Starting phenix.real_space_refine on Mon Oct 14 12:10:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/10_2024/8csr_26968.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/10_2024/8csr_26968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/10_2024/8csr_26968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/10_2024/8csr_26968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/10_2024/8csr_26968.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csr_26968/10_2024/8csr_26968.cif" } resolution = 2.54 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= 0.034 sd= 1.307 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 K 5 8.98 5 Fe 8 7.16 5 Zn 1 6.06 5 P 860 5.49 5 Mg 31 5.21 5 S 262 5.16 5 C 41007 2.51 5 N 12518 2.21 5 O 15176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 69868 Number of models: 1 Model: "" Number of chains: 42 Chain: "0" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1754 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "1" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2098 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Chain: "3" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 395 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "4" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4585 Classifications: {'peptide': 566} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 3 Chain: "5" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2568 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 23, 'TRANS': 295} Chain: "6" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Chain: "7" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3179 Classifications: {'peptide': 402} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 370} Chain breaks: 1 Chain: "8" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2543 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain: "A" Number of atoms: 18103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 853, 18103 Classifications: {'RNA': 853} Modifications used: {'rna2p_pur': 72, 'rna2p_pyr': 70, 'rna3p_pur': 369, 'rna3p_pyr': 342} Link IDs: {'rna2p': 142, 'rna3p': 710} Chain breaks: 7 Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1789 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "C" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1042 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1838 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 858 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "F" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1696 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain: "G" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2395 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain breaks: 1 Chain: "H" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1064 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 8, 'TRANS': 121} Chain breaks: 1 Chain: "I" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1019 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "J" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 97} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 296 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain breaks: 1 Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1363 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "M" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 913 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1570 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 21, 'TRANS': 168} Chain: "P" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "Q" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 744 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 83} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2382 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain: "S" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1100 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "T" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "U" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1468 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "V" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2946 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 9, 'TRANS': 349} Chain breaks: 1 Chain: "W" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "X" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2849 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 332} Chain: "Y" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1032 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "Z" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain breaks: 1 Chain: "7" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 78 Unusual residues: {' K': 5, ' MG': 29, 'NAD': 1} Classifications: {'undetermined': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15281 SG CYS 7 404 99.337 110.448 155.095 1.00 21.61 S ATOM 14802 SG CYS 7 347 103.548 106.157 151.868 1.00 33.65 S ATOM 14697 SG CYS 7 333 97.701 108.246 149.643 1.00 33.65 S ATOM 14744 SG CYS 7 339 102.851 111.667 149.873 1.00 22.31 S ATOM 52597 SG CYS O 94 114.604 154.274 96.076 1.00 33.35 S ATOM 52683 SG CYS O 105 117.312 154.723 93.600 1.00 30.33 S ATOM 52704 SG CYS O 108 116.268 157.728 95.504 1.00 33.70 S ATOM 52992 SG CYS O 143 113.819 156.215 92.920 1.00 27.63 S ATOM 53915 SG CYS P 65 124.894 65.287 50.727 1.00 44.36 S ATOM 54188 SG CYS P 100 122.292 68.029 51.443 1.00 39.26 S ATOM 41718 SG CYS E 105 124.498 69.800 46.609 1.00 66.97 S ATOM 53937 SG CYS P 68 126.831 67.048 46.459 1.00 46.08 S ATOM 50542 SG CYS M 26 92.897 165.851 74.463 1.00 29.96 S ATOM 59978 SG CYS T 149 96.305 165.835 75.402 1.00 33.06 S ATOM 59906 SG CYS T 139 95.579 167.184 68.963 1.00 31.31 S ATOM 59920 SG CYS T 141 98.314 166.742 71.425 1.00 31.18 S Time building chain proxies: 27.85, per 1000 atoms: 0.40 Number of scatterers: 69868 At special positions: 0 Unit cell: (216.648, 236.826, 216.648, 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 1 29.99 Fe 8 26.01 K 5 19.00 S 262 16.00 P 860 15.00 Mg 31 11.99 O 15176 8.00 N 12518 7.00 C 41007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 13.40 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 201 " pdb="FE2 FES P 201 " - pdb=" SG CYS E 105 " pdb="FE2 FES P 201 " - pdb=" SG CYS P 68 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 100 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 65 " pdb=" FES T 201 " pdb="FE1 FES T 201 " - pdb=" SG CYS M 26 " pdb="FE1 FES T 201 " - pdb=" SG CYS T 149 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 141 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 139 " pdb=" SF4 7 501 " pdb="FE3 SF4 7 501 " - pdb=" SG CYS 7 333 " pdb="FE2 SF4 7 501 " - pdb=" SG CYS 7 347 " pdb="FE4 SF4 7 501 " - pdb=" SG CYS 7 339 " pdb="FE1 SF4 7 501 " - pdb=" SG CYS 7 404 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 105 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 108 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 143 " Number of angles added : 6 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12058 Finding SS restraints... Secondary structure from input PDB file: 287 helices and 41 sheets defined 53.8% alpha, 11.9% beta 234 base pairs and 422 stacking pairs defined. Time for finding SS restraints: 21.76 Creating SS restraints... Processing helix chain '0' and resid 9 through 26 removed outlier: 3.884A pdb=" N GLU 0 13 " --> pdb=" O ARG 0 9 " (cutoff:3.500A) Processing helix chain '0' and resid 29 through 34 Processing helix chain '0' and resid 51 through 53 No H-bonds generated for 'chain '0' and resid 51 through 53' Processing helix chain '0' and resid 54 through 61 Processing helix chain '0' and resid 63 through 69 Processing helix chain '0' and resid 70 through 76 removed outlier: 7.669A pdb=" N LEU 0 73 " --> pdb=" O ARG 0 70 " (cutoff:3.500A) Processing helix chain '0' and resid 83 through 89 Processing helix chain '0' and resid 143 through 145 No H-bonds generated for 'chain '0' and resid 143 through 145' Processing helix chain '0' and resid 146 through 152 removed outlier: 3.506A pdb=" N ALA 0 152 " --> pdb=" O GLU 0 148 " (cutoff:3.500A) Processing helix chain '0' and resid 167 through 181 Processing helix chain '1' and resid 55 through 60 removed outlier: 3.641A pdb=" N GLU 1 58 " --> pdb=" O PRO 1 55 " (cutoff:3.500A) Processing helix chain '1' and resid 65 through 70 removed outlier: 4.022A pdb=" N VAL 1 69 " --> pdb=" O ASP 1 65 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR 1 70 " --> pdb=" O TRP 1 66 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 65 through 70' Processing helix chain '1' and resid 102 through 108 removed outlier: 3.635A pdb=" N LEU 1 106 " --> pdb=" O ASN 1 102 " (cutoff:3.500A) Processing helix chain '1' and resid 115 through 126 Processing helix chain '1' and resid 127 through 130 Processing helix chain '1' and resid 139 through 147 removed outlier: 4.000A pdb=" N LYS 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 169 removed outlier: 3.881A pdb=" N ARG 1 169 " --> pdb=" O PRO 1 166 " (cutoff:3.500A) Processing helix chain '1' and resid 178 through 180 No H-bonds generated for 'chain '1' and resid 178 through 180' Processing helix chain '1' and resid 183 through 195 Processing helix chain '1' and resid 214 through 234 removed outlier: 3.780A pdb=" N ASN 1 218 " --> pdb=" O LEU 1 214 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 242 Processing helix chain '1' and resid 256 through 273 Processing helix chain '1' and resid 287 through 302 Processing helix chain '1' and resid 305 through 321 Processing helix chain '3' and resid 154 through 181 Processing helix chain '4' and resid 68 through 78 removed outlier: 3.519A pdb=" N VAL 4 78 " --> pdb=" O LEU 4 74 " (cutoff:3.500A) Processing helix chain '4' and resid 99 through 124 Processing helix chain '4' and resid 125 through 128 Processing helix chain '4' and resid 137 through 141 Processing helix chain '4' and resid 153 through 164 Processing helix chain '4' and resid 165 through 179 Processing helix chain '4' and resid 184 through 199 Processing helix chain '4' and resid 242 through 251 Processing helix chain '4' and resid 255 through 269 Processing helix chain '4' and resid 271 through 285 Processing helix chain '4' and resid 290 through 304 Processing helix chain '4' and resid 308 through 326 Processing helix chain '4' and resid 331 through 343 Processing helix chain '4' and resid 344 through 348 removed outlier: 7.279A pdb=" N VAL 4 347 " --> pdb=" O ARG 4 344 " (cutoff:3.500A) Processing helix chain '4' and resid 349 through 363 Processing helix chain '4' and resid 368 through 380 removed outlier: 3.645A pdb=" N TYR 4 372 " --> pdb=" O SER 4 368 " (cutoff:3.500A) Processing helix chain '4' and resid 391 through 401 removed outlier: 4.217A pdb=" N ASP 4 395 " --> pdb=" O PHE 4 391 " (cutoff:3.500A) Processing helix chain '4' and resid 409 through 413 removed outlier: 4.251A pdb=" N ASP 4 413 " --> pdb=" O PRO 4 410 " (cutoff:3.500A) Processing helix chain '4' and resid 414 through 427 Processing helix chain '4' and resid 428 through 441 removed outlier: 3.658A pdb=" N ALA 4 432 " --> pdb=" O ASP 4 428 " (cutoff:3.500A) Processing helix chain '4' and resid 443 through 449 removed outlier: 4.257A pdb=" N GLY 4 449 " --> pdb=" O LYS 4 446 " (cutoff:3.500A) Processing helix chain '4' and resid 450 through 469 Processing helix chain '4' and resid 470 through 482 Processing helix chain '4' and resid 489 through 503 Processing helix chain '4' and resid 505 through 507 No H-bonds generated for 'chain '4' and resid 505 through 507' Processing helix chain '4' and resid 508 through 519 removed outlier: 3.569A pdb=" N ILE 4 512 " --> pdb=" O VAL 4 508 " (cutoff:3.500A) Processing helix chain '4' and resid 524 through 537 removed outlier: 3.556A pdb=" N ARG 4 528 " --> pdb=" O ARG 4 524 " (cutoff:3.500A) Processing helix chain '4' and resid 541 through 561 Processing helix chain '4' and resid 572 through 587 Processing helix chain '4' and resid 588 through 602 removed outlier: 3.781A pdb=" N ALA 4 592 " --> pdb=" O ARG 4 588 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG 4 600 " --> pdb=" O LEU 4 596 " (cutoff:3.500A) Processing helix chain '4' and resid 607 through 622 Processing helix chain '4' and resid 623 through 637 removed outlier: 3.544A pdb=" N ALA 4 627 " --> pdb=" O SER 4 623 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE 4 637 " --> pdb=" O LEU 4 633 " (cutoff:3.500A) Processing helix chain '4' and resid 638 through 640 No H-bonds generated for 'chain '4' and resid 638 through 640' Processing helix chain '4' and resid 641 through 653 Processing helix chain '4' and resid 656 through 667 Processing helix chain '5' and resid 17 through 25 Processing helix chain '5' and resid 40 through 51 Processing helix chain '5' and resid 67 through 76 Processing helix chain '5' and resid 87 through 89 No H-bonds generated for 'chain '5' and resid 87 through 89' Processing helix chain '5' and resid 90 through 101 Processing helix chain '5' and resid 122 through 126 removed outlier: 3.716A pdb=" N LEU 5 125 " --> pdb=" O SER 5 122 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS 5 126 " --> pdb=" O GLU 5 123 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 122 through 126' Processing helix chain '5' and resid 143 through 161 removed outlier: 4.171A pdb=" N THR 5 148 " --> pdb=" O PHE 5 144 " (cutoff:3.500A) Proline residue: 5 149 - end of helix Processing helix chain '5' and resid 162 through 167 removed outlier: 4.053A pdb=" N TYR 5 167 " --> pdb=" O PRO 5 164 " (cutoff:3.500A) Processing helix chain '5' and resid 178 through 185 Processing helix chain '5' and resid 194 through 202 Processing helix chain '5' and resid 213 through 217 Processing helix chain '5' and resid 241 through 254 Processing helix chain '5' and resid 259 through 265 removed outlier: 4.037A pdb=" N GLY 5 263 " --> pdb=" O TYR 5 259 " (cutoff:3.500A) Processing helix chain '5' and resid 266 through 268 No H-bonds generated for 'chain '5' and resid 266 through 268' Processing helix chain '5' and resid 272 through 285 Processing helix chain '5' and resid 291 through 295 Processing helix chain '5' and resid 296 through 313 Processing helix chain '5' and resid 321 through 328 removed outlier: 3.607A pdb=" N ARG 5 328 " --> pdb=" O GLU 5 324 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 50 Processing helix chain '6' and resid 91 through 109 Processing helix chain '6' and resid 114 through 121 removed outlier: 3.549A pdb=" N LEU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN 6 121 " --> pdb=" O LEU 6 117 " (cutoff:3.500A) Processing helix chain '6' and resid 145 through 170 removed outlier: 4.958A pdb=" N ALA 6 161 " --> pdb=" O GLN 6 157 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N HIS 6 162 " --> pdb=" O ARG 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 186 through 200 removed outlier: 4.276A pdb=" N LEU 6 190 " --> pdb=" O GLY 6 186 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL 6 199 " --> pdb=" O GLN 6 195 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 47 Processing helix chain '7' and resid 64 through 75 Processing helix chain '7' and resid 80 through 96 removed outlier: 3.505A pdb=" N GLU 7 84 " --> pdb=" O GLY 7 80 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 118 Processing helix chain '7' and resid 132 through 140 removed outlier: 3.590A pdb=" N LYS 7 140 " --> pdb=" O HIS 7 136 " (cutoff:3.500A) Processing helix chain '7' and resid 151 through 181 removed outlier: 6.256A pdb=" N ASP 7 164 " --> pdb=" O ALA 7 160 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY 7 165 " --> pdb=" O ALA 7 161 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 197 through 208 removed outlier: 3.536A pdb=" N ILE 7 206 " --> pdb=" O ALA 7 202 " (cutoff:3.500A) Processing helix chain '7' and resid 220 through 232 Processing helix chain '7' and resid 267 through 271 removed outlier: 3.604A pdb=" N LEU 7 271 " --> pdb=" O LEU 7 268 " (cutoff:3.500A) Processing helix chain '7' and resid 273 through 287 Processing helix chain '7' and resid 299 through 315 Processing helix chain '7' and resid 417 through 421 Processing helix chain '7' and resid 421 through 431 Processing helix chain '8' and resid 86 through 99 Processing helix chain '8' and resid 101 through 108 Processing helix chain '8' and resid 116 through 139 removed outlier: 3.772A pdb=" N GLN 8 121 " --> pdb=" O THR 8 117 " (cutoff:3.500A) Proline residue: 8 122 - end of helix Processing helix chain '8' and resid 139 through 145 removed outlier: 3.672A pdb=" N ILE 8 143 " --> pdb=" O GLN 8 139 " (cutoff:3.500A) Processing helix chain '8' and resid 154 through 163 removed outlier: 3.551A pdb=" N ALA 8 158 " --> pdb=" O VAL 8 154 " (cutoff:3.500A) Processing helix chain '8' and resid 167 through 189 removed outlier: 3.642A pdb=" N VAL 8 189 " --> pdb=" O ALA 8 185 " (cutoff:3.500A) Processing helix chain '8' and resid 203 through 219 removed outlier: 3.601A pdb=" N CYS 8 215 " --> pdb=" O ALA 8 211 " (cutoff:3.500A) Processing helix chain '8' and resid 241 through 251 Processing helix chain '8' and resid 251 through 256 Processing helix chain '8' and resid 271 through 276 Proline residue: 8 276 - end of helix Processing helix chain '8' and resid 277 through 288 removed outlier: 3.880A pdb=" N ALA 8 287 " --> pdb=" O GLN 8 283 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL 8 288 " --> pdb=" O ALA 8 284 " (cutoff:3.500A) Processing helix chain '8' and resid 308 through 310 No H-bonds generated for 'chain '8' and resid 308 through 310' Processing helix chain '8' and resid 311 through 319 removed outlier: 3.887A pdb=" N ALA 8 317 " --> pdb=" O HIS 8 313 " (cutoff:3.500A) Processing helix chain '8' and resid 320 through 322 No H-bonds generated for 'chain '8' and resid 320 through 322' Processing helix chain '8' and resid 326 through 335 Processing helix chain '8' and resid 352 through 362 Processing helix chain '8' and resid 362 through 368 removed outlier: 4.095A pdb=" N SER 8 368 " --> pdb=" O GLN 8 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.652A pdb=" N HIS B 69 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.928A pdb=" N PHE B 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 87 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 99 through 104 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 117 through 138 removed outlier: 3.542A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 206 through 215 removed outlier: 4.169A pdb=" N ARG B 210 " --> pdb=" O HIS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 274 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 81 through 100 Processing helix chain 'C' and resid 128 through 148 Processing helix chain 'D' and resid 263 through 277 removed outlier: 3.792A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.706A pdb=" N ASP D 287 " --> pdb=" O ARG D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 341 through 355 Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 374 through 378 Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'E' and resid 14 through 32 Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.979A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 removed outlier: 4.336A pdb=" N TYR F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 52' Processing helix chain 'F' and resid 59 through 72 removed outlier: 3.627A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 103 through 128 Processing helix chain 'F' and resid 132 through 137 removed outlier: 3.638A pdb=" N ALA F 135 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 175 through 192 Processing helix chain 'F' and resid 200 through 214 removed outlier: 3.705A pdb=" N HIS F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 230 Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.645A pdb=" N HIS F 238 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG F 240 " --> pdb=" O ALA F 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 93 Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 127 through 132 removed outlier: 4.070A pdb=" N ILE G 131 " --> pdb=" O HIS G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 154 Processing helix chain 'G' and resid 155 through 175 Processing helix chain 'G' and resid 201 through 210 Processing helix chain 'G' and resid 214 through 231 removed outlier: 3.768A pdb=" N TYR G 218 " --> pdb=" O SER G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 243 Processing helix chain 'G' and resid 300 through 304 Processing helix chain 'G' and resid 306 through 321 Proline residue: G 316 - end of helix removed outlier: 3.634A pdb=" N VAL G 320 " --> pdb=" O PRO G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 353 Processing helix chain 'G' and resid 354 through 356 No H-bonds generated for 'chain 'G' and resid 354 through 356' Processing helix chain 'G' and resid 357 through 367 Processing helix chain 'H' and resid 84 through 102 Processing helix chain 'H' and resid 150 through 163 Processing helix chain 'H' and resid 181 through 185 removed outlier: 3.561A pdb=" N LYS H 185 " --> pdb=" O GLU H 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'I' and resid 118 through 123 Processing helix chain 'I' and resid 124 through 141 Processing helix chain 'I' and resid 159 through 168 Processing helix chain 'J' and resid 32 through 40 Processing helix chain 'K' and resid 49 through 58 Processing helix chain 'K' and resid 107 through 117 Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.866A pdb=" N GLN L 77 " --> pdb=" O LYS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.966A pdb=" N VAL L 85 " --> pdb=" O ILE L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 93 Processing helix chain 'L' and resid 94 through 98 Processing helix chain 'L' and resid 99 through 116 removed outlier: 3.960A pdb=" N MET L 103 " --> pdb=" O ASN L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 146 removed outlier: 3.873A pdb=" N LYS L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 174 Processing helix chain 'L' and resid 174 through 186 Processing helix chain 'L' and resid 200 through 225 Processing helix chain 'M' and resid 69 through 79 Processing helix chain 'M' and resid 84 through 94 Processing helix chain 'M' and resid 100 through 124 Processing helix chain 'N' and resid 108 through 112 removed outlier: 3.601A pdb=" N SER N 112 " --> pdb=" O PRO N 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 61 removed outlier: 4.156A pdb=" N LEU O 59 " --> pdb=" O PRO O 55 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU O 60 " --> pdb=" O TRP O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 69 Processing helix chain 'O' and resid 119 through 125 removed outlier: 3.910A pdb=" N GLN O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 141 removed outlier: 3.838A pdb=" N THR O 140 " --> pdb=" O TYR O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 160 Processing helix chain 'O' and resid 190 through 196 Processing helix chain 'O' and resid 200 through 204 Processing helix chain 'O' and resid 209 through 220 Processing helix chain 'P' and resid 76 through 82 removed outlier: 3.554A pdb=" N GLN P 82 " --> pdb=" O GLN P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 98 Processing helix chain 'P' and resid 100 through 117 Processing helix chain 'P' and resid 126 through 130 Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 34 through 42 Processing helix chain 'Q' and resid 47 through 77 removed outlier: 4.103A pdb=" N ARG Q 77 " --> pdb=" O ASN Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 84 Processing helix chain 'R' and resid 86 through 91 Processing helix chain 'R' and