303 Processing helix chain 'e' and resid 326 through 335 Processing helix chain 'e' and resid 346 through 351 removed outlier: 3.611A pdb=" N ALA e 350 " --> pdb=" O SER e 346 " (cutoff:3.500A) Processing helix chain 'e' and resid 367 through 371 Processing helix chain 'e' and resid 373 through 388 Processing helix chain 'e' and resid 392 through 406 removed outlier: 4.026A pdb=" N MET e 405 " --> pdb=" O ASN e 401 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR e 406 " --> pdb=" O LYS e 402 " (cutoff:3.500A) Processing helix chain 'e' and resid 408 through 417 Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 77 through 85 removed outlier: 4.019A pdb=" N ARG A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU A 83 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 84 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 85 " --> pdb=" O TYR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 131 Processing helix chain 'A' and resid 202 through 213 removed outlier: 3.860A pdb=" N ILE A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 322 through 332 removed outlier: 4.488A pdb=" N ALA A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.328A pdb=" N GLU A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 399 through 426 removed outlier: 3.901A pdb=" N GLY A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 451 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.627A pdb=" N LEU A 459 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'U' and resid 34 through 50 removed outlier: 3.602A pdb=" N THR U 38 " --> pdb=" O GLY U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 88 Processing helix chain 'U' and resid 113 through 115 No H-bonds generated for 'chain 'U' and resid 113 through 115' Processing helix chain 'U' and resid 155 through 159 Processing helix chain 'U' and resid 212 through 230 Processing helix chain 'V' and resid 18 through 21 Processing helix chain 'V' and resid 34 through 49 removed outlier: 3.690A pdb=" N THR V 38 " --> pdb=" O GLY V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 87 removed outlier: 3.687A pdb=" N GLY V 87 " --> pdb=" O LEU V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 115 No H-bonds generated for 'chain 'V' and resid 113 through 115' Processing helix chain 'V' and resid 155 through 165 removed outlier: 3.835A pdb=" N HIS V 160 " --> pdb=" O SER V 156 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER V 161 " --> pdb=" O THR V 157 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU V 165 " --> pdb=" O SER V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 212 through 229 Processing helix chain 'V' and resid 230 through 232 No H-bonds generated for 'chain 'V' and resid 230 through 232' Processing helix chain 'V' and resid 256 through 261 removed outlier: 3.947A pdb=" N GLU V 261 " --> pdb=" O ASP V 258 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 272 Processing helix chain 'V' and resid 278 through 283 removed outlier: 3.750A pdb=" N GLN V 283 " --> pdb=" O GLY V 279 " (cutoff:3.500A) Processing helix chain 'V' and resid 296 through 310 Processing helix chain 'W' and resid 6 through 13 Processing helix chain 'W' and resid 15 through 31 removed outlier: 3.632A pdb=" N LEU W 19 " --> pdb=" O ASN W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 57 removed outlier: 3.758A pdb=" N ILE W 49 " --> pdb=" O LYS W 45 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY W 57 " --> pdb=" O GLU W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 80 Processing helix chain 'X' and resid 4 through 10 removed outlier: 3.647A pdb=" N ARG X 10 " --> pdb=" O THR X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 39 Processing helix chain 'X' and resid 42 through 46 removed outlier: 3.627A pdb=" N GLY X 45 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN X 46 " --> pdb=" O PRO X 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 42 through 46' Processing helix chain 'X' and resid 48 through 57 Processing helix chain 'X' and resid 81 through 89 Processing helix chain 'X' and resid 163 through 167 removed outlier: 3.736A pdb=" N SER X 166 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER X 167 " --> pdb=" O THR X 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 163 through 167' Processing helix chain 'X' and resid 206 through 213 removed outlier: 3.918A pdb=" N LEU X 213 " --> pdb=" O ILE X 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 225 Processing helix chain 'X' and resid 270 through 281 Processing helix chain 'X' and resid 288 through 294 removed outlier: 4.238A pdb=" N ILE X 292 " --> pdb=" O PRO X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 328 Processing helix chain 'X' and resid 346 through 353 Processing helix chain 'X' and resid 358 through 371 Processing helix chain 'X' and resid 379 through 389 removed outlier: 4.050A pdb=" N PHE X 389 " --> pdb=" O PHE X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 409 Processing helix chain 'X' and resid 421 through 437 Processing helix chain 'X' and resid 455 through 480 Processing helix chain 'X' and resid 494 through 508 removed outlier: 4.388A pdb=" N ILE X 498 " --> pdb=" O ASN X 494 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE X 505 " --> pdb=" O ALA X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 519 through 528 removed outlier: 3.774A pdb=" N ARG X 528 " --> pdb=" O ILE X 524 " (cutoff:3.500A) Processing helix chain 'X' and resid 544 through 549 Processing helix chain 'X' and resid 551 through 555 Processing helix chain 'X' and resid 609 through 613 Processing helix chain 'X' and resid 675 through 688 removed outlier: 3.660A pdb=" N ASN X 684 " --> pdb=" O LEU X 680 " (cutoff:3.500A) Processing helix chain 'X' and resid 703 through 712 removed outlier: 4.427A pdb=" N ALA X 707 " --> pdb=" O GLY X 703 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER X 712 " --> pdb=" O VAL X 708 " (cutoff:3.500A) Processing helix chain 'X' and resid 820 through 826 Processing helix chain 'X' and resid 858 through 863 Processing helix chain 'X' and resid 896 through 904 Processing helix chain 'X' and resid 942 through 979 Processing helix chain 'X' and resid 982 through 990 Processing helix chain 'X' and resid 992 through 996 removed outlier: 3.980A pdb=" N ASP X 995 " --> pdb=" O LEU X 992 " (cutoff:3.500A) Processing helix chain 'X' and resid 1003 through 1038 removed outlier: 4.860A pdb=" N ASN X1009 " --> pdb=" O GLU X1005 " (cutoff:3.500A) Processing helix chain 'X' and resid 1101 through 1107 removed outlier: 4.341A pdb=" N SER X1105 " --> pdb=" O LEU X1101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG X1106 " --> pdb=" O GLY X1102 " (cutoff:3.500A) Processing helix chain 'X' and resid 1109 through 1134 removed outlier: 3.511A pdb=" N LEU X1113 " --> pdb=" O ILE X1109 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN X1134 " --> pdb=" O ALA X1130 " (cutoff:3.500A) Processing helix chain 'X' and resid 1137 through 1150 removed outlier: 3.575A pdb=" N LEU X1141 " --> pdb=" O GLU X1137 " (cutoff:3.500A) Processing helix chain 'X' and resid 1167 through 1177 removed outlier: 3.593A pdb=" N ARG X1171 " --> pdb=" O GLU X1167 " (cutoff:3.500A) Processing helix chain 'X' and resid 1191 through 1202 removed outlier: 3.599A pdb=" N ILE X1195 " --> pdb=" O LYS X1191 " (cutoff:3.500A) Processing helix chain 'X' and resid 1260 through 1264 Processing helix chain 'X' and resid 1271 through 1281 removed outlier: 3.819A pdb=" N VAL X1275 " --> pdb=" O GLY X1271 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR X1281 " --> pdb=" O ALA X1277 " (cutoff:3.500A) Processing helix chain 'X' and resid 1283 through 1292 Processing helix chain 'X' and resid 1297 through 1310 removed outlier: 3.818A pdb=" N THR X1302 " --> pdb=" O VAL X1298 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP X1310 " --> pdb=" O LYS X1306 " (cutoff:3.500A) Processing helix chain 'X' and resid 1320 through 1334 removed outlier: 3.644A pdb=" N ASN X1324 " --> pdb=" O PRO X1320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 33 Processing helix chain 'Y' and resid 96 through 101 removed outlier: 3.953A pdb=" N GLU Y 100 " --> pdb=" O LYS Y 96 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 117 removed outlier: 3.785A pdb=" N PHE Y 116 " --> pdb=" O HIS Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 123 through 129 Processing helix chain 'Y' and resid 131 through 140 Processing helix chain 'Y' and resid 161 through 168 removed outlier: 3.634A pdb=" N ALA Y 168 " --> pdb=" O GLN Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 180 through 190 Processing helix chain 'Y' and resid 195 through 208 Processing helix chain 'Y' and resid 211 through 230 Processing helix chain 'Y' and resid 233 through 238 Processing helix chain 'Y' and resid 246 through 250 removed outlier: 3.588A pdb=" N LEU Y 249 " --> pdb=" O PRO Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 285 removed outlier: 4.341A pdb=" N LEU Y 285 " --> pdb=" O ARG Y 281 " (cutoff:3.500A) Processing helix chain 'Y' and resid 289 through 308 removed outlier: 4.379A pdb=" N LEU Y 299 " --> pdb=" O GLU Y 295 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP Y 304 " --> pdb=" O GLN Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 334 Processing helix chain 'Y' and resid 370 through 377 Processing helix chain 'Y' and resid 377 through 388 Processing helix chain 'Y' and resid 393 through 404 Processing helix chain 'Y' and resid 408 through 