resid 107 through 126 Processing helix chain 'R' and resid 146 through 149 Processing helix chain 'R' and resid 166 through 170 removed outlier: 3.606A pdb=" N ARG R 170 " --> pdb=" O HIS R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 197 Processing helix chain 'R' and resid 207 through 210 removed outlier: 3.525A pdb=" N PHE R 210 " --> pdb=" O PRO R 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 207 through 210' Processing helix chain 'R' and resid 211 through 221 Processing helix chain 'R' and resid 223 through 235 Processing helix chain 'R' and resid 239 through 257 Processing helix chain 'R' and resid 258 through 262 Processing helix chain 'R' and resid 267 through 278 Processing helix chain 'R' and resid 281 through 291 Processing helix chain 'R' and resid 293 through 308 Processing helix chain 'R' and resid 311 through 321 Processing helix chain 'R' and resid 324 through 335 removed outlier: 3.748A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 356 Processing helix chain 'S' and resid 11 through 22 Processing helix chain 'S' and resid 31 through 38 Processing helix chain 'S' and resid 65 through 78 removed outlier: 4.203A pdb=" N ARG S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE S 70 " --> pdb=" O HIS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 109 Processing helix chain 'S' and resid 113 through 129 Processing helix chain 'T' and resid 7 through 11 Processing helix chain 'T' and resid 12 through 18 Processing helix chain 'T' and resid 38 through 40 No H-bonds generated for 'chain 'T' and resid 38 through 40' Processing helix chain 'T' and resid 41 through 51 Processing helix chain 'T' and resid 51 through 59 Processing helix chain 'T' and resid 94 through 107 Processing helix chain 'T' and resid 109 through 124 removed outlier: 3.994A pdb=" N LEU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER T 124 " --> pdb=" O LYS T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 143 Processing helix chain 'T' and resid 156 through 159 Processing helix chain 'T' and resid 160 through 165 Processing helix chain 'U' and resid 35 through 39 removed outlier: 3.502A pdb=" N ILE U 39 " --> pdb=" O LYS U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 88 Processing helix chain 'U' and resid 88 through 164 Processing helix chain 'U' and resid 165 through 167 No H-bonds generated for 'chain 'U' and resid 165 through 167' Processing helix chain 'U' and resid 172 through 182 Processing helix chain 'V' and resid 31 through 36 Processing helix chain 'V' and resid 37 through 42 Processing helix chain 'V' and resid 49 through 63 Processing helix chain 'V' and resid 68 through 78 removed outlier: 3.513A pdb=" N ILE V 72 " --> pdb=" O SER V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 97 removed outlier: 3.508A pdb=" N ASP V 86 " --> pdb=" O ARG V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 104 Processing helix chain 'V' and resid 105 through 119 Processing helix chain 'V' and resid 121 through 131 Processing helix chain 'V' and resid 131 through 136 Processing helix chain 'V' and resid 140 through 154 Processing helix chain 'V' and resid 156 through 171 Processing helix chain 'V' and resid 175 through 191 Processing helix chain 'V' and resid 197 through 215 Proline residue: V 211 - end of helix removed outlier: 3.948A pdb=" N LYS V 214 " --> pdb=" O LEU V 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN V 215 " --> pdb=" O PRO V 211 " (cutoff:3.500A) Processing helix chain 'V' and resid 217 through 239 Processing helix chain 'V' and resid 239 through 245 removed outlier: 3.547A pdb=" N VAL V 243 " --> pdb=" O GLY V 239 " (cutoff:3.500A) Processing helix chain 'V' and resid 254 through 268 Processing helix chain 'V' and resid 277 through 291 Processing helix chain 'V' and resid 326 through 344 Processing helix chain 'V' and resid 351 through 406 removed outlier: 5.479A pdb=" N SER V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THR V 366 " --> pdb=" O GLU V 362 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA V 406 " --> pdb=" O GLN V 402 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 86 Processing helix chain 'W' and resid 87 through 93 removed outlier: 3.922A pdb=" N GLY W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 134 Processing helix chain 'X' and resid 55 through 59 removed outlier: 3.686A pdb=" N HIS X 59 " --> pdb=" O PRO X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 64 Processing helix chain 'X' and resid 71 through 79 Processing helix chain 'X' and resid 84 through 95 removed outlier: 3.799A pdb=" N MET X 89 " --> pdb=" O PRO X 85 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN X 90 " --> pdb=" O ARG X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 114 Processing helix chain 'X' and resid 133 through 148 removed outlier: 3.651A pdb=" N GLN X 148 " --> pdb=" O PHE X 144 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 162 Processing helix chain 'X' and resid 180 through 195 removed outlier: 3.848A pdb=" N ASN X 190 " --> pdb=" O THR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 202 removed outlier: 4.325A pdb=" N GLN X 201 " --> pdb=" O ARG X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 232 removed outlier: 4.230A pdb=" N VAL X 225 " --> pdb=" O PRO X 221 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 254 removed outlier: 3.961A pdb=" N SER X 252 " --> pdb=" O LYS X 248 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 268 Processing helix chain 'X' and resid 283 through 286 Processing helix chain 'X' and resid 287 through 298 removed outlier: 3.854A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET X 297 " --> pdb=" O LEU X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 324 through 338 removed outlier: 7.397A pdb=" N LYS X 331 " --> pdb=" O GLU X 327 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLU X 332 " --> pdb=" O LEU X 328 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY X 333 " --> pdb=" O LEU X 329 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 363 Processing helix chain 'X' and resid 373 through 385 Processing helix chain 'X' and resid 387 through 397 removed outlier: 4.043A pdb=" N TYR X 397 " --> pdb=" O ARG X 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 277 through 289 removed outlier: 3.512A pdb=" N THR Y 288 " --> pdb=" O LYS Y 284 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) Processing helix chain 'Y' and resid 296 through 308 Processing helix chain 'Y' and resid 322 through 326 Processing helix chain 'Y' and resid 327 through 333 removed outlier: 3.762A pdb=" N HIS Y 331 " --> pdb=" O GLU Y 327 " (cutoff:3.500A) Processing helix chain 'Y' and resid 334 through 338 Processing helix chain 'Y' and resid 345 through 360 removed outlier: 3.573A pdb=" N HIS Y 349 " --> pdb=" O GLY Y 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS Y 360 " --> pdb=" O CYS Y 356 " (cutoff:3.500A) Processing helix chain 'Y' and resid 365 through 383 Processing helix chain 'Z' and resid 5 through 20 Processing helix chain 'Z' and resid 31 through 39 removed outlier: 3.583A pdb=" N GLU Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 69 removed outlier: 3.580A pdb=" N LEU Z 61 " --> pdb=" O THR Z 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE Z 67 " --> pdb=" O GLN Z 63 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU Z 68 " --> pdb=" O THR Z 64 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 123 through 124 Processing sheet with id=AA2, first strand: chain '0' and resid 123 through 124 removed outlier: 5.980A pdb=" N ILE 0 117 " --> pdb=" O LEU 0 97 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU 0 97 " --> pdb=" O ILE 0 117 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR 0 119 " --> pdb=" O TRP 0 95 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP 0 95 " --> pdb=" O THR 0 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain '1' and resid 198 through 199 removed outlier: 3.736A pdb=" N VAL 1 204 " --> pdb=" O CYS 1 199 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG H 75 " --> pdb=" O THR H 175 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU H 177 " --> pdb=" O TYR H 73 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR H 73 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU H 72 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR H 149 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS H 74 " --> pdb=" O HIS H 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.041A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '4' and resid 61 through 65 removed outlier: 4.590A pdb=" N LYS 4 62 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 105 through 109 removed outlier: 3.637A pdb=" N GLN 5 171 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE 5 210 " --> pdb=" O VAL 5 227 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS 5 229 " --> pdb=" O HIS 5 208 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N HIS 5 208 " --> pdb=" O HIS 5 229 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N THR 5 231 " --> pdb=" O VAL 5 206 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL 5 206 " --> pdb=" O THR 5 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '6' and resid 124 through 129 removed outlier: 6.868A pdb=" N TYR 6 139 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL 6 127 " --> pdb=" O ARG 6 137 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG 6 137 " --> pdb=" O VAL 6 127 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N CYS 6 136 " --> pdb=" O VAL 6 180 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL 6 182 " --> pdb=" O CYS 6 136 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA 6 138 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP 6 184 " --> pdb=" O ALA 6 138 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TRP 6 140 " --> pdb=" O ASP 6 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '7' and resid 36 through 37 Processing sheet with id=AB1, first strand: chain '7' and resid 245 through 248 removed outlier: 6.586A pdb=" N LEU 7 189 " --> pdb=" O MET 7 215 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL 7 217 " --> pdb=" O LEU 7 189 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP 7 191 " --> pdb=" O VAL 7 217 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA 7 265 " --> pdb=" O PHE 7 192 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE 7 259 " --> pdb=" O GLY 7 289 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N PHE 7 291 " --> pdb=" O PHE 7 259 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL 7 261 " --> pdb=" O PHE 7 291 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL 7 293 " --> pdb=" O VAL 7 261 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL 7 263 " --> pdb=" O VAL 7 293 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL 7 295 " --> pdb=" O VAL 7 263 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA 7 265 " --> pdb=" O VAL 7 295 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN 7 297 " --> pdb=" O ALA 7 265 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS 7 290 " --> pdb=" O ARG 7 376 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA 7 375 " --> pdb=" O VAL 7 329 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL 7 329 " --> pdb=" O ALA 7 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '7' and resid 245 through 248 removed outlier: 6.586A pdb=" N LEU 7 189 " --> pdb=" O MET 7 215 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL 7 217 " --> pdb=" O LEU 7 189 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP 7 191 " --> pdb=" O VAL 7 217 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA 7 265 " --> pdb=" O PHE 7 192 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE 7 259 " --> pdb=" O GLY 7 289 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N PHE 7 291 " --> pdb=" O PHE 7 259 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL 7 261 " --> pdb=" O PHE 7 291 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL 7 293 " --> pdb=" O VAL 7 261 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL 7 263 " --> pdb=" O VAL 7 293 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL 7 295 " --> pdb=" O VAL 7 263 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA 7 265 " --> pdb=" O VAL 7 295 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN 7 297 " --> pdb=" O ALA 7 265 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS 7 290 " --> pdb=" O ARG 7 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '7' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain '7' and resid 387 through 388 Processing sheet with id=AB5, first strand: chain '8' and resid 296 through 297 removed outlier: 6.007A pdb=" N SER 8 63 " --> pdb=" O CYS 8 146 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA 8 148 " --> pdb=" O SER 8 63 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR 8 345 " --> pdb=" O SER 8 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '8' and resid 257 through 262 removed outlier: 8.155A pdb=" N CYS 8 235 " --> pdb=" O TYR 8 230 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N TYR 8 230 " --> pdb=" O CYS 8 235 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL 8 237 " --> pdb=" O SER 8 228 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N VAL 8 324 " --> pdb=" O GLU 8 226 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER 8 228 " --> pdb=" O VAL 8 324 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 91 through 94 removed outlier: 5.838A pdb=" N LEU B 91 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 116 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N HIS B 93 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 108 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.441A pdb=" N LEU B 143 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR B 219 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL B 236 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY B 221 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AC1, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.886A pdb=" N LEU C 104 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU C 124 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL C 122 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 110 through 113 Processing sheet with id=AC3, first strand: chain 'D' and resid 219 through 228 removed outlier: 6.386A pdb=" N LEU D 244 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL D 225 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG D 242 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN D 227 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER D 240 " --> pdb=" O ASN D 227 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 294 through 298 Processing sheet with id=AC5, first strand: chain 'D' and resid 382 through 385 removed outlier: 6.846A pdb=" N VAL D 370 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 53 removed outlier: 5.338A pdb=" N VAL E 36 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR E 69 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP E 38 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR E 63 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU E 44 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY E 61 " --> pdb=" O GLU E 44 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA E 46 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ASN E 59 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 14.417A pdb=" N GLN E 57 " --> pdb=" O PRO E 48 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LYS E 11 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL E 88 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 156 through 162 removed outlier: 3.627A pdb=" N VAL F 170 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 197 through 199 Processing sheet with id=AC9, first strand: chain 'G' and resid 261 through 262 removed outlier: 6.007A pdb=" N LYS G 294 " --> pdb=" O CYS G 330 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL G 332 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 106 through 111 removed outlier: 6.343A pdb=" N ALA I 86 " --> pdb=" O VAL I 150 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LYS I 152 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE I 88 " --> pdb=" O LYS I 152 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE I 147 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER I 174 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 57 through 68 removed outlier: 5.685A pdb=" N VAL J 62 " --> pdb=" O ARG J 84 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG J 84 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS J 64 " --> pdb=" O ARG J 82 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N LEU J 123 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL J 92 " --> pdb=" O LEU J 123 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL J 125 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE J 94 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 82 through 83 removed outlier: 6.832A pdb=" N TYR M 32 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER M 53 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE M 34 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS R 183 " --> pdb=" O VAL R 141 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL R 141 " --> pdb=" O LYS R 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 12 through 22 removed outlier: 15.642A pdb=" N TRP N 12 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 11.954A pdb=" N LEU N 33 " --> pdb=" O TRP N 12 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL N 14 " --> pdb=" O THR N 31 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR N 31 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS N 27 " --> pdb=" O ILE N 18 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR N 20 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR N 25 " --> pdb=" O THR N 20 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL N 77 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N PHE N 50 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS N 79 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU N 81 " --> pdb=" O ARG N 67 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG N 67 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU N 83 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE N 63 " --> pdb=" O VAL N 85 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 100 through 101 Processing sheet with id=AD6, first strand: chain 'T' and resid 63 through 68 removed outlier: 6.684A pdb=" N LYS T 28 " --> pdb=" O GLN T 63 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N MET T 65 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET T 30 " --> pdb=" O MET T 65 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE T 67 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL T 32 " --> pdb=" O PHE T 67 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR T 79 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET T 30 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG T 77 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL T 32 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE T 75 " --> pdb=" O VAL T 32 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 190 through 191 Processing sheet with id=AD8, first strand: chain 'V' and resid 275 through 276 removed outlier: 6.280A pdb=" N LEU V 275 " --> pdb=" O GLU V 348 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'W' and resid 122 through 125 removed outlier: 6.646A pdb=" N ASP W 111 " --> pdb=" O ILE W 107 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE W 107 " --> pdb=" O ASP W 111 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TYR W 113 " --> pdb=" O PHE W 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS W 98 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG W 139 " --> pdb=" O ILE W 172 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE W 172 " --> pdb=" O ARG W 139 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG W 141 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN W 166 " --> pdb=" O LEU W 145 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 150 through 151 Processing sheet with id=AE2, first strand: chain 'X' and resid 67 through 70 removed outlier: 4.469A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 151 through 155 removed outlier: 6.405A pdb=" N LEU X 258 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL X 307 " --> pdb=" O LEU X 258 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL X 260 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA X 309 " --> pdb=" O VAL X 260 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL X 262 " --> pdb=" O ALA X 309 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG X 123 " --> pdb=" O ILE X 341 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE X 343 " --> pdb=" O ARG X 123 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU X 125 " --> pdb=" O ILE X 343 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL X 345 " --> pdb=" O LEU X 125 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR X 127 " --> pdb=" O VAL X 345 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'X' and resid 208 through 209 2589 hydrogen bonds defined for protein. 7392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 578 hydrogen bonds 1040 hydrogen bond angles 0 basepair planarities 234 basepair parallelities 422 stacking parallelities Total time for adding SS restraints: 41.39 Time building geometry restraints manager: 15.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 28522 1.39 - 1.62: 44144 1.62 - 1.85: 409 1.85 - 2.08: 0 2.08 - 2.32: 20 Bond restraints: 73095 Sorted by residual: bond pdb=" N1 GDP X 503 " pdb=" C2 GDP X 503 " ideal model delta sigma weight residual 1.337 1.558 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CG PRO Y 346 " pdb=" CD PRO Y 346 " ideal model delta sigma weight residual 1.503 1.162 0.341 3.40e-02 8.65e+02 1.00e+02 bond pdb=" C6 GDP X 503 " pdb=" O6 GDP X 503 " ideal model delta sigma weight residual 1.250 1.417 -0.167 2.00e-02 2.50e+03 6.97e+01 bond pdb=" C5A NAD A1735 " pdb=" N7A NAD A1735 " ideal model delta sigma weight residual 1.372 1.513 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C5 GDP X 503 " pdb=" C4 GDP X 503 " ideal model delta sigma weight residual 1.490 1.349 0.141 2.00e-02 2.50e+03 4.96e+01 ... (remaining 73090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 102639 4.16 - 8.33: 205 8.33 - 12.49: 12 12.49 - 16.65: 5 16.65 - 20.82: 2 Bond angle restraints: 102863 Sorted by residual: angle pdb=" N PRO Y 346 " pdb=" CD PRO Y 346 " pdb=" CG PRO Y 346 " ideal model delta sigma weight residual 103.20 87.07 16.13 1.50e+00 4.44e-01 1.16e+02 angle pdb=" N PRO G 96 " pdb=" CD PRO G 96 " pdb=" CG PRO G 96 " ideal model delta sigma weight residual 103.20 87.79 15.41 1.50e+00 4.44e-01 1.06e+02 angle pdb=" CA PRO Y 346 " pdb=" N PRO Y 346 " pdb=" CD PRO Y 346 " ideal model delta sigma weight residual 112.00 98.15 13.85 1.40e+00 5.10e-01 9.79e+01 angle pdb=" CA PRO G 96 " pdb=" CB PRO G 96 " pdb=" CG PRO G 96 " ideal model delta sigma weight residual 104.50 89.45 15.05 1.90e+00 2.77e-01 6.27e+01 angle pdb=" O1A NAD A1735 " pdb=" PA NAD A1735 " pdb=" O2A NAD A1735 " ideal model delta sigma weight residual 122.64 101.82 20.82 3.00e+00 1.11e-01 4.81e+01 ... (remaining 102858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 42592 34.81 - 69.62: 2252 69.62 - 104.43: 349 104.43 - 139.24: 11 139.24 - 174.06: 7 Dihedral angle restraints: 45211 sinusoidal: 26624 harmonic: 18587 Sorted by residual: dihedral pdb=" CA LYS J 72 " pdb=" C LYS J 72 " pdb=" N PRO J 73 " pdb=" CA PRO J 73 " ideal model delta harmonic sigma weight residual 180.00 111.16 68.84 0 5.00e+00 4.00e-02 1.90e+02 dihedral pdb=" O4' C A 870 " pdb=" C1' C A 870 " pdb=" N1 C A 870 " pdb=" C2 C A 870 " ideal model delta sinusoidal sigma weight residual 200.00 40.15 159.85 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' C A1233 " pdb=" C1' C A1233 " pdb=" N1 C A1233 " pdb=" C2 C A1233 " ideal model delta sinusoidal sigma weight residual 200.00 46.11 153.89 1 1.50e+01 4.44e-03 8.10e+01 ... (remaining 45208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.198: 12009 4.198 - 8.396: 0 8.396 - 12.594: 0 12.594 - 16.792: 0 16.792 - 20.990: 4 Chirality restraints: 12013 Sorted by residual: chirality pdb="FE1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S3 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.44 -20.99 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE3 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.38 -20.94 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE4 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S3 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.34 20.90 2.00e-01 2.50e+01 1.09e+04 ... (remaining 12010 not shown) Planarity restraints: 10016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 72 " 0.062 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO J 73 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO J 73 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO J 73 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Y 345 " 0.069 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO Y 346 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO Y 346 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO Y 346 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 375 " 0.031 2.00e-02 2.50e+03 2.27e-02 1.29e+01 pdb=" CG TRP Y 375 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 375 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 375 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 375 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 375 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 375 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 375 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 375 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 375 " 0.015 2.00e-02 2.50e+03 ... (remaining 10013 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.56: 481 2.56 - 3.20: 60946 3.20 - 3.85: 147381 3.85 - 4.49: 205814 4.49 - 5.14: 300189 Nonbonded interactions: 714811 Sorted by model distance: nonbonded pdb="MG MG A1720 " pdb=" O HOH A1808 " model vdw 1.910 2.170 nonbonded pdb="MG MG A1720 " pdb=" O HOH A1823 " model vdw 1.922 2.170 nonbonded pdb=" OP1 A A 801 " pdb="MG MG A1716 " model vdw 1.925 2.170 nonbonded pdb="MG MG A1709 " pdb=" O HOH A1811 " model vdw 1.925 2.170 nonbonded pdb=" OP1 A A 816 " pdb="MG MG A1717 " model vdw 1.930 2.170 ... (remaining 714806 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 2.260 Check model and map are aligned: 0.400 Set scattering table: 0.520 Process input model: 167.540 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.341 73095 Z= 0.284 Angle : 0.654 20.815 102863 Z= 0.344 Chirality : 0.384 20.990 12013 Planarity : 0.005 0.095 10016 Dihedral : 18.518 174.056 33153 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.19 (0.11), residues: 6259 helix: 1.54 (0.09), residues: 2975 sheet: -0.16 (0.19), residues: 662 loop : 0.32 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP Y 375 HIS 0.018 0.001 HIS I 183 PHE 0.043 0.002 PHE V 196 TYR 0.028 0.002 TYR V 226 ARG 0.014 0.001 ARG T 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1053 time to evaluate : 5.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 183 GLN cc_start: 0.7433 (mt0) cc_final: 0.7163 (mt0) REVERT: D 361 GLN cc_start: 0.8832 (mt0) cc_final: 0.8516 (mt0) REVERT: D 424 ASN cc_start: 0.8301 (m-40) cc_final: 0.8045 (m110) REVERT: E 45 ARG cc_start: 0.8387 (ptp-170) cc_final: 0.8103 (ptp-170) REVERT: J 89 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7359 (ttp-110) REVERT: J 114 ARG cc_start: 0.8328 (ptm-80) cc_final: 0.8054 (ptt180) REVERT: L 144 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7011 (mt-10) REVERT: O 62 GLU cc_start: 0.6714 (tp30) cc_final: 0.6473 (tp30) REVERT: P 49 ASP cc_start: 0.7907 (m-30) cc_final: 0.7617 (m-30) REVERT: P 137 ASN cc_start: 0.7628 (m110) cc_final: 0.7067 (p0) REVERT: R 77 SER cc_start: 0.7968 (p) cc_final: 0.7758 (p) REVERT: S 50 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7178 (mtp85) REVERT: T 95 ASN cc_start: 0.8535 (p0) cc_final: 0.8335 (p0) REVERT: U 183 SER cc_start: 0.7854 (t) cc_final: 0.7464 (p) outliers start: 0 outliers final: 0 residues processed: 1053 average time/residue: 1.7639 time to fit residues: 2345.9124 Evaluate side-chains 685 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 685 time to evaluate : 5.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 595 optimal weight: 9.9990 chunk 534 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 360 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 552 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 336 optimal weight: 7.9990 chunk 411 optimal weight: 4.9990 chunk 640 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 192 ASN 4 90 GLN 4 346 HIS 5 171 GLN 5 316 GLN 6 43 ASN 6 115 GLN 6 165 HIS 6 175 ASN 6 187 ASN 7 39 ASN 7 60 HIS 7 69 ASN 7 209 GLN 7 290 HIS ** 7 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 398 HIS 7 400 HIS 8 111 GLN 8 145 ASN 8 222 ASN ** 8 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 302 HIS 8 313 HIS 8 380 HIS B 64 ASN B 69 HIS B 74 ASN C 60 HIS C 115 ASN D 415 GLN E 57 GLN E 58 HIS F 146 HIS ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS H 109 HIS H 183 HIS I 141 GLN I 183 HIS I 184 ASN K 119 GLN L 169 ASN O 103 ASN O 225 GLN R 86 ASN R 221 GLN R 350 GLN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 GLN U 110 GLN U 133 GLN V 188 HIS V 377 GLN X 114 ASN ** X 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 159 HIS X 176 GLN X 363 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.289 73095 Z= 0.428 Angle : 0.862 51.008 102863 Z= 0.505 Chirality : 0.120 6.319 12013 Planarity : 0.005 0.067 10016 Dihedral : 19.625 175.313 19976 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.24 % Allowed : 8.84 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.10), residues: 6259 helix: 1.57 (0.09), residues: 3019 sheet: -0.01 (0.19), residues: 640 loop : 0.23 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP Y 375 HIS 0.017 0.002 HIS R 247 PHE 0.046 0.002 PHE 4 294 TYR 0.030 0.002 TYR V 91 ARG 0.009 0.001 ARG 8 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 731 time to evaluate : 5.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 144 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5840 (pt0) REVERT: 4 650 MET cc_start: 0.4793 (mpt) cc_final: 0.4366 (ppp) REVERT: 5 313 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6680 (mt-10) REVERT: 6 47 LYS cc_start: 0.7938 (tppt) cc_final: 0.7621 (tppp) REVERT: 6 106 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6881 (t70) REVERT: 7 30 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7797 (mm) REVERT: 8 193 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7774 (mtm) REVERT: 8 262 MET cc_start: 0.6390 (tpt) cc_final: 0.6073 (tpp) REVERT: 8 272 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6879 (mtp180) REVERT: C 126 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7192 (pt0) REVERT: D 424 ASN cc_start: 0.8390 (m-40) cc_final: 0.8131 (m-40) REVERT: E 40 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: G 211 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7136 (mt-10) REVERT: J 89 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7309 (ttp-110) REVERT: M 114 ARG cc_start: 0.7935 (mmt90) cc_final: 0.7699 (mtt-85) REVERT: N 23 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7753 (mt0) REVERT: O 54 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: O 65 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7456 (tp-100) REVERT: P 120 MET cc_start: 0.9245 (ttt) cc_final: 0.8967 (ttt) REVERT: P 134 LYS cc_start: 0.8206 (tttm) cc_final: 0.7820 (ttmm) REVERT: P 137 ASN cc_start: 0.7758 (m110) cc_final: 0.7177 (p0) REVERT: Q 38 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6979 (t70) REVERT: R 341 TYR cc_start: 0.7463 (t80) cc_final: 0.7015 (t80) REVERT: T 9 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8198 (tp) REVERT: T 66 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.7577 (mpp) REVERT: U 101 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7005 (tt0) REVERT: U 132 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5700 (tm-30) REVERT: U 183 SER cc_start: 0.8038 (t) cc_final: 0.7584 (p) REVERT: U 185 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7697 (tttt) REVERT: X 73 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6532 (mm-40) outliers start: 125 outliers final: 50 residues processed: 796 average time/residue: 1.6683 time to fit residues: 1701.4360 Evaluate side-chains 728 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 661 time to evaluate : 5.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 62 SER Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 119 ILE Chi-restraints excluded: chain 1 residue 140 ASP Chi-restraints excluded: chain 1 residue 144 GLU Chi-restraints excluded: chain 1 residue 303 GLU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 395 ASP Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 420 MET Chi-restraints excluded: chain 4 residue 422 ILE Chi-restraints excluded: chain 4 residue 426 LEU Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 313 GLU Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 109 CYS Chi-restraints excluded: chain 6 residue 128 SER Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 209 GLN Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 153 SER Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 164 LYS Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 149 ASP Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain X residue 255 MET Chi-restraints excluded: chain Y residue 376 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 355 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 532 optimal weight: 5.9990 chunk 435 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 641 optimal weight: 1.9990 chunk 692 optimal weight: 0.7980 chunk 571 optimal weight: 0.4980 chunk 636 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 514 optimal weight: 5.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 108 ASN 0 192 ASN 5 316 GLN 7 209 GLN 8 70 GLN ** 8 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 313 HIS B 64 ASN B 69 HIS B 74 ASN C 60 HIS C 115 ASN E 57 GLN F 169 GLN F 196 HIS ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS I 184 ASN K 113 HIS O 225 GLN R 86 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 358 GLN W 135 GLN X 54 ASN X 81 HIS Y 285 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 73095 Z= 0.264 Angle : 0.773 50.572 102863 Z= 0.466 Chirality : 0.121 6.423 12013 Planarity : 0.004 0.062 10016 Dihedral : 19.510 175.861 19976 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.01 % Allowed : 10.49 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.58 (0.11), residues: 6259 helix: 1.91 (0.09), residues: 3023 sheet: 0.17 (0.20), residues: 631 loop : 0.36 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Y 375 HIS 0.008 0.001 HIS 7 52 PHE 0.037 0.001 PHE 4 294 TYR 0.020 0.001 TYR V 91 ARG 0.009 0.000 ARG O 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 723 time to evaluate : 5.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 107 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7969 (tm130) REVERT: 5 127 ARG cc_start: 0.6691 (mtp85) cc_final: 0.6490 (mtp85) REVERT: 5 313 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: 6 47 LYS cc_start: 0.7917 (tppt) cc_final: 0.7556 (tppp) REVERT: 6 106 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6816 (t70) REVERT: 7 30 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7681 (mm) REVERT: 7 178 ARG cc_start: 0.7505 (tmm-80) cc_final: 0.7205 (tmm-80) REVERT: 7 215 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6466 (tpp) REVERT: 8 272 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6705 (mtp180) REVERT: D 424 ASN cc_start: 0.8354 (m-40) cc_final: 0.8082 (m110) REVERT: E 40 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: G 280 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6684 (mttm) REVERT: H 113 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.7020 (ttp-110) REVERT: J 89 ARG cc_start: 0.7621 (ttp-110) cc_final: 0.7308 (ttp-110) REVERT: J 114 ARG cc_start: 0.8416 (ptm-80) cc_final: 0.8183 (ptt180) REVERT: K 112 ARG cc_start: 0.3947 (ptp90) cc_final: 0.3550 (ptt-90) REVERT: O 65 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7568 (tp-100) REVERT: P 137 ASN cc_start: 0.7749 (m110) cc_final: 0.7223 (p0) REVERT: R 203 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8108 (mtmt) REVERT: R 341 TYR cc_start: 0.7451 (t80) cc_final: 0.7047 (t80) REVERT: S 36 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: S 50 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7376 (mtp85) REVERT: U 101 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: U 127 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6415 (mt-10) REVERT: U 183 SER cc_start: 0.7983 (t) cc_final: 0.7504 (p) REVERT: U 185 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7651 (tttt) REVERT: V 91 TYR cc_start: 0.8501 (m-80) cc_final: 0.8262 (m-80) REVERT: X 73 GLN cc_start: 0.6784 (OUTLIER) cc_final: 0.6501 (mm-40) REVERT: Y 285 GLN cc_start: 0.6930 (tt0) cc_final: 0.6245 (mp10) outliers start: 112 outliers final: 42 residues processed: 777 average time/residue: 1.6954 time to fit residues: 1679.7630 Evaluate side-chains 713 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 657 time to evaluate : 5.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 1 residue 153 SER Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 3 residue 176 ILE Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 395 ASP Chi-restraints excluded: chain 4 residue 422 ILE Chi-restraints excluded: chain 4 residue 431 LEU Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 313 GLU Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 185 LYS Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 118 LEU Chi-restraints excluded: chain 7 residue 209 GLN Chi-restraints excluded: chain 7 residue 215 MET Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 216 GLU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Y residue 376 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 633 optimal weight: 10.0000 chunk 482 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 chunk 430 optimal weight: 5.9990 chunk 643 optimal weight: 3.9990 chunk 681 optimal weight: 5.9990 chunk 336 optimal weight: 0.8980 chunk 610 optimal weight: 1.9990 chunk 183 optimal weight: 0.0170 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN ** 4 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 540 HIS 5 316 GLN 6 183 GLN 7 209 GLN 8 61 GLN ** 8 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 313 HIS B 64 ASN B 69 HIS B 74 ASN C 60 HIS C 115 ASN E 54 HIS E 57 GLN F 196 HIS H 109 HIS O 225 GLN R 86 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 54 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.239 73095 Z= 0.315 Angle : 0.792 50.692 102863 Z= 0.473 Chirality : 0.122 6.463 12013 Planarity : 0.004 0.062 10016 Dihedral : 19.445 175.936 19976 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.43 % Allowed : 11.60 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.58 (0.11), residues: 6259 helix: 1.91 (0.09), residues: 3021 sheet: 0.23 (0.20), residues: 629 loop : 0.35 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 3 177 HIS 0.008 0.001 HIS 7 383 PHE 0.041 0.002 PHE 4 294 TYR 0.024 0.002 TYR V 91 ARG 0.010 0.000 ARG O 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 687 time to evaluate : 5.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 107 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7890 (tm130) REVERT: 4 395 ASP cc_start: 0.5059 (OUTLIER) cc_final: 0.4813 (m-30) REVERT: 5 127 ARG cc_start: 0.6758 (mtp85) cc_final: 0.6542 (mtp85) REVERT: 6 47 LYS cc_start: 0.7948 (tppt) cc_final: 0.7732 (tppp) REVERT: 6 106 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6884 (t0) REVERT: 7 30 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7811 (mm) REVERT: 7 226 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7183 (tp) REVERT: 8 193 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7839 (mtm) REVERT: 8 262 MET cc_start: 0.6309 (tpt) cc_final: 0.5996 (tpp) REVERT: 8 272 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6799 (mtp180) REVERT: 8 274 MET cc_start: 0.7026 (mmt) cc_final: 0.6172 (mmt) REVERT: D 424 ASN cc_start: 0.8356 (m-40) cc_final: 0.8112 (m110) REVERT: E 40 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7028 (mp0) REVERT: G 280 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6782 (mttm) REVERT: J 89 ARG cc_start: 0.7691 (ttp-110) cc_final: 0.7373 (ttp-110) REVERT: O 54 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: O 65 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7596 (tp-100) REVERT: P 137 ASN cc_start: 0.7697 (m110) cc_final: 0.7245 (p0) REVERT: R 203 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8116 (mtmt) REVERT: S 36 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: T 66 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: U 101 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: U 127 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6433 (mt-10) REVERT: U 132 GLU cc_start: 0.5920 (OUTLIER) cc_final: 0.5712 (tm-30) REVERT: U 183 SER cc_start: 0.8010 (t) cc_final: 0.7522 (p) REVERT: U 185 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7658 (tttt) REVERT: V 196 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6028 (t80) REVERT: X 73 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6544 (mm-40) REVERT: X 81 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.6239 (p-80) REVERT: Y 259 PHE cc_start: 0.5450 (OUTLIER) cc_final: 0.4433 (t80) REVERT: Y 285 GLN cc_start: 0.6915 (tt0) cc_final: 0.6342 (mp10) outliers start: 136 outliers final: 55 residues processed: 762 average time/residue: 1.7563 time to fit residues: 1742.2737 Evaluate side-chains 714 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 639 time to evaluate : 5.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 62 SER Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 153 SER Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 1 residue 252 ILE Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 3 residue 176 ILE Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 395 ASP Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 422 ILE Chi-restraints excluded: chain 4 residue 599 PHE Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 109 CYS Chi-restraints excluded: chain 6 residue 126 LYS Chi-restraints excluded: chain 6 residue 128 SER Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 183 GLN Chi-restraints excluded: chain 6 residue 185 LYS Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 82 THR Chi-restraints excluded: chain 7 residue 209 GLN Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 182 GLU Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 164 LYS Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 101 GLU Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 196 PHE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 376 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 567 optimal weight: 10.0000 chunk 386 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 507 optimal weight: 0.8980 chunk 281 optimal weight: 10.0000 chunk 581 optimal weight: 0.0050 chunk 471 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 347 optimal weight: 5.9990 chunk 611 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN 4 562 GLN 5 316 GLN 7 144 HIS 7 209 GLN ** 8 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 313 HIS B 64 ASN B 74 ASN C 60 HIS C 115 ASN E 57 GLN F 196 HIS ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 ASN J 106 GLN O 225 GLN R 86 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 135 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 73095 Z= 0.279 Angle : 0.772 50.678 102863 Z= 0.465 Chirality : 0.121 6.412 12013 Planarity : 0.004 0.060 10016 Dihedral : 19.406 176.114 19976 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.36 % Allowed : 12.57 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.67 (0.11), residues: 6259 helix: 1.99 (0.09), residues: 3017 sheet: 0.24 (0.20), residues: 633 loop : 0.40 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 3 177 HIS 0.007 0.001 HIS 7 52 PHE 0.040 0.001 PHE 4 294 TYR 0.021 0.001 TYR V 91 ARG 0.010 0.000 ARG O 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 680 time to evaluate : 5.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8893 (mp) REVERT: 0 107 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7850 (tm130) REVERT: 4 395 ASP cc_start: 0.5081 (OUTLIER) cc_final: 0.4864 (m-30) REVERT: 5 127 ARG cc_start: 0.6702 (mtp85) cc_final: 0.6493 (mtp85) REVERT: 5 313 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6554 (mt-10) REVERT: 6 47 LYS cc_start: 0.7926 (tppt) cc_final: 0.7613 (tppp) REVERT: 7 30 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7842 (mm) REVERT: 7 226 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7106 (tp) REVERT: 8 193 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7791 (mtm) REVERT: 8 262 MET cc_start: 0.6360 (tpt) cc_final: 0.6035 (tpp) REVERT: 8 272 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6835 (mtp180) REVERT: D 424 ASN cc_start: 0.8324 (m-40) cc_final: 0.8045 (m110) REVERT: E 40 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: G 280 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6765 (mttm) REVERT: O 54 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6231 (mp0) REVERT: O 65 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7563 (tp-100) REVERT: P 137 ASN cc_start: 0.7740 (m110) cc_final: 0.7251 (p0) REVERT: Q 38 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6915 (t0) REVERT: R 203 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8225 (mtmt) REVERT: S 50 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7531 (mtp85) REVERT: T 14 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: T 66 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.7547 (mpp) REVERT: T 157 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8129 (mmtp) REVERT: U 127 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6438 (mt-10) REVERT: U 132 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5722 (tm-30) REVERT: U 183 SER cc_start: 0.7960 (t) cc_final: 0.7491 (p) REVERT: U 185 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7647 (tttt) REVERT: V 196 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.5897 (t80) REVERT: X 73 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6563 (mm-40) REVERT: X 81 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.6088 (p-80) REVERT: Y 259 PHE cc_start: 0.5483 (OUTLIER) cc_final: 0.4467 (t80) REVERT: Y 285 GLN cc_start: 0.7005 (tt0) cc_final: 0.6369 (mp10) REVERT: Y 303 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6762 (tp-100) REVERT: Y 323 ASP cc_start: 0.5891 (t0) cc_final: 0.5430 (t0) outliers start: 132 outliers final: 57 residues processed: 753 average time/residue: 1.6436 time to fit residues: 1588.1766 Evaluate side-chains 727 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 648 time to evaluate : 5.