416 Processing helix chain 'Y' and resid 430 through 432 No H-bonds generated for 'chain 'Y' and resid 430 through 432' Processing helix chain 'Y' and resid 453 through 458 removed outlier: 3.629A pdb=" N TYR Y 457 " --> pdb=" O VAL Y 453 " (cutoff:3.500A) Processing helix chain 'Y' and resid 473 through 483 Processing helix chain 'Y' and resid 503 through 515 Processing helix chain 'Y' and resid 529 through 539 Processing helix chain 'Y' and resid 574 through 580 Processing helix chain 'Y' and resid 597 through 613 Processing helix chain 'Y' and resid 614 through 636 removed outlier: 3.523A pdb=" N VAL Y 618 " --> pdb=" O LEU Y 614 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE Y 619 " --> pdb=" O LYS Y 615 " (cutoff:3.500A) Processing helix chain 'Y' and resid 649 through 671 Processing helix chain 'Y' and resid 674 through 702 removed outlier: 3.836A pdb=" N ASP Y 684 " --> pdb=" O ASN Y 680 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE Y 685 " --> pdb=" O LYS Y 681 " (cutoff:3.500A) Processing helix chain 'Y' and resid 720 through 728 removed outlier: 3.684A pdb=" N SER Y 728 " --> pdb=" O MET Y 724 " (cutoff:3.500A) Processing helix chain 'Y' and resid 733 through 742 Processing helix chain 'Y' and resid 768 through 804 removed outlier: 3.996A pdb=" N LYS Y 781 " --> pdb=" O HIS Y 777 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY Y 782 " --> pdb=" O GLY Y 778 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR Y 786 " --> pdb=" O GLY Y 782 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA Y 787 " --> pdb=" O LEU Y 783 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN Y 792 " --> pdb=" O LEU Y 788 " (cutoff:3.500A) Processing helix chain 'Y' and resid 835 through 840 Processing helix chain 'Y' and resid 865 through 875 Processing helix chain 'Y' and resid 896 through 900 Processing helix chain 'Y' and resid 914 through 925 removed outlier: 4.003A pdb=" N ILE Y 918 " --> pdb=" O ALA Y 914 " (cutoff:3.500A) Processing helix chain 'Y' and resid 926 through 930 Processing helix chain 'Y' and resid 1137 through 1147 Processing helix chain 'Y' and resid 1216 through 1225 Processing helix chain 'Y' and resid 1226 through 1245 removed outlier: 3.702A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1249 through 1261 removed outlier: 4.442A pdb=" N ILE Y1253 " --> pdb=" O ASN Y1249 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Y1261 " --> pdb=" O VAL Y1257 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1282 through 1294 removed outlier: 4.161A pdb=" N GLU Y1291 " --> pdb=" O ILE Y1287 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU Y1292 " --> pdb=" O ALA Y1288 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA Y1294 " --> pdb=" O ARG Y1290 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1308 through 1315 removed outlier: 3.572A pdb=" N LEU Y1314 " --> pdb=" O THR Y1310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1327 through 1339 Processing helix chain 'Y' and resid 1347 through 1352 Processing helix chain 'Y' and resid 1360 through 1373 removed outlier: 4.125A pdb=" N ALA Y1364 " --> pdb=" O GLY Y1360 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR Y1365 " --> pdb=" O THR Y1361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'f' and resid 49 through 57 removed outlier: 8.012A pdb=" N TYR f 80 " --> pdb=" O LEU f 113 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N LYS f 115 " --> pdb=" O TYR f 80 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS f 100 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL f 116 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER f 98 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU f 118 " --> pdb=" O THR f 96 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR f 96 " --> pdb=" O GLU f 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'f' and resid 227 through 230 removed outlier: 7.708A pdb=" N VAL f 228 " --> pdb=" O LEU f 204 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL f 206 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER f 230 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU f 208 " --> pdb=" O SER f 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'f' and resid 227 through 230 removed outlier: 7.708A pdb=" N VAL f 228 " --> pdb=" O LEU f 204 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL f 206 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER f 230 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU f 208 " --> pdb=" O SER f 230 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLY f 174 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA f 319 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE f 176 " --> pdb=" O ALA f 319 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N GLU f 342 " --> pdb=" O ASN f 361 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN f 361 " --> pdb=" O GLU f 342 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS f 344 " --> pdb=" O ASP f 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'f' and resid 284 through 285 removed outlier: 3.983A pdb=" N VAL f 289 " --> pdb=" O LEU f 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 49 through 57 removed outlier: 8.013A pdb=" N TYR a 80 " --> pdb=" O LEU a 113 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N LYS a 115 " --> pdb=" O TYR a 80 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS a 100 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL a 116 " --> pdb=" O SER a 98 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N SER a 98 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU a 118 " --> pdb=" O THR a 96 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR a 96 " --> pdb=" O GLU a 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 227 through 230 removed outlier: 7.708A pdb=" N VAL a 228 " --> pdb=" O LEU a 204 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL a 206 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER a 230 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU a 208 " --> pdb=" O SER a 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 227 through 230 removed outlier: 7.708A pdb=" N VAL a 228 " --> pdb=" O LEU a 204 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL a 206 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER a 230 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU a 208 " --> pdb=" O SER a 230 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLY a 174 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA a 319 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE a 176 " --> pdb=" O ALA a 319 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N GLU a 342 " --> pdb=" O ASN a 361 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ASN a 361 " --> pdb=" O GLU a 342 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS a 344 " --> pdb=" O ASP a 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 284 through 285 removed outlier: 3.984A pdb=" N VAL a 289 " --> pdb=" O LEU a 285 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 49 through 57 removed outlier: 8.012A pdb=" N TYR b 80 " --> pdb=" O LEU b 113 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N LYS b 115 " --> pdb=" O TYR b 80 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS b 100 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL b 116 " --> pdb=" O SER b 98 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER b 98 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU b 118 " --> pdb=" O THR b 96 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR b 96 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 227 through 230 removed outlier: 7.709A pdb=" N VAL b 228 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL b 206 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER b 230 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU b 208 " --> pdb=" O SER b 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 227 through 230 removed outlier: 7.709A pdb=" N VAL b 228 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL b 206 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER b 230 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU b 208 " --> pdb=" O SER b 230 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLY b 174 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA b 319 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE b 176 " --> pdb=" O ALA b 319 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N GLU b 342 " --> pdb=" O ASN b 361 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN b 361 " --> pdb=" O GLU b 342 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS b 344 " --> pdb=" O ASP b 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 284 through 285 removed outlier: 3.984A pdb=" N VAL b 289 " --> pdb=" O LEU b 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 49 through 57 removed outlier: 8.013A pdb=" N TYR c 80 " --> pdb=" O LEU c 113 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N LYS c 115 " --> pdb=" O TYR c 80 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS c 100 " --> pdb=" O LEU c 114 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL c 116 " --> pdb=" O SER c 98 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER c 98 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU c 118 " --> pdb=" O THR c 96 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR c 96 " --> pdb=" O GLU c 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 227 through 230 