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 62 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 140 ASP Chi-restraints excluded: chain 1 residue 153 SER Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 3 residue 176 ILE Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 365 ILE Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 395 ASP Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 422 ILE Chi-restraints excluded: chain 4 residue 431 LEU Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 4 residue 599 PHE Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 313 GLU Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 118 LEU Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 288 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain T residue 164 LYS Chi-restraints excluded: chain U residue 89 VAL Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 196 PHE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 310 LEU Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 11 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 229 optimal weight: 10.0000 chunk 613 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 400 optimal weight: 0.1980 chunk 168 optimal weight: 4.9990 chunk 682 optimal weight: 0.0870 chunk 566 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 358 optimal weight: 5.9990 overall best weight: 1.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN 5 316 GLN 6 183 GLN ** 6 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 107 GLN 8 111 GLN ** 8 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 313 HIS B 64 ASN B 74 ASN C 60 HIS E 57 GLN F 196 HIS ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN K 55 ASN O 155 GLN O 207 GLN O 225 GLN R 86 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 122 GLN V 87 HIS X 54 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.238 73095 Z= 0.275 Angle : 0.768 50.645 102863 Z= 0.463 Chirality : 0.121 6.404 12013 Planarity : 0.004 0.058 10016 Dihedral : 19.368 175.978 19976 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.40 % Allowed : 13.28 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.76 (0.11), residues: 6259 helix: 2.06 (0.09), residues: 3014 sheet: 0.29 (0.20), residues: 634 loop : 0.46 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 3 177 HIS 0.007 0.001 HIS 7 52 PHE 0.039 0.001 PHE 4 294 TYR 0.021 0.001 TYR V 91 ARG 0.011 0.000 ARG 6 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 690 time to evaluate : 5.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8872 (mp) REVERT: 4 468 MET cc_start: 0.6902 (mpt) cc_final: 0.6663 (mmt) REVERT: 5 313 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6516 (mt-10) REVERT: 6 47 LYS cc_start: 0.7995 (tppt) cc_final: 0.7698 (tppp) REVERT: 6 106 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.7023 (t0) REVERT: 7 30 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7815 (mm) REVERT: 7 226 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7182 (tp) REVERT: 8 193 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7785 (mtm) REVERT: 8 272 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6833 (mtp180) REVERT: D 424 ASN cc_start: 0.8341 (m-40) cc_final: 0.8062 (m110) REVERT: E 40 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: G 280 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6694 (mttm) REVERT: J 71 LYS cc_start: 0.8533 (ptmt) cc_final: 0.8299 (ptmt) REVERT: K 112 ARG cc_start: 0.4152 (ptt180) cc_final: 0.3672 (ptp-170) REVERT: M 102 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8358 (mmm) REVERT: O 65 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7559 (tp-100) REVERT: P 137 ASN cc_start: 0.7710 (m110) cc_final: 0.7296 (p0) REVERT: R 203 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8237 (mtmt) REVERT: S 50 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7545 (mtp85) REVERT: T 14 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: T 66 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.7479 (mpp) REVERT: T 70 MET cc_start: 0.8484 (mtp) cc_final: 0.8003 (mtp) REVERT: T 157 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8145 (mmtp) REVERT: U 127 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6429 (mt-10) REVERT: U 132 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5793 (tm-30) REVERT: U 183 SER cc_start: 0.7953 (t) cc_final: 0.7467 (p) REVERT: U 185 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7640 (tttt) REVERT: V 91 TYR cc_start: 0.8578 (m-80) cc_final: 0.8305 (m-80) REVERT: V 196 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.5735 (t80) REVERT: X 73 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6536 (mm-40) REVERT: X 81 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.5868 (p90) REVERT: Y 259 PHE cc_start: 0.5436 (OUTLIER) cc_final: 0.4434 (t80) REVERT: Z 68 LEU cc_start: 0.4973 (OUTLIER) cc_final: 0.4306 (mt) outliers start: 134 outliers final: 69 residues processed: 766 average time/residue: 1.6744 time to fit residues: 1641.5575 Evaluate side-chains 731 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 640 time to evaluate : 5.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 62 SER Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 143 CYS Chi-restraints excluded: chain 1 residue 153 SER Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 1 residue 322 VAL Chi-restraints excluded: chain 3 residue 176 ILE Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 395 ASP Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 422 ILE Chi-restraints excluded: chain 4 residue 431 LEU Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 4 residue 599 PHE Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 170 THR Chi-restraints excluded: chain 5 residue 313 GLU Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 128 SER Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 180 VAL Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 107 GLN Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 288 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 153 SER Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 93 TYR Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain O residue 54 GLU Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 164 LYS Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain V residue 196 PHE Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 310 LEU Chi-restraints excluded: chain Y residue 315 ILE Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 68 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 657 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 388 optimal weight: 0.8980 chunk 498 optimal weight: 0.9980 chunk 385 optimal weight: 7.9990 chunk 574 optimal weight: 0.9980 chunk 380 optimal weight: 4.9990 chunk 679 optimal weight: 6.9990 chunk 425 optimal weight: 1.9990 chunk 414 optimal weight: 0.9980 chunk 313 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN 5 316 GLN 6 43 ASN 6 183 GLN 6 187 ASN 7 49 HIS ** 8 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 313 HIS B 64 ASN B 74 ASN C 60 HIS E 57 GLN F 196 HIS ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 207 GLN O 225 GLN R 86 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 135 GLN X 54 ASN X 81 HIS ** Y 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 73095 Z= 0.263 Angle : 0.765 50.627 102863 Z= 0.461 Chirality : 0.121 6.386 12013 Planarity : 0.004 0.060 10016 Dihedral : 19.340 176.255 19976 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.29 % Allowed : 13.69 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.82 (0.11), residues: 6259 helix: 2.11 (0.09), residues: 3011 sheet: 0.31 (0.20), residues: 636 loop : 0.48 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 3 177 HIS 0.006 0.001 HIS 7 52 PHE 0.043 0.001 PHE 4 294 TYR 0.022 0.001 TYR H 93 ARG 0.015 0.000 ARG G 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 682 time to evaluate : 5.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8855 (mp) REVERT: 4 468 MET cc_start: 0.6869 (mpt) cc_final: 0.6609 (mmt) REVERT: 5 313 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6489 (mt-10) REVERT: 6 47 LYS cc_start: 0.7985 (tppt) cc_final: 0.7689 (tppp) REVERT: 7 30 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7646 (mm) REVERT: 7 226 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7107 (tp) REVERT: 8 193 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7769 (mtm) REVERT: 8 272 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6746 (mtp180) REVERT: D 424 ASN cc_start: 0.8311 (m-40) cc_final: 0.8019 (m110) REVERT: E 40 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: G 280 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6686 (mttm) REVERT: H 113 ARG cc_start: 0.7085 (ttp-110) cc_final: 0.6831 (ttp-110) REVERT: J 71 LYS cc_start: 0.8534 (ptmt) cc_final: 0.8331 (ptmt) REVERT: M 102 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8245 (mmm) REVERT: M 114 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7615 (mtt-85) REVERT: O 65 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7559 (tp-100) REVERT: P 54 MET cc_start: 0.8662 (ptp) cc_final: 0.8390 (ptm) REVERT: P 134 LYS cc_start: 0.8141 (tttm) cc_final: 0.7752 (tttm) REVERT: P 137 ASN cc_start: 0.7800 (m110) cc_final: 0.7358 (p0) REVERT: Q 38 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6911 (t0) REVERT: R 203 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8246 (mtmt) REVERT: S 50 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7552 (mtp85) REVERT: T 14 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: T 66 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.7406 (mpp) REVERT: T 70 MET cc_start: 0.8449 (mtp) cc_final: 0.7925 (mtp) REVERT: T 157 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8146 (mmtp) REVERT: U 127 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6433 (mt-10) REVERT: U 132 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5758 (tm-30) REVERT: U 134 ARG cc_start: 0.6444 (ttp-110) cc_final: 0.6168 (mtm110) REVERT: U 183 SER cc_start: 0.7930 (t) cc_final: 0.7455 (p) REVERT: U 185 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7629 (tttt) REVERT: V 91 TYR cc_start: 0.8549 (m-80) cc_final: 0.8285 (m-80) REVERT: W 109 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: X 73 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6536 (mm-40) REVERT: Y 259 PHE cc_start: 0.5441 (OUTLIER) cc_final: 0.4447 (t80) REVERT: Y 284 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6346 (mtpp) REVERT: Z 68 LEU cc_start: 0.4855 (OUTLIER) cc_final: 0.4204 (mt) outliers start: 128 outliers final: 61 residues processed: 750 average time/residue: 1.6737 time to fit residues: 1615.4435 Evaluate side-chains 733 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 650 time to evaluate : 5.