removed outlier: 7.708A pdb=" N VAL c 228 " --> pdb=" O LEU c 204 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL c 206 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER c 230 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU c 208 " --> pdb=" O SER c 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 227 through 230 removed outlier: 7.708A pdb=" N VAL c 228 " --> pdb=" O LEU c 204 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL c 206 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER c 230 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU c 208 " --> pdb=" O SER c 230 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLY c 174 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA c 319 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE c 176 " --> pdb=" O ALA c 319 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N GLU c 342 " --> pdb=" O ASN c 361 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN c 361 " --> pdb=" O GLU c 342 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS c 344 " --> pdb=" O ASP c 359 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 284 through 285 removed outlier: 3.984A pdb=" N VAL c 289 " --> pdb=" O LEU c 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 49 through 57 removed outlier: 8.012A pdb=" N TYR d 80 " --> pdb=" O LEU d 113 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N LYS d 115 " --> pdb=" O TYR d 80 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS d 100 " --> pdb=" O LEU d 114 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL d 116 " --> pdb=" O SER d 98 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER d 98 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU d 118 " --> pdb=" O THR d 96 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR d 96 " --> pdb=" O GLU d 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.708A pdb=" N VAL d 228 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL d 206 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER d 230 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU d 208 " --> pdb=" O SER d 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.708A pdb=" N VAL d 228 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL d 206 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER d 230 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU d 208 " --> pdb=" O SER d 230 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLY d 174 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA d 319 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE d 176 " --> pdb=" O ALA d 319 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N GLU d 342 " --> pdb=" O ASN d 361 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN d 361 " --> pdb=" O GLU d 342 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS d 344 " --> pdb=" O ASP d 359 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 284 through 285 removed outlier: 3.984A pdb=" N VAL d 289 " --> pdb=" O LEU d 285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 49 through 57 removed outlier: 8.012A pdb=" N TYR e 80 " --> pdb=" O LEU e 113 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N LYS e 115 " --> pdb=" O TYR e 80 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS e 100 " --> pdb=" O LEU e 114 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL e 116 " --> pdb=" O SER e 98 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER e 98 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU e 118 " --> pdb=" O THR e 96 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR e 96 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 227 through 230 removed outlier: 7.709A pdb=" N VAL e 228 " --> pdb=" O LEU e 204 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL e 206 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER e 230 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU e 208 " --> pdb=" O SER e 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 227 through 230 removed outlier: 7.709A pdb=" N VAL e 228 " --> pdb=" O LEU e 204 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL e 206 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER e 230 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU e 208 " --> pdb=" O SER e 230 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLY e 174 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA e 319 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE e 176 " --> pdb=" O ALA e 319 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N GLU e 342 " --> pdb=" O ASN e 361 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN e 361 " --> pdb=" O GLU e 342 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N HIS e 344 " --> pdb=" O ASP e 359 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 284 through 285 removed outlier: 3.984A pdb=" N VAL e 289 " --> pdb=" O LEU e 285 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 137 through 138 removed outlier: 3.691A pdb=" N ILE A 138 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY A 181 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 196 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 142 through 145 removed outlier: 4.890A pdb=" N VAL A 142 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASP A 153 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 222 through 229 removed outlier: 4.978A pdb=" N ILE A 223 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS A 239 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL A 274 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE A 236 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 293 through 299 Processing sheet with id=AD2, first strand: chain 'U' and resid 12 through 15 removed outlier: 6.396A pdb=" N THR U 27 " --> pdb=" O VAL U 14 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N HIS U 23 " --> pdb=" O THR U 207 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR U 207 " --> pdb=" O HIS U 23 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS U 25 " --> pdb=" O MET U 205 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N MET U 205 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR U 27 " --> pdb=" O ILE U 203 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE U 203 " --> pdb=" O THR U 27 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU U 29 " --> pdb=" O LEU U 201 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU U 201 " --> pdb=" O GLU U 29 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'U' and resid 52 through 53 removed outlier: 3.913A pdb=" N GLY U 53 " --> pdb=" O GLY U 149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 97 through 104 removed outlier: 3.629A pdb=" N GLU U 58 " --> pdb=" O LYS U 145 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN U 147 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL U 56 " --> pdb=" O GLN U 147 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 90 through 91 Processing sheet with id=AD6, first strand: chain 'U' and resid 108 through 111 Processing sheet with id=AD7, first strand: chain 'V' and resid 16 through 17 Processing sheet with id=AD8, first strand: chain 'V' and resid 53 through 61 removed outlier: 6.095A pdb=" N CYS V 54 " --> pdb=" O GLY V 149 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY V 149 " --> pdb=" O CYS V 54 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET V 142 " --> pdb=" O LEU V 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 90 through 92 Processing sheet with id=AE1, first strand: chain 'V' and resid 110 through 111 removed outlier: 6.790A pdb=" N VAL V 110 " --> pdb=" O ILE V 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'V' and resid 152 through 153 Processing sheet with id=AE3, first strand: chain 'X' and resid 13 through 14 removed outlier: 6.326A pdb=" N LYS X 13 " --> pdb=" O ALA X1183 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 67 through 75 removed outlier: 6.886A pdb=" N LYS X 99 " --> pdb=" O VAL X 71 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR X 73 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG X 97 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU X 75 " --> pdb=" O PRO X 95 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA X 94 " --> pdb=" O GLU X 126 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU X 126 " --> pdb=" O ALA X 94 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU X 96 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE X 104 " --> pdb=" O ASP X 116 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP X 116 " --> pdb=" O ILE X 104 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 136 through 137 Processing sheet with id=AE6, first strand: chain 'X' and resid 451 through 454 removed outlier: 6.525A pdb=" N SER X 147 " --> pdb=" O SER X 531 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 154 through 160 removed outlier: 3.536A pdb=" N LEU X 204 " --> pdb=" O VAL X 196 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 229 through 230 Processing sheet with id=AE9, first strand: chain 'X' and resid 580 through 581 removed outlier: 5.940A pdb=" N GLU X 602 " --> pdb=" O LYS X 593 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 580 through 581 Processing sheet with id=AF2, first strand: chain 'X' and resid 616 through 617 removed outlier: 3.875A pdb=" N ILE X 616 " --> pdb=" O ARG X 637 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG X 637 " --> pdb=" O ILE X 616 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 716 through 717 removed outlier: 6.579A pdb=" N ALA X 716 " --> pdb=" O LEU X 783 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 748 through 752 removed outlier: 5.695A pdb=" N LYS X 735 " --> pdb=" O VAL X 724 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL X 724 " --> pdb=" O LYS X 735 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 757 through 758 removed outlier: 3.502A pdb=" N THR X 757 " --> pdb=" O ILE X 765 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 798 through 804 removed outlier: 8.681A pdb=" N ILE X1096 " --> pdb=" O ASN X 799 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG X 801 " --> pdb=" O ILE X1096 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU X1098 " --> pdb=" O ARG X 801 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA X 803 " --> pdb=" O LEU X1098 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE X 816 " --> pdb=" O SER X1077 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE X1079 " --> pdb=" O ILE X 816 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL X 818 " --> pdb=" O ILE X1079 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 830 through 841 removed outlier: 6.367A pdb=" N THR X 830 " --> pdb=" O LYS X1057 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS X1057 " --> pdb=" O THR X 830 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N HIS X 832 " --> pdb=" O ALA X1055 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA X1055 " --> pdb=" O HIS X 832 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN X 834 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR X1053 " --> pdb=" O GLN X 834 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU X 836 " --> pdb=" O LYS X1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS X1051 " --> pdb=" O LEU X 836 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS X 838 " --> pdb=" O ILE X1049 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE X1049 " --> pdb=" O CYS X 838 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER X 840 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU X1047 " --> pdb=" O THR X 935 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR X 935 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE X1049 " --> pdb=" O VAL X 933 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL X 933 " --> pdb=" O ILE X1049 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS X1051 " --> pdb=" O VAL X 931 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL X 931 " --> pdb=" O LYS X1051 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR X1053 " --> pdb=" O ILE X 929 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 1087 through 1088 Processing sheet with id=AF9, first strand: chain 'X' and resid 1244 through 1246 Processing sheet with id=AG1, first strand: chain 'X' and resid 1244 through 1246 removed outlier: 7.709A pdb=" N ILE Y 447 " --> pdb=" O ARG Y 352 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL Y 354 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU Y 449 " --> pdb=" O VAL Y 354 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N THR Y 356 " --> pdb=" O LEU Y 449 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 34 through 37 removed outlier: 7.441A pdb=" N HIS Y 104 " --> pdb=" O PHE Y 35 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU Y 37 " --> pdb=" O HIS Y 104 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLU Y 106 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU Y 107 " --> pdb=" O THR Y 240 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR Y 240 " --> pdb=" O LEU Y 107 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 145 through 147 removed outlier: 3.558A pdb=" N VAL Y 145 " --> pdb=" O LYS Y 179 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP Y 177 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 526 through 527 Processing sheet with id=AG5, first strand: chain 'Y' and resid 809 through 811 Processing sheet with id=AG6, first strand: chain 'Y' and resid 819 through 822 Processing sheet with id=AG7, first strand: chain 'Y' and resid 957 through 961 removed outlier: 3.690A pdb=" N GLU Y 981 " --> pdb=" O SER Y 961 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU Y 993 " --> pdb=" O LEU Y 984 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id=AG9, first strand: chain 'Y' and resid 1099 through 1100 removed outlier: 4.334A pdb=" N LYS Y1079 " --> pdb=" O ARG Y1036 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG Y1036 " --> pdb=" O LYS Y1079 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Y1035 " --> pdb=" O VAL Y1113 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL Y1113 " --> pdb=" O VAL Y1035 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 1059 through 1060 removed outlier: 3.687A pdb=" N ARG Y1123 " --> pdb=" O ILE Y1106 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 1162 through 1164 removed outlier: 3.529A pdb=" N LEU Y1175 " --> pdb=" O GLU Y1188 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU Y1188 " --> pdb=" O LEU Y1175 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 1280 through 1281 2146 hydrogen bonds defined for protein. 6045 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 23.94 Time building geometry restraints manager: 12.17 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: 14463 1.33 - 1.45: 7926 1.45 - 1.57: 29491 1.57 - 1.69: 193 1.69 - 1.81: 408 Bond restraints: 52481 Sorted by residual: bond pdb=" F2 BEF a1002 " pdb="BE BEF a1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" F2 BEF e1002 " pdb="BE BEF e1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF d1002 " pdb="BE BEF d1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF b1002 " pdb="BE BEF b1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 52476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 70614 2.54 - 5.08: 531 5.08 - 7.61: 66 7.61 - 10.15: 9 10.15 - 12.69: 6 Bond angle restraints: 71226 Sorted by residual: angle pdb=" C LEU Y 268 " pdb=" N TYR Y 269 " pdb=" CA TYR Y 269 " ideal model delta sigma weight residual 122.06 113.83 8.23 1.86e+00 2.89e-01 1.96e+01 angle pdb=" C SER Y 119 " pdb=" N LEU Y 120 " pdb=" CA LEU Y 120 " ideal model delta sigma weight residual 121.80 132.15 -10.35 2.44e+00 1.68e-01 1.80e+01 angle pdb=" F2 BEF d1002 " pdb="BE BEF d1002 " pdb=" F3 BEF d1002 " ideal model delta sigma weight residual 119.96 107.27 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 107.30 12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" F2 BEF b1002 " pdb="BE BEF b1002 " pdb=" F3 BEF b1002 " ideal model delta sigma weight residual 119.96 107.36 12.60 3.00e+00 1.11e-01 1.76e+01 ... (remaining 71221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 31315 35.35 - 70.71: 865 70.71 - 106.06: 65 106.06 - 141.41: 5 141.41 - 176.77: 8 Dihedral angle restraints: 32258 sinusoidal: 14100 harmonic: 18158 Sorted by residual: dihedral pdb=" CA LEU Y 120 " pdb=" C LEU Y 120 " pdb=" N PRO Y 121 " pdb=" CA PRO Y 121 " ideal model delta harmonic sigma weight residual 180.00 126.09 53.91 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" C4' U R 23 " pdb=" C3' U R 23 " pdb=" C2' U R 23 " pdb=" C1' U R 23 " ideal model delta sinusoidal sigma weight residual -35.00 34.87 -69.87 1 8.00e+00 1.56e-02 9.84e+01 dihedral pdb=" C5' U R 23 " pdb=" C4' U R 23 " pdb=" C3' U R 23 " pdb=" O3' U R 23 " ideal model delta sinusoidal sigma weight residual 147.00 81.08 65.92 1 8.00e+00 1.56e-02 8.88e+01 ... (remaining 32255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 7022 0.058 - 0.116: 1064 0.116 - 0.175: 63 0.175 - 0.233: 2 0.233 - 0.291: 1 Chirality restraints: 8152 Sorted by residual: chirality pdb=" C3' U R 23 " pdb=" C4' U R 23 " pdb=" O3' U R 23 " pdb=" C2' U R 23 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' U R 23 " pdb=" C3' U R 23 " pdb=" O2' U R 23 " pdb=" C1' U R 23 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR Y 269 " pdb=" N TYR Y 269 " pdb=" C TYR Y 269 " pdb=" CB TYR Y 269 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 8149 not shown) Planarity restraints: 8987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Y 120 " 0.061 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO Y 121 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO Y 121 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO Y 121 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU Y 658 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C GLU Y 658 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU Y 658 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA Y 659 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO Y 288 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C PRO Y 288 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO Y 288 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP Y 289 " 0.011 2.00e-02 2.50e+03 ... (remaining 8984 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 592 2.54 - 3.13: 40956 3.13 - 3.72: 84083 3.72 - 4.31: 112303 4.31 - 4.90: 179496 Nonbonded interactions: 417430 Sorted by model distance: nonbonded pdb=" O1B ADP a1000 " pdb="MG MG a1001 " model vdw 1.954 2.170 nonbonded pdb="MG MG a1001 " pdb=" O HOH a1101 " model vdw 1.981 2.170 nonbonded pdb=" O2B ADP d1000 " pdb="MG MG d1001 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR a 185 " pdb="MG MG a1001 " model vdw 2.003 2.170 nonbonded pdb=" O2B ADP e1000 " pdb="MG MG e1001 " model vdw 2.009 2.170 ... (remaining 417425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and resid 1 through 417) selection = (chain 'b' and resid 1 through 417) selection = (chain 'c' and resid 1 through 417) selection = (chain 'd' and resid 1 through 417) selection = (chain 'e' and resid 1 through 417) selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 1.620 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 114.010 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.210 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.003 0.086 52481 Z= 0.167 Angle : 0.588 12.688 71226 Z= 0.323 Chirality : 0.041 0.291 8152 Planarity : 0.004 0.093 8987 Dihedral : 15.512 176.765 20536 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.34 % Rotamer: Outliers : 3.12 % Allowed : 5.80 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -3.15 (0.09), residues: 6289 helix: -1.23 (0.10), residues: 2316 sheet: -2.14 (0.15), residues: 800 loop : -2.79 (0.10), residues: 3173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X1276 HIS 0.003 0.000 HIS b 239 PHE 0.021 0.001 PHE Y 141 TYR 0.020 0.001 TYR Y 269 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 385 time to evaluate : 4.626 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: f 186 MET cc_start: 0.8763 (pmm) cc_final: 0.8379 (pmm) REVERT: f 217 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8706 (p) REVERT: f 396 MET cc_start: 0.8848 (tpt) cc_final: 0.8558 (tpp) REVERT: b 31 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8731 (tmtt) REVERT: c 21 MET cc_start: 0.8439 (mmm) cc_final: 0.8044 (mtt) REVERT: c 137 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.5231 (t) REVERT: d 266 SER cc_start: 0.6825 (OUTLIER) cc_final: 0.6542 (t) REVERT: d 318 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7925 (p) REVERT: e 186 MET cc_start: 0.8501 (pmm) cc_final: 0.8251 (pmm) REVERT: e 266 SER cc_start: 0.6420 (OUTLIER) cc_final: 0.4573 (t) REVERT: e 312 SER cc_start: 0.6341 (OUTLIER) cc_final: 0.5528 (t) REVERT: e 320 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9104 (mm) REVERT: e 374 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.9089 (mm110) REVERT: e 396 MET cc_start: 0.9287 (tpt) cc_final: 0.9059 (mmm) REVERT: A 288 MET cc_start: 0.7497 (mtm) cc_final: 0.6497 (ppp) REVERT: A 334 TRP cc_start: 0.7827 (m-10) cc_final: 0.7080 (m-10) REVERT: A 339 MET cc_start: 0.6063 (mmt) cc_final: 0.5244 (mpp) REVERT: V 236 ASP cc_start: 0.8138 (m-30) cc_final: 0.7794 (p0) REVERT: W 22 VAL cc_start: 0.9580 (t) cc_final: 0.9311 (t) REVERT: W 26 ARG cc_start: 0.9378 (tpt90) cc_final: 0.9160 (tpt90) REVERT: W 30 MET cc_start: 0.9378 (ptm) cc_final: 0.9058 (ptm) REVERT: W 39 VAL cc_start: 0.7339 (t) cc_final: 0.6707 (p) REVERT: W 53 GLU cc_start: 0.8904 (pt0) cc_final: 0.8492 (mt-10) REVERT: W 61 ASN cc_start: 0.9061 (t0) cc_final: 0.8836 (t0) REVERT: W 64 LEU cc_start: 0.8116 (pp) cc_final: 0.7834 (pp) REVERT: X 1230 MET cc_start: 0.6392 (ttm) cc_final: 0.5803 (ttm) REVERT: Y 115 TRP cc_start: 0.8970 (m-10) cc_final: 0.8686 (m-10) REVERT: Y 166 LEU cc_start: 0.9067 (tp) cc_final: 0.8762 (pp) outliers start: 168 outliers final: 33 residues processed: 535 average time/residue: 0.5410 time to fit residues: 471.7277 Evaluate side-chains 316 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 274 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 534 optimal weight: 20.0000 chunk 479 optimal weight: 8.9990 chunk 266 optimal weight: 0.9980 chunk 163 optimal weight: 0.0060 chunk 323 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 496 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 301 optimal weight: 6.9990 chunk 369 optimal weight: 10.0000 chunk 574 optimal weight: 2.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 256 HIS f 401 ASN a 256 HIS a 401 ASN b 256 HIS b 401 ASN ** c 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 256 HIS c 401 ASN d 220 GLN d 241 GLN d 256 HIS d 401 ASN e 220 GLN ** e 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN e 401 ASN A 70 GLN A 88 ASN A 133 HIS A 157 ASN A 172 ASN A 313 ASN A 330 GLN A 349 GLN A 412 ASN A 428 ASN A 462 GLN U 37 HIS U 132 HIS U 147 GLN V 93 GLN W 43 ASN X 41 GLN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 214 ASN X 238 GLN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 343 HIS X 604 HIS ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 808 ASN X 932 GLN X1008 GLN X1010 GLN X1013 GLN X1256 GLN Y 80 HIS ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 335 GLN Y 365 GLN Y 488 ASN Y 545 HIS Y 702 GLN Y 865 HIS ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1259 GLN Y1326 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 52481 Z= 0.215 Angle : 0.596 9.707 71226 Z= 0.304 Chirality : 0.041 0.218 8152 Planarity : 0.004 0.090 8987 Dihedral : 13.191 177.155 8057 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.10), residues: 6289 helix: -0.03 (0.11), residues: 2333 sheet: -1.89 (0.16), residues: 821 loop : -2.30 (0.10), residues: 3135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Y1020 HIS 0.005 0.001 HIS c 42 PHE 0.033 0.001 PHE f 412 TYR 0.034 0.001 TYR Y 269 ARG 0.011 0.000 ARG Y 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 297 time to evaluate : 4.607 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: f 219 MET cc_start: 0.8069 (mmp) cc_final: 0.7862 (mmm) REVERT: f 396 MET cc_start: 0.8858 (tpt) cc_final: 0.8577 (tpp) REVERT: a 29 MET cc_start: 0.2342 (ptt) cc_final: 0.1395 (ptp) REVERT: a 343 LEU cc_start: 0.8722 (mt) cc_final: 0.8499 (mt) REVERT: b 21 MET cc_start: 0.6970 (mtp) cc_final: 0.6501 (mtp) REVERT: b 186 MET cc_start: 0.6986 (pmm) cc_final: 0.6724 (pmm) REVERT: b 380 MET cc_start: 0.8998 (mtm) cc_final: 0.8667 (mtm) REVERT: c 21 MET cc_start: 0.8562 (mmm) cc_final: 0.8202 (mtt) REVERT: c 186 MET cc_start: 0.7724 (ptp) cc_final: 0.7336 (ptp) REVERT: c 397 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8837 (pp20) REVERT: e 186 MET cc_start: 0.8435 (pmm) cc_final: 0.8200 (pmm) REVERT: e 396 MET cc_start: 0.9412 (tpt) cc_final: 0.9138 (mmm) REVERT: A 288 MET cc_start: 0.7620 (mtm) cc_final: 0.5627 (tpt) REVERT: A 334 TRP cc_start: 0.7589 (m-10) cc_final: 0.7356 (m-10) REVERT: A 339 MET cc_start: 0.5965 (mmt) cc_final: 0.5196 (mpp) REVERT: A 428 ASN cc_start: -0.1190 (OUTLIER) cc_final: -0.1947 (p0) REVERT: V 236 ASP cc_start: 0.8261 (m-30) cc_final: 0.7818 (p0) REVERT: W 26 ARG cc_start: 0.9596 (tpt90) cc_final: 0.9181 (tpt90) REVERT: W 30 MET cc_start: 0.9209 (ptm) cc_final: 0.8889 (ptm) REVERT: X 681 MET cc_start: 0.8376 (pmm) cc_final: 0.7952 (pmm) REVERT: Y 192 MET cc_start: 0.8284 (mmp) cc_final: 0.7718 (mmm) REVERT: Y 697 MET cc_start: 0.8371 (ttp) cc_final: 0.8043 (ttm) REVERT: Y 1040 MET cc_start: 0.6606 (mtm) cc_final: 0.5858 (mpp) REVERT: Y 1145 PHE cc_start: 0.7627 (m-80) cc_final: 0.7002 (m-80) REVERT: Y 1260 MET cc_start: 0.7837 (tpt) cc_final: 0.7290 (tpt) outliers start: 6 outliers final: 0 residues processed: 303 average time/residue: 0.5732 time to fit residues: 288.0346 Evaluate side-chains 263 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 4.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 319 optimal weight: 10.0000 chunk 178 optimal weight: 40.0000 chunk 478 optimal weight: 5.9990 chunk 391 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 575 optimal weight: 10.0000 chunk 622 optimal weight: 20.0000 chunk 512 optimal weight: 8.9990 chunk 571 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 461 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 HIS f 190 ASN f 275 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 HIS a 190 ASN a 275 ASN ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN b 275 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS c 172 GLN c 190 ASN c 275 ASN c 344 HIS ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 90 ASN d 190 ASN d 256 HIS d 275 ASN d 295 HIS ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 GLN A 88 ASN A 149 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN U 208 ASN ** V 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 283 GLN X 36 GLN X 65 ASN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 628 HIS ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1023 HIS ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 335 GLN ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 805 GLN ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1044 GLN Y1244 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 52481 Z= 0.363 Angle : 0.752 14.763 71226 Z= 0.385 Chirality : 0.043 0.220 8152 Planarity : 0.005 0.102 8987 Dihedral : 13.312 172.508 8057 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.07 % Allowed : 5.37 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.10), residues: 6289 helix: -0.06 (0.10), residues: 2382 sheet: -1.79 (0.16), residues: 838 loop : -2.04 (0.11), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 115 HIS 0.010 0.002 HIS Y 777 PHE 0.044 0.002 PHE f 412 TYR 0.026 0.002 TYR b 274 ARG 0.020 0.001 ARG V 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 274 time to evaluate : 4.948 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: f 219 MET cc_start: 0.8647 (mmp) cc_final: 0.8405 (mmm) REVERT: f 327 MET cc_start: 0.9105 (ptp) cc_final: 0.8314 (pmm) REVERT: f 341 MET cc_start: 0.7777 (tmm) cc_final: 0.7576 (tmm) REVERT: f 343 LEU cc_start: 0.8888 (mt) cc_final: 0.8676 (mt) REVERT: f 396 MET cc_start: 0.8750 (tpt) cc_final: 0.8461 (tpp) REVERT: f 405 MET cc_start: 0.8520 (ptt) cc_final: 0.8315 (ppp) REVERT: f 416 MET cc_start: 0.9141 (mpp) cc_final: 0.8884 (mpp) REVERT: a 29 MET cc_start: 0.3010 (ptt) cc_final: 0.1765 (ptp) REVERT: a 245 MET cc_start: 0.8600 (mmm) cc_final: 0.8374 (mmm) REVERT: a 341 MET cc_start: 0.7861 (tmm) cc_final: 0.7349 (tmm) REVERT: b 21 MET cc_start: 0.7543 (mtp) cc_final: 0.7322 (mtp) REVERT: b 186 MET cc_start: 0.7866 (pmm) cc_final: 0.7443 (pmm) REVERT: b 380 MET cc_start: 0.9000 (mtm) cc_final: 0.8613 (mtp) REVERT: b 390 MET cc_start: 0.8516 (ptm) cc_final: 0.7943 (ptt) REVERT: c 21 MET cc_start: 0.8886 (mmm) cc_final: 0.8560 (mtt) REVERT: c 29 MET cc_start: 0.8420 (ptm) cc_final: 0.7512 (ptp) REVERT: c 219 MET cc_start: 0.7837 (mmm) cc_final: 0.7625 (mmm) REVERT: c 380 MET cc_start: 0.8908 (mtm) cc_final: 0.8531 (mtp) REVERT: d 186 MET cc_start: 0.8339 (ptp) cc_final: 0.7941 (ptt) REVERT: e 1 MET cc_start: 0.7870 (ppp) cc_final: 0.7334 (ppp) REVERT: e 21 MET cc_start: 0.8960 (mtp) cc_final: 0.8359 (tpp) REVERT: e 186 MET cc_start: 0.8549 (pmm) cc_final: 0.8277 (pmm) REVERT: A 288 MET cc_start: 0.7611 (mtm) cc_final: 0.7303 (ppp) REVERT: V 236 ASP cc_start: 0.8218 (m-30) cc_final: 0.7813 (p0) REVERT: W 26 ARG cc_start: 0.9494 (tpt90) cc_final: 0.9028 (tpt90) REVERT: W 41 GLU cc_start: 0.8952 (tt0) cc_final: 0.8751 (tt0) REVERT: W 71 GLU cc_start: 0.9138 (pp20) cc_final: 0.8868 (pp20) REVERT: X 315 MET cc_start: 0.8961 (tpp) cc_final: 0.8709 (mmm) REVERT: X 681 MET cc_start: 0.8634 (pmm) cc_final: 0.8218 (pmm) REVERT: Y 166 LEU cc_start: 0.9378 (tp) cc_final: 0.9146 (pp) REVERT: Y 192 MET cc_start: 0.8296 (mmp) cc_final: 0.7615 (mmm) REVERT: Y 697 MET cc_start: 0.8491 (ttp) cc_final: 0.8182 (ttm) REVERT: Y 1040 MET cc_start: 0.7239 (mtm) cc_final: 0.6658 (mtt) REVERT: Y 1145 PHE cc_start: 0.8295 (m-80) cc_final: 0.7613 (m-80) REVERT: Y 1260 MET cc_start: 0.8033 (tpt) cc_final: 0.7576 (tpp) outliers start: 4 outliers final: 0 residues processed: 276 average time/residue: 0.5417 time to fit residues: 251.8853 Evaluate side-chains 236 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 4.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 568 optimal weight: 7.9990 chunk 432 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 386 optimal weight: 40.0000 chunk 577 optimal weight: 9.9990 chunk 611 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 547 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 241 GLN ** f 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN a 256 HIS ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS b 256 HIS ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 295 HIS ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 488 ASN Y 805 GLN ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 52481 Z= 0.270 Angle : 0.637 9.738 71226 Z= 0.324 Chirality : 0.042 0.235 8152 Planarity : 0.004 0.099 8987 Dihedral : 13.112 171.539 8057 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % Twisted General : 0.02 % 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: -1.52 (0.10), residues: 6289 helix: 0.27 (0.11), residues: 2412 sheet: -1.77 (0.16), residues: 839 loop : -1.85 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 115 HIS 0.010 0.001 HIS V 160 PHE 0.028 0.002 PHE f 412 TYR 0.030 0.002 TYR Y 269 ARG 0.012 0.001 ARG W 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 258 time to evaluate : 4.721 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: f 219 MET cc_start: 0.8581 (mmp) cc_final: 0.8255 (mmm) REVERT: f 327 MET cc_start: 0.9178 (ptp) cc_final: 0.8951 (ptm) REVERT: a 29 MET cc_start: 0.2334 (ptt) cc_final: 0.1106 (ptp) REVERT: a 245 MET cc_start: 0.8528 (mmm) cc_final: 0.8220 (mmm) REVERT: a 341 MET cc_start: 0.7951 (tmm) cc_final: 0.7506 (tmm) REVERT: a 343 LEU cc_start: 0.8880 (mt) cc_final: 0.8634 (mt) REVERT: b 21 MET cc_start: 0.7609 (mtp) cc_final: 0.7409 (mtp) REVERT: b 380 MET cc_start: 0.8996 (mtm) cc_final: 0.8570 (ptp) REVERT: b 390 MET cc_start: 0.8522 (ptm) cc_final: 0.8194 (ptp) REVERT: c 21 MET cc_start: 0.8963 (mmm) cc_final: 0.8667 (mtt) REVERT: c 29 MET cc_start: 0.8365 (ptm) cc_final: 0.7382 (ptp) REVERT: c 219 MET cc_start: 0.7725 (mmm) cc_final: 0.7446 (mmm) REVERT: c 380 MET cc_start: 0.8981 (mtm) cc_final: 0.8576 (mtp) REVERT: d 219 MET cc_start: 0.7599 (mmp) cc_final: 0.6939 (mmm) REVERT: e 1 MET cc_start: 0.8165 (ppp) cc_final: 0.7709 (ppp) REVERT: e 147 MET cc_start: 0.8610 (mmp) cc_final: 0.8315 (mmm) REVERT: e 197 TYR cc_start: 0.9148 (t80) cc_final: 0.8944 (t80) REVERT: e 396 MET cc_start: 0.9217 (mmp) cc_final: 0.8762 (mmm) REVERT: e 405 MET cc_start: 0.9533 (pmm) cc_final: 0.9310 (pmm) REVERT: V 236 ASP cc_start: 0.8183 (m-30) cc_final: 0.7651 (p0) REVERT: W 11 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: W 26 ARG cc_start: 0.9501 (tpt90) cc_final: 0.8322 (tpt90) REVERT: W 30 MET cc_start: 0.9075 (ptp) cc_final: 0.8780 (ptp) REVERT: W 67 ARG cc_start: 0.8760 (ttp-170) cc_final: 0.8535 (ptt180) REVERT: X 315 MET cc_start: 0.8789 (tpp) cc_final: 0.8486 (mmm) REVERT: X 1119 MET cc_start: 0.8395 (tpp) cc_final: 0.8152 (tpp) REVERT: X 1232 MET cc_start: 0.7943 (mmm) cc_final: 0.7651 (mmm) REVERT: Y 298 MET cc_start: 0.2780 (ttt) cc_final: 0.2521 (ttt) REVERT: Y 1145 PHE cc_start: 0.8419 (m-80) cc_final: 0.7734 (m-80) REVERT: Y 1260 MET cc_start: 0.7964 (tpt) cc_final: 0.7466 (tpp) outliers start: 4 outliers final: 2 residues processed: 262 average time/residue: 0.5677 time to fit residues: 252.4105 Evaluate side-chains 238 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 4.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 509 optimal weight: 5.9990 chunk 347 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 455 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 522 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 549 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 90 ASN a 172 GLN ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 2 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 GLN X 238 GLN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 761 GLN ** X 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 805 GLN ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 52481 Z= 0.311 Angle : 0.686 12.335 71226 Z= 0.348 Chirality : 0.042 0.270 8152 Planarity : 0.005 0.101 8987 Dihedral : 13.171 172.253 8057 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.10), residues: 6289 helix: 0.33 (0.10), residues: 2412 sheet: -1.76 (0.16), residues: 823 loop : -1.70 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 115 HIS 0.010 0.001 HIS Y 777 PHE 0.032 0.002 PHE f 412 TYR 0.021 0.002 TYR Y 269 ARG 0.009 0.001 ARG f 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 4.665 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: f 1 MET cc_start: 0.8631 (ppp) cc_final: 0.8296 (ppp) REVERT: f 327 MET cc_start: 0.9170 (ptp) cc_final: 0.8850 (ptm) REVERT: f 396 MET cc_start: 0.8737 (mmm) cc_final: 0.8345 (tpp) REVERT: a 29 MET cc_start: 0.2456 (ptt) cc_final: 0.2238 (ptt) REVERT: a 245 MET cc_start: 0.8628 (mmm) cc_final: 0.8124 (mmm) REVERT: a 343 LEU cc_start: 0.8938 (mt) cc_final: 0.8657 (mt) REVERT: b 21 MET cc_start: 0.7615 (mtp) cc_final: 0.7390 (mtp) REVERT: b 186 MET cc_start: 0.8164 (pmm) cc_final: 0.7756 (pmm) REVERT: b 380 MET cc_start: 0.9011 (mtm) cc_final: 0.8607 (mtp) REVERT: b 390 MET cc_start: 0.8507 (ptm) cc_final: 0.7895 (ptm) REVERT: c 21 MET cc_start: 0.9019 (mmm) cc_final: 0.8726 (mtt) REVERT: c 219 MET cc_start: 0.7818 (mmm) cc_final: 0.7288 (mmm) REVERT: c 327 MET cc_start: 0.8136 (mmm) cc_final: 0.7732 (mmm) REVERT: c 380 MET cc_start: 0.8990 (mtm) cc_final: 0.8560 (mtp) REVERT: d 29 MET cc_start: 0.8194 (pmm) cc_final: 0.7732 (pmm) REVERT: d 219 MET cc_start: 0.8111 (mmp) cc_final: 0.7285 (mmm) REVERT: e 1 MET cc_start: 0.8246 (ppp) cc_final: 0.7791 (ppp) REVERT: e 147 MET cc_start: 0.8757 (mmp) cc_final: 0.8510 (mmm) REVERT: e 197 TYR cc_start: 0.9197 (t80) cc_final: 0.8996 (t80) REVERT: e 396 MET cc_start: 0.9143 (mmp) cc_final: 0.8806 (mmm) REVERT: U 51 MET cc_start: 0.8695 (mmm) cc_final: 0.8413 (mmm) REVERT: V 142 MET cc_start: 0.8454 (pmm) cc_final: 0.8225 (pmm) REVERT: V 236 ASP cc_start: 0.8397 (m-30) cc_final: 0.7743 (p0) REVERT: W 26 ARG cc_start: 0.9611 (tpt90) cc_final: 0.8976 (tpt90) REVERT: W 30 MET cc_start: 0.9088 (ptp) cc_final: 0.8778 (ptt) REVERT: X 315 MET cc_start: 0.8779 (tpp) cc_final: 0.8415 (mmm) REVERT: X 681 MET cc_start: 0.8578 (pmm) cc_final: 0.8080 (pmm) REVERT: X 1232 MET cc_start: 0.8105 (mmm) cc_final: 0.7659 (mmm) REVERT: Y 192 MET cc_start: 0.7646 (mmm) cc_final: 0.7015 (mmm) REVERT: Y 237 MET cc_start: 0.8731 (ttt) cc_final: 0.8242 (tpt) REVERT: Y 1145 PHE cc_start: 0.8591 (m-80) cc_final: 0.8004 (m-80) outliers start: 1 outliers final: 1 residues processed: 249 average time/residue: 0.5233 time to fit residues: 221.1082 Evaluate side-chains 233 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 4.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 205 optimal weight: 10.0000 chunk 551 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 359 optimal weight: 0.0050 chunk 151 optimal weight: 20.0000 chunk 612 optimal weight: 5.9990 chunk 508 optimal weight: 5.9990 chunk 283 optimal weight: 40.0000 chunk 50 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 193 GLN ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN d 90 ASN ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 25 ASN A 2 ASN V 37 HIS V 160 HIS ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 238 GLN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 798 GLN ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 52481 Z= 0.209 Angle : 0.607 9.836 71226 Z= 0.307 Chirality : 0.042 0.242 8152 Planarity : 0.004 0.099 8987 Dihedral : 13.016 174.529 8057 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.74 % Rotamer: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.11), residues: 6289 helix: 0.53 (0.11), residues: 2453 sheet: -1.63 (0.16), residues: 837 loop : -1.62 (0.11), residues: 2999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X1276 HIS 0.006 0.001 HIS Y 777 PHE 0.022 0.001 PHE f 412 TYR 0.031 0.001 TYR Y 269 ARG 0.008 0.000 ARG f 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 250 time to evaluate : 4.640 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: f 327 MET cc_start: 0.9164 (ptp) cc_final: 0.8959 (ptm) REVERT: f 396 MET cc_start: 0.8700 (mmm) cc_final: 0.8296 (tpp) REVERT: f 416 MET cc_start: 0.9168 (mpp) cc_final: 0.8951 (mpp) REVERT: a 29 MET cc_start: 0.1980 (ptt) cc_final: 0.0816 (ptp) REVERT: a 245 MET cc_start: 0.8580 (mmm) cc_final: 0.8158 (mmm) REVERT: a 341 MET cc_start: 0.8094 (tmm) cc_final: 0.7777 (tmm) REVERT: b 21 MET cc_start: 0.7499 (mtp) cc_final: 0.7277 (mtp) REVERT: b 390 MET cc_start: 0.8295 (ptm) cc_final: 0.7766 (ptp) REVERT: c 21 MET cc_start: 0.8972 (mmm) cc_final: 0.8711 (mtt) REVERT: c 219 MET cc_start: 0.7978 (mmm) cc_final: 0.7426 (mmm) REVERT: c 327 MET cc_start: 0.8104 (mmm) cc_final: 0.7678 (mmm) REVERT: d 219 MET cc_start: 0.8095 (mmp) cc_final: 0.7412 (mmm) REVERT: e 147 MET cc_start: 0.8763 (mmp) cc_final: 0.8537 (mmm) REVERT: e 396 MET cc_start: 0.9177 (mmp) cc_final: 0.8842 (mmm) REVERT: e 405 MET cc_start: 0.9513 (pmm) cc_final: 0.9296 (pmm) REVERT: e 416 MET cc_start: 0.9115 (ppp) cc_final: 0.8890 (ppp) REVERT: V 236 ASP cc_start: 0.8323 (m-30) cc_final: 0.7701 (p0) REVERT: W 26 ARG cc_start: 0.9589 (tpt90) cc_final: 0.8729 (tpt90) REVERT: W 30 MET cc_start: 0.8990 (ptp) cc_final: 0.8699 (ptt) REVERT: X 315 MET cc_start: 0.8803 (tpp) cc_final: 0.8490 (mmm) REVERT: X 681 MET cc_start: 0.8593 (pmm) cc_final: 0.8167 (pmm) REVERT: X 1119 MET cc_start: 0.8239 (tpp) cc_final: 0.7935 (tpp) REVERT: X 1232 MET cc_start: 0.7933 (mmm) cc_final: 0.7719 (mmm) REVERT: Y 192 MET cc_start: 0.7562 (mmm) cc_final: 0.6923 (mmm) REVERT: Y 484 MET cc_start: 0.7848 (mmp) cc_final: 0.7576 (mmm) REVERT: Y 1145 PHE cc_start: 0.8449 (m-80) cc_final: 0.8024 (m-80) outliers start: 2 outliers final: 2 residues processed: 252 average time/residue: 0.5285 time to fit residues: 225.1201 Evaluate side-chains 233 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 590 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 348 optimal weight: 20.0000 chunk 447 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 515 optimal weight: 50.0000 chunk 341 optimal weight: 0.0010 chunk 610 optimal weight: 0.9990 chunk 381 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 281 optimal weight: 0.6980 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 241 GLN ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 HIS A 337 ASN V 147 GLN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 832 HIS ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1157 GLN ** X1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1044 GLN Y1227 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 52481 Z= 0.167 Angle : 0.592 10.603 71226 Z= 0.297 Chirality : 0.042 0.248 8152 Planarity : 0.004 0.095 8987 Dihedral : 12.871 175.229 8057 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -0.93 (0.11), residues: 6289 helix: 0.76 (0.11), residues: 2437 sheet: -1.49 (0.16), residues: 850 loop : -1.51 (0.11), residues: 3002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 115 HIS 0.005 0.001 HIS Y 450 PHE 0.023 0.001 PHE f 412 TYR 0.033 0.001 TYR Y 269 ARG 0.008 0.000 ARG b 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 4.626 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: f 1 MET cc_start: 0.8355 (ppp) cc_final: 0.7929 (ppp) REVERT: f 219 MET cc_start: 0.8619 (mmp) cc_final: 0.8290 (mmm) REVERT: f 396 MET cc_start: 0.8681 (mmm) cc_final: 0.8261 (tpp) REVERT: a 29 MET cc_start: 0.1654 (ptt) cc_final: 0.0662 (ptp) REVERT: a 245 MET cc_start: 0.8569 (mmm) cc_final: 0.8163 (mmm) REVERT: a 343 LEU cc_start: 0.8889 (mt) cc_final: 0.8628 (mt) REVERT: b 21 MET cc_start: 0.7367 (mtp) cc_final: 0.7157 (mtp) REVERT: b 219 MET cc_start: 0.8572 (mmp) cc_final: 0.8278 (mmm) REVERT: b 390 MET cc_start: 0.8156 (ptm) cc_final: 0.7564 (ptp) REVERT: c 21 MET cc_start: 0.8912 (mmm) cc_final: 0.8671 (mtt) REVERT: c 29 MET cc_start: 0.8442 (ptm) cc_final: 0.7827 (ptt) REVERT: c 219 MET cc_start: 0.7950 (mmm) cc_final: 0.7487 (mmm) REVERT: c 327 MET cc_start: 0.8138 (mmm) cc_final: 0.7689 (mmm) REVERT: d 219 MET cc_start: 0.8066 (mmp) cc_final: 0.7453 (mmm) REVERT: d 341 MET cc_start: 0.8833 (tpt) cc_final: 0.8371 (tpp) REVERT: e 186 MET cc_start: 0.8742 (pmm) cc_final: 0.8537 (pmm) REVERT: e 390 MET cc_start: 0.8873 (ptt) cc_final: 0.7734 (ptt) REVERT: e 396 MET cc_start: 0.9335 (mmp) cc_final: 0.9104 (mmm) REVERT: e 405 MET cc_start: 0.9497 (pmm) cc_final: 0.9282 (pmm) REVERT: e 416 MET cc_start: 0.9100 (ppp) cc_final: 0.8891 (ppp) REVERT: A 339 MET cc_start: 0.7379 (mpp) cc_final: 0.7066 (pmm) REVERT: V 236 ASP cc_start: 0.8291 (m-30) cc_final: 0.7728 (p0) REVERT: W 26 ARG cc_start: 0.9606 (tpt90) cc_final: 0.8786 (tpt90) REVERT: W 30 MET cc_start: 0.9002 (ptp) cc_final: 0.8652 (ptt) REVERT: X 315 MET cc_start: 0.8743 (tpp) cc_final: 0.8498 (mmm) REVERT: X 681 MET cc_start: 0.8524 (pmm) cc_final: 0.8198 (pmm) REVERT: X 1119 MET cc_start: 0.8261 (tpp) cc_final: 0.8005 (tpp) REVERT: X 1273 MET cc_start: 0.8166 (ttp) cc_final: 0.7563 (ttp) REVERT: Y 192 MET cc_start: 0.7475 (mmm) cc_final: 0.7111 (mmm) REVERT: Y 237 MET cc_start: 0.8019 (ttt) cc_final: 0.7804 (tpt) REVERT: Y 298 MET cc_start: 0.2283 (ttp) cc_final: 0.1771 (ptm) REVERT: Y 1145 PHE cc_start: 0.8404 (m-80) cc_final: 0.7832 (m-80) REVERT: Y 1260 MET cc_start: 0.8044 (tpt) cc_final: 0.7680 (tpp) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.5296 time to fit residues: 224.7840 Evaluate side-chains 229 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 377 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 364 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 387 optimal weight: 8.9990 chunk 415 optimal weight: 4.9990 chunk 301 optimal weight: 0.0570 chunk 56 optimal weight: 20.0000 chunk 479 optimal weight: 0.7980 overall best weight: 3.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 172 GLN ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1157 GLN ** X1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 702 GLN Y 805 GLN ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 52481 Z= 0.206 Angle : 0.610 11.186 71226 Z= 0.307 Chirality : 0.042 0.240 8152 Planarity : 0.004 0.095 8987 Dihedral : 12.838 175.236 8057 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.20 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -0.90 (0.11), residues: 6289 helix: 0.76 (0.11), residues: 2455 sheet: -1.48 (0.17), residues: 870 loop : -1.48 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 409 HIS 0.006 0.001 HIS Y 777 PHE 0.015 0.001 PHE Y 141 TYR 0.029 0.001 TYR Y 269 ARG 0.008 0.000 ARG f 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 4.720 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: f 1 MET cc_start: 0.8693 (ppp) cc_final: 0.8303 (ppp) REVERT: f 219 MET cc_start: 0.8622 (mmp) cc_final: 0.8277 (mmm) REVERT: f 396 MET cc_start: 0.8699 (mmm) cc_final: 0.8287 (tpp) REVERT: a 29 MET cc_start: 0.1839 (ptt) cc_final: 0.0954 (ptp) REVERT: a 245 MET cc_start: 0.8585 (mmm) cc_final: 0.8173 (mmm) REVERT: a 341 MET cc_start: 0.8016 (tmm) cc_final: 0.7604 (tmm) REVERT: a 343 LEU cc_start: 0.8889 (mt) cc_final: 0.8654 (mt) REVERT: b 21 MET cc_start: 0.7384 (mtp) cc_final: 0.7181 (mtp) REVERT: b 186 MET cc_start: 0.8048 (pmm) cc_final: 0.7579 (pmm) REVERT: b 219 MET cc_start: 0.8548 (mmp) cc_final: 0.8343 (mmm) REVERT: b 380 MET cc_start: 0.9044 (mtm) cc_final: 0.8516 (ptp) REVERT: b 390 MET cc_start: 0.8207 (ptm) cc_final: 0.7375 (ptm) REVERT: c 21 MET cc_start: 0.8980 (mmm) cc_final: 0.8721 (mtt) REVERT: c 29 MET cc_start: 0.8488 (ptm) cc_final: 0.7747 (ptp) REVERT: c 219 MET cc_start: 0.8026 (mmm) cc_final: 0.7446 (mmm) REVERT: d 219 MET cc_start: 0.8085 (mmp) cc_final: 0.7523 (mmm) REVERT: d 390 MET cc_start: 0.8890 (ptp) cc_final: 0.8638 (ptp) REVERT: e 21 MET cc_start: 0.9058 (mtp) cc_final: 0.8543 (ttp) REVERT: e 390 MET cc_start: 0.8870 (ptt) cc_final: 0.7845 (ptt) REVERT: e 396 MET cc_start: 0.9357 (mmp) cc_final: 0.9125 (mmm) REVERT: e 416 MET cc_start: 0.9120 (ppp) cc_final: 0.8885 (ppp) REVERT: A 361 LYS cc_start: 0.8304 (mmtt) cc_final: 0.8062 (mptt) REVERT: V 236 ASP cc_start: 0.8341 (m-30) cc_final: 0.7839 (p0) REVERT: W 26 ARG cc_start: 0.9541 (tpt90) cc_final: 0.8737 (tpm170) REVERT: W 30 MET cc_start: 0.9023 (ptp) cc_final: 0.8802 (ptt) REVERT: X 315 MET cc_start: 0.8826 (tpp) cc_final: 0.8571 (mmm) REVERT: X 681 MET cc_start: 0.8558 (pmm) cc_final: 0.8167 (pmm) REVERT: Y 137 ARG cc_start: 0.9443 (ptm160) cc_final: 0.9183 (ttp80) REVERT: Y 192 MET cc_start: 0.7399 (mmm) cc_final: 0.7053 (mmm) REVERT: Y 298 MET cc_start: 0.3747 (ttp) cc_final: 0.3323 (ttp) REVERT: Y 484 MET cc_start: 0.8258 (mmm) cc_final: 0.7619 (mmm) REVERT: Y 747 MET cc_start: 0.7917 (ttm) cc_final: 0.7693 (ttt) REVERT: Y 1145 PHE cc_start: 0.8588 (m-80) cc_final: 0.8033 (m-80) REVERT: Y 1260 MET cc_start: 0.8117 (tpt) cc_final: 0.7834 (tpp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.5320 time to fit residues: 222.1242 Evaluate side-chains 227 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 4.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 554 optimal weight: 0.4980 chunk 584 optimal weight: 6.9990 chunk 533 optimal weight: 10.0000 chunk 568 optimal weight: 5.9990 chunk 342 optimal weight: 0.0980 chunk 247 optimal weight: 20.0000 chunk 446 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 513 optimal weight: 20.0000 chunk 537 optimal weight: 9.9990 chunk 566 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN ** d 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 25 ASN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 330 HIS ** X 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 702 GLN ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1326 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 52481 Z= 0.208 Angle : 0.615 11.134 71226 Z= 0.309 Chirality : 0.042 0.247 8152 Planarity : 0.004 0.094 8987 Dihedral : 12.822 174.577 8057 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -0.88 (0.11), residues: 6289 helix: 0.75 (0.11), residues: 2458 sheet: -1.41 (0.17), residues: 862 loop : -1.46 (0.11), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 409 HIS 0.006 0.001 HIS Y 777 PHE 0.013 0.001 PHE Y 141 TYR 0.031 0.001 TYR Y 269 ARG 0.007 0.000 ARG f 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 4.651 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: f 1 MET cc_start: 0.8766 (ppp) cc_final: 0.8506 (ppp) REVERT: f 396 MET cc_start: 0.8741 (mmm) cc_final: 0.8354 (tpp) REVERT: a 29 MET cc_start: 0.1861 (ptt) cc_final: 0.0968 (ptp) REVERT: a 245 MET cc_start: 0.8575 (mmm) cc_final: 0.8149 (mmm) REVERT: a 341 MET cc_start: 0.8128 (tmm) cc_final: 0.7741 (tmm) REVERT: b 21 MET cc_start: 0.7456 (mtp) cc_final: 0.7253 (mtp) REVERT: b 186 MET cc_start: 0.8073 (pmm) cc_final: 0.7532 (pmm) REVERT: b 219 MET cc_start: 0.8484 (mmp) cc_final: 0.8257 (mmm) REVERT: b 390 MET cc_start: 0.8190 (ptm) cc_final: 0.7737 (ptp) REVERT: c 29 MET cc_start: 0.8459 (ptm) cc_final: 0.7694 (ptp) REVERT: c 219 MET cc_start: 0.8079 (mmm) cc_final: 0.7474 (mmm) REVERT: c 327 MET cc_start: 0.8542 (mmm) cc_final: 0.8309 (mmm) REVERT: d 29 MET cc_start: 0.7910 (pmm) cc_final: 0.7522 (pmm) REVERT: d 219 MET cc_start: 0.8171 (mmp) cc_final: 0.7695 (mmm) REVERT: d 327 MET cc_start: 0.8406 (ptm) cc_final: 0.8002 (ppp) REVERT: d 396 MET cc_start: 0.9014 (mmp) cc_final: 0.8806 (mmm) REVERT: e 21 MET cc_start: 0.9046 (mtp) cc_final: 0.8352 (ttp) REVERT: e 390 MET cc_start: 0.8832 (ptt) cc_final: 0.7756 (ptt) REVERT: e 396 MET cc_start: 0.9302 (mmp) cc_final: 0.9019 (mmm) REVERT: e 416 MET cc_start: 0.9180 (ppp) cc_final: 0.8937 (ppp) REVERT: A 339 MET cc_start: 0.7365 (mpp) cc_final: 0.7048 (pmm) REVERT: A 361 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8097 (mptt) REVERT: V 236 ASP cc_start: 0.8340 (m-30) cc_final: 0.7843 (p0) REVERT: W 26 ARG cc_start: 0.9617 (tpt90) cc_final: 0.8985 (tpm170) REVERT: X 315 MET cc_start: 0.8822 (tpp) cc_final: 0.8552 (mmm) REVERT: X 515 MET cc_start: 0.9021 (pmm) cc_final: 0.8506 (pmm) REVERT: X 1119 MET cc_start: 0.8026 (tpp) cc_final: 0.7765 (tpp) REVERT: X 1273 MET cc_start: 0.8155 (ttp) cc_final: 0.7684 (ttp) REVERT: Y 137 ARG cc_start: 0.9497 (ptm160) cc_final: 0.9238 (ttp80) REVERT: Y 192 MET cc_start: 0.7571 (mmm) cc_final: 0.7183 (mmm) REVERT: Y 298 MET cc_start: 0.3977 (ttp) cc_final: 0.3551 (ttp) REVERT: Y 747 MET cc_start: 0.7960 (ttm) cc_final: 0.7692 (ttt) REVERT: Y 1145 PHE cc_start: 0.8669 (m-80) cc_final: 0.8117 (m-80) REVERT: Y 1260 MET cc_start: 0.8092 (tpt) cc_final: 0.7823 (tpp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.5375 time to fit residues: 222.8571 Evaluate side-chains 231 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 4.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 373 optimal weight: 6.9990 chunk 601 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 417 optimal weight: 5.9990 chunk 630 optimal weight: 40.0000 chunk 580 optimal weight: 7.9990 chunk 502 optimal weight: 10.0000 chunk 52 optimal weight: 0.0980 chunk 387 optimal weight: 9.9990 chunk 307 optimal weight: 2.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN V 208 ASN ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 618 GLN ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1295 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 52481 Z= 0.219 Angle : 0.624 14.410 71226 Z= 0.313 Chirality : 0.042 0.255 8152 Planarity : 0.004 0.094 8987 Dihedral : 12.813 174.216 8057 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.41 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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: -0.87 (0.11), residues: 6289 helix: 0.74 (0.11), residues: 2464 sheet: -1.39 (0.17), residues: 848 loop : -1.44 (0.11), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 183 HIS 0.007 0.001 HIS Y 777 PHE 0.013 0.001 PHE Y 141 TYR 0.030 0.001 TYR Y 269 ARG 0.014 0.000 ARG X1034 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12578 Ramachandran restraints generated. 6289 Oldfield, 0 Emsley, 6289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 4.649 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: f 219 MET cc_start: 0.8659 (mmp) cc_final: 0.8256 (mmm) REVERT: f 396 MET cc_start: 0.8701 (mmm) cc_final: 0.8321 (tpp) REVERT: a 21 MET cc_start: 0.5016 (mmp) cc_final: 0.2127 (mtt) REVERT: a 29 MET cc_start: 0.2002 (ptt) cc_final: 0.1103 (ptp) REVERT: a 245 MET cc_start: 0.8567 (mmm) cc_final: 0.8187 (mmm) REVERT: a 341 MET cc_start: 0.8150 (tmm) cc_final: 0.7774 (tmm) REVERT: b 21 MET cc_start: 0.7508 (mtp) cc_final: 0.7300 (mtp) REVERT: b 186 MET cc_start: 0.8102 (pmm) cc_final: 0.7524 (pmm) REVERT: b 219 MET cc_start: 0.8380 (mmp) cc_final: 0.8103 (mmm) REVERT: b 390 MET cc_start: 0.8209 (ptm) cc_final: 0.7772 (ptp) REVERT: c 21 MET cc_start: 0.7849 (mtt) cc_final: 0.7601 (mtp) REVERT: c 29 MET cc_start: 0.8465 (ptm) cc_final: 0.7645 (ptp) REVERT: c 219 MET cc_start: 0.8102 (mmm) cc_final: 0.7521 (mmm) REVERT: c 327 MET cc_start: 0.8531 (mmm) cc_final: 0.8249 (mmm) REVERT: d 29 MET cc_start: 0.7931 (pmm) cc_final: 0.7581 (pmm) REVERT: d 219 MET cc_start: 0.8216 (mmp) cc_final: 0.7713 (mmm) REVERT: d 327 MET cc_start: 0.8423 (ptm) cc_final: 0.7984 (ppp) REVERT: d 390 MET cc_start: 0.8735 (pmm) cc_final: 0.8187 (pmm) REVERT: d 396 MET cc_start: 0.8966 (mmp) cc_final: 0.8721 (mmm) REVERT: e 186 MET cc_start: 0.8674 (pmm) cc_final: 0.8383 (pmm) REVERT: e 390 MET cc_start: 0.8900 (ptt) cc_final: 0.7831 (ptt) REVERT: e 396 MET cc_start: 0.9352 (mmp) cc_final: 0.8931 (tpt) REVERT: e 416 MET cc_start: 0.9125 (ppp) cc_final: 0.8856 (ppp) REVERT: A 1 MET cc_start: 0.8209 (mtp) cc_final: 0.7993 (mtp) REVERT: A 339 MET cc_start: 0.7188 (mpp) cc_final: 0.6872 (pmm) REVERT: A 361 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7978 (mptt) REVERT: V 236 ASP cc_start: 0.8393 (m-30) cc_final: 0.7851 (p0) REVERT: W 26 ARG cc_start: 0.9595 (tpt90) cc_final: 0.8448 (tpt90) REVERT: W 30 MET cc_start: 0.9031 (ptp) cc_final: 0.8236 (ptt) REVERT: X 315 MET cc_start: 0.8850 (tpp) cc_final: 0.8567 (mmm) REVERT: X 515 MET cc_start: 0.9038 (pmm) cc_final: 0.8180 (pmm) REVERT: X 1119 MET cc_start: 0.8105 (tpp) cc_final: 0.7844 (tpp) REVERT: X 1273 MET cc_start: 0.8253 (ttp) cc_final: 0.7797 (ttp) REVERT: X 1304 MET cc_start: 0.8483 (mmp) cc_final: 0.8187 (mmm) REVERT: Y 137 ARG cc_start: 0.9522 (ptm160) cc_final: 0.9255 (ttp80) REVERT: Y 192 MET cc_start: 0.7396 (mmm) cc_final: 0.7046 (mmm) REVERT: Y 747 MET cc_start: 0.7997 (ttm) cc_final: 0.7667 (ttt) REVERT: Y 1145 PHE cc_start: 0.8751 (m-80) cc_final: 0.8214 (m-80) REVERT: Y 1260 MET cc_start: 0.8099 (tpt) cc_final: 0.7842 (tpp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.5355 time to fit residues: 222.0568 Evaluate side-chains 229 residues out of total 5379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 398 optimal weight: 9.9990 chunk 534 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 463 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 502 optimal weight: 0.7980 chunk 210 optimal weight: 20.0000 chunk 516 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Y 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.035648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.022782 restraints weight = 751646.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.023148 restraints weight = 487009.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.023528 restraints weight = 359604.334| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 52481 Z= 0.211 Angle : 0.623 11.830 71226 Z= 0.314 Chirality : 0.042 0.234 8152 Planarity : 0.004 0.094 8987 Dihedral : 12.779 174.194 8057 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.12 % Twisted Proline : 0.40 % 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 (0.11), residues: 6289 helix: 0.75 (0.11), residues: 2457 sheet: -1.35 (0.17), residues: 841 loop : -1.39 (0.11), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 580 HIS 0.006 0.001 HIS Y 777 PHE 0.015 0.001 PHE Y 141 TYR 0.031 0.001 TYR Y 269 ARG 0.008 0.000 ARG X1034 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7361.48 seconds wall clock time: 131 minutes 20.07 seconds (7880.07 seconds total)