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 143 CYS Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 3 residue 176 ILE Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 422 ILE Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 170 THR Chi-restraints excluded: chain 5 residue 313 GLU Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 128 SER Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 180 VAL Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 288 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 101 ASP Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 193 MET Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 121 ILE Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 284 LYS Chi-restraints excluded: chain Y residue 310 LEU Chi-restraints excluded: chain Y residue 315 ILE Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 68 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 420 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 405 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 432 optimal weight: 3.9990 chunk 462 optimal weight: 4.9990 chunk 335 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 534 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN ** 4 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 316 GLN 6 43 ASN 6 183 GLN 7 209 GLN ** 8 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 313 HIS B 64 ASN B 74 ASN C 60 HIS C 115 ASN C 116 GLN E 57 GLN F 196 HIS ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 ASN J 106 GLN K 55 ASN O 207 GLN R 86 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 73095 Z= 0.338 Angle : 0.803 50.702 102863 Z= 0.477 Chirality : 0.122 6.463 12013 Planarity : 0.004 0.055 10016 Dihedral : 19.342 175.714 19976 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.17 % Allowed : 14.18 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.11), residues: 6259 helix: 1.95 (0.09), residues: 3010 sheet: 0.27 (0.20), residues: 632 loop : 0.41 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 3 177 HIS 0.008 0.001 HIS 7 398 PHE 0.045 0.002 PHE 4 294 TYR 0.025 0.002 TYR 4 272 ARG 0.011 0.001 ARG 7 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 658 time to evaluate : 5.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8810 (mp) REVERT: 4 468 MET cc_start: 0.6834 (mpt) cc_final: 0.6512 (mmt) REVERT: 6 47 LYS cc_start: 0.7946 (tppt) cc_final: 0.7633 (tppp) REVERT: 7 30 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7911 (mm) REVERT: 8 262 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5979 (tpp) REVERT: 8 272 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6845 (mtp180) REVERT: D 424 ASN cc_start: 0.8323 (m-40) cc_final: 0.8043 (m110) REVERT: E 40 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: G 280 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6768 (mttm) REVERT: K 112 ARG cc_start: 0.4009 (ptt180) cc_final: 0.3602 (ptp-170) REVERT: O 54 GLU cc_start: 0.6341 (mt-10) cc_final: 0.6026 (mp0) REVERT: O 65 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7579 (tp-100) REVERT: P 137 ASN cc_start: 0.7713 (m110) cc_final: 0.7350 (p0) REVERT: R 203 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8228 (mtmt) REVERT: R 299 ASN cc_start: 0.8557 (m-40) cc_final: 0.8324 (m110) REVERT: S 36 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: T 14 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: T 66 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.7473 (mpp) REVERT: T 70 MET cc_start: 0.8467 (mtp) cc_final: 0.8030 (mtp) REVERT: T 157 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8198 (mmtp) REVERT: U 127 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: U 132 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5666 (tm-30) REVERT: U 134 ARG cc_start: 0.6438 (ttp-110) cc_final: 0.6162 (mtm110) REVERT: U 183 SER cc_start: 0.7989 (t) cc_final: 0.7498 (p) REVERT: U 185 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7652 (tttt) REVERT: X 73 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6577 (mm-40) REVERT: Y 259 PHE cc_start: 0.5510 (OUTLIER) cc_final: 0.4516 (t80) REVERT: Y 284 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6430 (mtpp) REVERT: Z 68 LEU cc_start: 0.5019 (OUTLIER) cc_final: 0.4329 (mt) outliers start: 121 outliers final: 63 residues processed: 733 average time/residue: 1.6874 time to fit residues: 1589.8956 Evaluate side-chains 717 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 636 time to evaluate : 5.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 91 VAL Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 143 CYS Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 3 residue 176 ILE Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 420 MET Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 170 THR Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 180 VAL Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 209 GLN Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 288 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 101 ASP Chi-restraints excluded: chain 8 residue 153 SER Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 262 MET Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 187 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 137 LEU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 284 LYS Chi-restraints excluded: chain Y residue 310 LEU Chi-restraints excluded: chain Y residue 315 ILE Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 68 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 618 optimal weight: 0.0570 chunk 650 optimal weight: 0.8980 chunk 593 optimal weight: 7.9990 chunk 633 optimal weight: 6.9990 chunk 381 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 chunk 497 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 572 optimal weight: 1.9990 chunk 598 optimal weight: 10.0000 chunk 631 optimal weight: 0.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 24 GLN 0 192 ASN ** 4 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 316 GLN 6 43 ASN 6 183 GLN 6 187 ASN 7 383 HIS ** 8 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 313 HIS B 64 ASN B 74 ASN C 60 HIS C 115 ASN E 57 GLN F 196 HIS ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 ASN O 155 GLN O 207 GLN R 86 ASN S 47 GLN S 61 GLN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 135 GLN X 81 HIS ** Y 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 372 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 73095 Z= 0.259 Angle : 0.771 50.615 102863 Z= 0.464 Chirality : 0.121 6.379 12013 Planarity : 0.004 0.051 10016 Dihedral : 19.306 175.997 19976 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.88 % Allowed : 14.73 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 1.81 (0.11), residues: 6259 helix: 2.09 (0.09), residues: 3008 sheet: 0.36 (0.20), residues: 631 loop : 0.48 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 3 177 HIS 0.008 0.001 HIS 7 52 PHE 0.053 0.001 PHE 4 294 TYR 0.024 0.001 TYR 4 272 ARG 0.014 0.000 ARG 7 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12518 Ramachandran restraints generated. 6259 Oldfield, 0 Emsley, 6259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 663 time to evaluate : 8.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8868 (mp) REVERT: 4 468 MET cc_start: 0.6792 (mpt) cc_final: 0.6469 (mmt) REVERT: 5 313 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6246 (mp0) REVERT: 7 30 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7792 (mm) REVERT: 8 262 MET cc_start: 0.6222 (tpt) cc_final: 0.6008 (tpp) REVERT: 8 272 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6790 (mtp180) REVERT: C 138 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.5856 (t80) REVERT: D 424 ASN cc_start: 0.8304 (m-40) cc_final: 0.8022 (m110) REVERT: E 40 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: G 280 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6677 (mttm) REVERT: K 112 ARG cc_start: 0.3960 (ptt180) cc_final: 0.3542 (ptp-170) REVERT: M 102 MET cc_start: 0.8581 (tpt) cc_final: 0.8305 (mmm) REVERT: O 65 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7572 (tp-100) REVERT: P 54 MET cc_start: 0.8693 (ptp) cc_final: 0.8329 (ptm) REVERT: P 134 LYS cc_start: 0.8232 (tttm) cc_final: 0.7844 (tttm) REVERT: P 137 ASN cc_start: 0.7733 (m110) cc_final: 0.7376 (p0) REVERT: R 203 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8217 (mtmt) REVERT: R 299 ASN cc_start: 0.8610 (m-40) cc_final: 0.8397 (m110) REVERT: S 36 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: S 50 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7551 (mtp85) REVERT: T 14 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: T 66 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.7385 (mpp) REVERT: T 70 MET cc_start: 0.8489 (mtp) cc_final: 0.7928 (mtp) REVERT: T 157 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8185 (mmtp) REVERT: U 127 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: U 132 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5667 (tm-30) REVERT: U 134 ARG cc_start: 0.6432 (ttp-110) cc_final: 0.6158 (mtm110) REVERT: U 183 SER cc_start: 0.7927 (t) cc_final: 0.7454 (p) REVERT: U 185 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7621 (tttt) REVERT: V 91 TYR cc_start: 0.8538 (m-80) cc_final: 0.8288 (m-80) REVERT: W 109 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: X 73 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6562 (mm-40) REVERT: X 81 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.5917 (p90) REVERT: Y 259 PHE cc_start: 0.5541 (OUTLIER) cc_final: 0.4564 (t80) REVERT: Z 31 MET cc_start: 0.4736 (ppp) cc_final: 0.4399 (ppp) REVERT: Z 68 LEU cc_start: 0.4882 (OUTLIER) cc_final: 0.4216 (mt) outliers start: 105 outliers final: 55 residues processed: 721 average time/residue: 1.6792 time to fit residues: 1572.5693 Evaluate side-chains 719 residues out of total 5586 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 644 time to evaluate : 5.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 36 VAL Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 143 CYS Chi-restraints excluded: chain 1 residue 190 LEU Chi-restraints excluded: chain 1 residue 207 ILE Chi-restraints excluded: chain 3 residue 176 ILE Chi-restraints excluded: chain 4 residue 204 SER Chi-restraints excluded: chain 4 residue 376 ILE Chi-restraints excluded: chain 4 residue 422 ILE Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 5 residue 23 LYS Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 170 THR Chi-restraints excluded: chain 5 residue 313 GLU Chi-restraints excluded: chain 6 residue 45 LEU Chi-restraints excluded: chain 6 residue 172 THR Chi-restraints excluded: chain 6 residue 180 VAL Chi-restraints excluded: chain 6 residue 183 GLN Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 31 VAL Chi-restraints excluded: chain 7 residue 210 SER Chi-restraints excluded: chain 7 residue 288 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 101 ASP Chi-restraints excluded: chain 8 residue 172 LEU Chi-restraints excluded: chain 8 residue 205 ASN Chi-restraints excluded: chain 8 residue 260 THR Chi-restraints excluded: chain 8 residue 272 ARG Chi-restraints excluded: chain 8 residue 297 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 132 TYR Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain D residue 417 MET Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 333 SER Chi-restraints excluded: chain G residue 338 SER Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 183 HIS Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 124 GLN Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 181 ILE Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 73 GLU Chi-restraints excluded: chain R residue 203 LYS Chi-restraints excluded: chain S residue 36 ASP Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 157 LYS Chi-restraints excluded: chain U residue 127 GLU Chi-restraints excluded: chain U residue 132 GLU Chi-restraints excluded: chain U residue 185 LYS Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 259 PHE Chi-restraints excluded: chain Y residue 376 PHE Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 68 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 705 random chunks: chunk 415 optimal weight: 2.9990 chunk 669 optimal weight: 0.0470 chunk 408 optimal weight: 0.9990 chunk 317 optimal weight: 6.9990 chunk 465 optimal weight: 2.9990 chunk 702 optimal weight: 20.0000 chunk 646 optimal weight: 9.9990 chunk 559 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 432 optimal weight: 0.7980 chunk 342 optimal weight: 7.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: