Starting phenix.real_space_refine on Sat Sep 28 10:52:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/09_2024/8csp_26966_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/09_2024/8csp_26966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/09_2024/8csp_26966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/09_2024/8csp_26966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/09_2024/8csp_26966_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csp_26966/09_2024/8csp_26966_neut.cif" } resolution = 2.66 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= 0.045 sd= 1.467 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 4 8.98 5 Fe 8 7.16 5 Zn 1 6.06 5 P 742 5.49 5 Mg 28 5.21 5 S 265 5.16 5 C 41157 2.51 5 N 12380 2.21 5 O 14717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 69302 Number of models: 1 Model: "" Number of chains: 40 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: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2195 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} 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: "7" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3145 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 366} 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: "9" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3558 Classifications: {'peptide': 446} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 411} Chain breaks: 3 Chain: "A" Number of atoms: 15655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 15655 Classifications: {'RNA': 737} Modifications used: {'rna2p_pur': 66, 'rna2p_pyr': 55, 'rna3p_pur': 319, 'rna3p_pyr': 297} Link IDs: {'rna2p': 120, 'rna3p': 616} Chain breaks: 10 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: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 839 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1724 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} 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: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1045 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain breaks: 1 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: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 283 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain breaks: 2 Chain: "L" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1091 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} 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: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} 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: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1043 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} 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: "a" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1785 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 140 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Unusual residues: {' K': 4, ' MG': 26} Classifications: {'undetermined': 30} Link IDs: {None: 29} 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: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13955 SG CYS 7 404 103.800 107.113 162.091 1.00 19.15 S ATOM 13476 SG CYS 7 347 107.604 102.804 158.325 1.00 21.64 S ATOM 13371 SG CYS 7 333 101.532 105.232 156.913 1.00 21.41 S ATOM 13418 SG CYS 7 339 106.934 108.394 156.771 1.00 17.22 S ATOM 41502 SG CYS E 105 121.431 74.068 47.737 1.00 62.84 S ATOM 52658 SG CYS P 100 120.981 71.746 51.293 1.00 45.38 S ATOM 52407 SG CYS P 68 125.132 70.663 46.031 1.00 49.31 S ATOM 51067 SG CYS O 94 111.543 159.763 99.764 1.00 33.91 S ATOM 51153 SG CYS O 105 114.435 160.302 97.614 1.00 31.13 S ATOM 51174 SG CYS O 108 113.443 163.172 99.444 1.00 33.64 S ATOM 51462 SG CYS O 143 110.983 161.803 96.642 1.00 27.23 S ATOM 49012 SG CYS M 26 90.632 170.806 77.118 1.00 30.16 S ATOM 57710 SG CYS T 149 94.046 170.946 78.053 1.00 30.67 S ATOM 57638 SG CYS T 139 93.456 172.025 71.615 1.00 29.36 S ATOM 57652 SG CYS T 141 96.186 171.853 74.307 1.00 28.65 S Time building chain proxies: 28.07, per 1000 atoms: 0.41 Number of scatterers: 69302 At special positions: 0 Unit cell: (223.02, 244.26, 221.958, 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 4 19.00 S 265 16.00 P 742 15.00 Mg 28 11.99 O 14717 8.00 N 12380 7.00 C 41157 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.75 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS P 68 " pdb="FE1 FES E 201 " - pdb=" SG CYS P 100 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 105 " 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="FE4 SF4 7 501 " - pdb=" SG CYS 7 339 " pdb="FE2 SF4 7 501 " - pdb=" SG CYS 7 347 " pdb="FE1 SF4 7 501 " - pdb=" SG CYS 7 404 " Number of angles added : 23 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 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12600 Finding SS restraints... Secondary structure from input PDB file: 299 helices and 48 sheets defined 52.0% alpha, 12.9% beta 211 base pairs and 363 stacking pairs defined. Time for finding SS restraints: 23.53 Creating SS restraints... Processing helix chain '0' and resid 9 through 25 removed outlier: 3.950A 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: 7.700A pdb=" N LEU 0 73 " --> pdb=" O ARG 0 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU 0 76 " --> pdb=" O LEU 0 73 " (cutoff:3.500A) Processing helix chain '0' and resid 83 through 89 Processing helix chain '0' and resid 146 through 152 Processing helix chain '0' and resid 167 through 181 Processing helix chain '1' and resid 55 through 60 removed outlier: 3.566A pdb=" N GLU 1 58 " --> pdb=" O PRO 1 55 " (cutoff:3.500A) Processing helix chain '1' and resid 65 through 70 removed outlier: 3.840A pdb=" N VAL 1 69 " --> pdb=" O ASP 1 65 " (cutoff:3.500A) Processing helix chain '1' and resid 102 through 107 Processing helix chain '1' and resid 115 through 126 removed outlier: 3.558A pdb=" N ALA 1 125 " --> pdb=" O LYS 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 127 through 130 Processing helix chain '1' and resid 139 through 147 removed outlier: 3.773A pdb=" N LYS 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 169 removed outlier: 3.791A 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 235 removed outlier: 3.712A pdb=" N ASN 1 218 " --> pdb=" O LEU 1 214 " (cutoff:3.500A) Processing helix chain '1' and resid 239 through 243 removed outlier: 3.542A pdb=" N SER 1 242 " --> pdb=" O TRP 1 239 " (cutoff:3.500A) Processing helix chain '1' and resid 256 through 274 Processing helix chain '1' and resid 286 through 302 Processing helix chain '1' and resid 305 through 321 Processing helix chain '4' and resid 68 through 78 removed outlier: 3.783A 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 removed outlier: 3.622A pdb=" N MET 4 141 " --> pdb=" O PRO 4 138 " (cutoff:3.500A) Processing helix chain '4' and resid 153 through 163 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 removed outlier: 3.523A pdb=" N TYR 4 259 " --> pdb=" O ASN 4 255 " (cutoff:3.500A) 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 removed outlier: 3.792A pdb=" N PHE 4 335 " --> pdb=" O ASN 4 331 " (cutoff:3.500A) Processing helix chain '4' and resid 344 through 348 removed outlier: 6.957A pdb=" N VAL 4 347 " --> pdb=" O ARG 4 344 " (cutoff:3.500A) Processing helix chain '4' and resid 349 through 364 Processing helix chain '4' and resid 368 through 380 Processing helix chain '4' and resid 391 through 401 removed outlier: 3.945A pdb=" N ASP 4 395 " --> pdb=" O PHE 4 391 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 413 No H-bonds generated for 'chain '4' and resid 411 through 413' Processing helix chain '4' and resid 414 through 427 Processing helix chain '4' and resid 428 through 440 removed outlier: 3.646A pdb=" N ALA 4 432 " --> pdb=" O ASP 4 428 " (cutoff:3.500A) Processing helix chain '4' and resid 443 through 449 removed outlier: 4.233A 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 504 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 Processing helix chain '4' and resid 524 through 537 Processing helix chain '4' and resid 541 through 561 Processing helix chain '4' and resid 572 through 586 Processing helix chain '4' and resid 588 through 603 removed outlier: 3.688A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) Processing helix chain '4' and resid 607 through 622 Processing helix chain '4' and resid 623 through 637 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 90 through 101 Processing helix chain '5' and resid 116 through 120 removed outlier: 3.926A pdb=" N LYS 5 119 " --> pdb=" O LYS 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 122 through 126 removed outlier: 3.669A pdb=" N LEU 5 125 " --> pdb=" O SER 5 122 " (cutoff:3.500A) removed outlier: 3.688A 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: 3.955A 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: 3.966A 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: 3.965A 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 269 through 271 No H-bonds generated for 'chain '5' and resid 269 through 271' Processing helix chain '5' and resid 272 through 284 Processing helix chain '5' and resid 291 through 295 Processing helix chain '5' and resid 296 through 313 Processing helix chain '5' and resid 314 through 320 removed outlier: 3.997A pdb=" N PHE 5 318 " --> pdb=" O PRO 5 315 " (cutoff:3.500A) Processing helix chain '5' and resid 321 through 327 Processing helix chain '7' and resid 42 through 47 removed outlier: 3.632A pdb=" N LYS 7 46 " --> pdb=" O GLY 7 42 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG 7 47 " --> pdb=" O PHE 7 43 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 42 through 47' Processing helix chain '7' and resid 48 through 52 removed outlier: 3.627A pdb=" N GLN 7 51 " --> pdb=" O PRO 7 48 " (cutoff:3.500A) Processing helix chain '7' and resid 64 through 76 Processing helix chain '7' and resid 80 through 97 removed outlier: 3.507A pdb=" N GLU 7 84 " --> pdb=" O GLY 7 80 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 116 Processing helix chain '7' and resid 134 through 142 Processing helix chain '7' and resid 151 through 181 removed outlier: 6.219A pdb=" N ASP 7 164 " --> pdb=" O ALA 7 160 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLY 7 165 " --> pdb=" O ALA 7 161 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 197 through 208 Processing helix chain '7' and resid 220 through 232 Processing helix chain '7' and resid 267 through 271 Processing helix chain '7' and resid 273 through 287 Processing helix chain '7' and resid 299 through 315 Processing helix chain '7' and resid 416 through 421 Processing helix chain '7' and resid 421 through 431 Processing helix chain '8' and resid 86 through 99 removed outlier: 3.544A pdb=" N LEU 8 90 " --> pdb=" O ARG 8 86 " (cutoff:3.500A) Processing helix chain '8' and resid 101 through 108 removed outlier: 3.539A pdb=" N LEU 8 105 " --> pdb=" O ASP 8 101 " (cutoff:3.500A) Processing helix chain '8' and resid 116 through 139 removed outlier: 3.850A 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: 3.721A pdb=" N ILE 8 143 " --> pdb=" O GLN 8 139 " (cutoff:3.500A) Processing helix chain '8' and resid 154 through 163 removed outlier: 3.648A pdb=" N ALA 8 158 " --> pdb=" O VAL 8 154 " (cutoff:3.500A) Processing helix chain '8' and resid 167 through 189 removed outlier: 3.630A pdb=" N VAL 8 189 " --> pdb=" O ALA 8 185 " (cutoff:3.500A) Processing helix chain '8' and resid 203 through 219 removed outlier: 3.972A 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: 3.649A pdb=" N LEU 8 281 " --> pdb=" O ALA 8 277 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA 8 287 " --> pdb=" O GLN 8 283 " (cutoff:3.500A) removed outlier: 4.173A 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: 3.726A 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 367 Processing helix chain '9' and resid 74 through 78 Processing helix chain '9' and resid 86 through 115 removed outlier: 4.218A pdb=" N GLN 9 90 " --> pdb=" O THR 9 86 " (cutoff:3.500A) Processing helix chain '9' and resid 180 through 193 Processing helix chain '9' and resid 197 through 205 Processing helix chain '9' and resid 205 through 210 Processing helix chain '9' and resid 230 through 232 No H-bonds generated for 'chain '9' and resid 230 through 232' Processing helix chain '9' and resid 233 through 238 Processing helix chain '9' and resid 259 through 275 removed outlier: 3.585A pdb=" N ALA 9 275 " --> pdb=" O ASP 9 271 " (cutoff:3.500A) Processing helix chain '9' and resid 323 through 332 Processing helix chain '9' and resid 346 through 349 Processing helix chain '9' and resid 350 through 360 Processing helix chain '9' and resid 370 through 375 removed outlier: 3.570A pdb=" N ALA 9 375 " --> pdb=" O ALA 9 371 " (cutoff:3.500A) Processing helix chain '9' and resid 396 through 401 removed outlier: 3.886A pdb=" N MET 9 400 " --> pdb=" O THR 9 396 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE 9 401 " --> pdb=" O PRO 9 397 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 396 through 401' Processing helix chain '9' and resid 505 through 510 removed outlier: 4.101A pdb=" N LEU 9 509 " --> pdb=" O CYS 9 505 " (cutoff:3.500A) Processing helix chain '9' and resid 511 through 519 Processing helix chain '9' and resid 571 through 582 removed outlier: 4.425A pdb=" N ASP 9 575 " --> pdb=" O LEU 9 571 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA 9 576 " --> pdb=" O ASP 9 572 " (cutoff:3.500A) Processing helix chain '9' and resid 592 through 600 removed outlier: 3.564A pdb=" N MET 9 597 " --> pdb=" O GLY 9 593 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY 9 599 " --> pdb=" O GLU 9 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.528A pdb=" N HIS B 69 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.891A pdb=" N GLU B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.002A 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: 3.588A 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 183 Processing helix chain 'B' and resid 206 through 215 removed outlier: 4.132A 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 24 removed outlier: 3.678A pdb=" N ALA C 24 " --> pdb=" O LEU C 21 " (cutoff:3.500A) 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: 3.823A pdb=" N HIS D 277 " --> pdb=" O ASN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.512A 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: 4.047A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 58 Processing helix chain 'F' and resid 59 through 72 removed outlier: 3.541A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 3.525A 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 133 through 137 removed outlier: 3.507A pdb=" N THR F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 133 through 137' Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 175 through 192 Processing helix chain 'F' and resid 200 through 214 removed outlier: 3.622A pdb=" N HIS F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 232 Processing helix chain 'G' and resid 70 through 93 Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 118 through 122 removed outlier: 3.671A pdb=" N ARG G 122 " --> pdb=" O LYS G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 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: 3.615A 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 320 removed outlier: 3.556A pdb=" N ARG G 310 " --> pdb=" O ILE G 306 " (cutoff:3.500A) Proline residue: G 316 - end of helix removed outlier: 3.586A 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 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 Processing helix chain 'J' and resid 32 through 40 Processing helix chain 'K' and resid 49 through 58 Processing helix chain 'K' and resid 112 through 117 Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.789A pdb=" N GLN L 77 " --> pdb=" O LYS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 93 Processing helix chain 'L' and resid 94 through 98 removed outlier: 3.600A pdb=" N ALA L 98 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 removed outlier: 4.020A pdb=" N MET L 103 " --> pdb=" O ASN L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 144 Processing helix chain 'L' and resid 149 through 174 Processing helix chain 'L' and resid 174 through 185 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 Processing helix chain 'O' and resid 55 through 61 removed outlier: 4.213A pdb=" N LEU O 59 " --> pdb=" O PRO O 55 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU O 60 " --> pdb=" O TRP O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 68 removed outlier: 3.537A pdb=" N GLN O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 124 Processing helix chain 'O' and resid 125 through 127 No H-bonds generated for 'chain 'O' and resid 125 through 127' Processing helix chain 'O' and resid 136 through 141 removed outlier: 3.908A 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 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 '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 185 through 197 Processing helix chain 'R' and resid 207 through 210 removed outlier: 3.569A 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 336 removed outlier: 3.744A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA R 336 " --> pdb=" O ALA R 332 " (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: 4.134A pdb=" N ARG S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) removed outlier: 3.911A 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: 4.010A pdb=" N LEU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) removed outlier: 4.171A 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 164 removed outlier: 6.061A pdb=" N GLY T 161 " --> pdb=" O GLU T 158 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS T 162 " --> pdb=" O MET T 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 39 removed outlier: 3.651A pdb=" N ILE U 39 " --> pdb=" O LYS U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 87 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: 3.514A pdb=" N ILE V 72 " --> pdb=" O SER V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 97 removed outlier: 3.560A 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 213 Proline residue: V 211 - end of helix Processing helix chain 'V' and resid 217 through 239 Processing helix chain 'V' and resid 239 through 245 removed outlier: 3.566A 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 345 Processing helix chain 'V' and resid 351 through 406 removed outlier: 5.775A pdb=" N SER V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THR V 366 " --> pdb=" O GLU V 362 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 86 Processing helix chain 'W' and resid 87 through 93 removed outlier: 3.906A 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: 3.887A pdb=" N HIS X 59 " --> pdb=" O PRO X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 64 removed outlier: 3.531A pdb=" N GLU X 64 " --> pdb=" O ASP X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 78 Processing helix chain 'X' and resid 84 through 95 removed outlier: 3.786A pdb=" N MET X 89 " --> pdb=" O PRO X 85 " (cutoff:3.500A) removed outlier: 3.729A 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 Processing helix chain 'X' and resid 157 through 163 removed outlier: 4.025A pdb=" N LYS X 163 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 180 through 195 removed outlier: 3.771A pdb=" N ASN X 190 " --> pdb=" O THR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 202 removed outlier: 4.241A pdb=" N GLN X 201 " --> pdb=" O ARG X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 232 removed outlier: 4.180A pdb=" N VAL X 225 " --> pdb=" O PRO X 221 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG X 232 " --> pdb=" O GLN X 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 254 removed outlier: 3.928A 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: 3.521A pdb=" N LEU X 293 " --> pdb=" O LEU X 289 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET X 297 " --> pdb=" O LEU X 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS X 298 " --> pdb=" O ARG X 294 " (cutoff:3.500A) Processing helix chain 'X' and resid 324 through 338 removed outlier: 6.927A pdb=" N LYS X 331 " --> pdb=" O GLU X 327 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLU X 332 " --> pdb=" O LEU X 328 " (cutoff:3.500A) removed outlier: 3.602A 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: 4.017A pdb=" N TYR X 397 " --> pdb=" O ARG X 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 277 through 289 removed outlier: 3.529A pdb=" N THR Y 288 " --> pdb=" O LYS Y 284 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) Processing helix chain 'Y' and resid 296 through 307 Processing helix chain 'Y' and resid 327 through 333 removed outlier: 3.772A pdb=" N HIS Y 331 " --> pdb=" O GLU Y 327 " (cutoff:3.500A) Processing helix chain 'Y' and resid 334 through 339 removed outlier: 3.635A pdb=" N HIS Y 337 " --> pdb=" O LEU Y 334 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU Y 339 " --> pdb=" O LYS Y 336 " (cutoff:3.500A) Processing helix chain 'Y' and resid 345 through 360 Processing helix chain 'Y' and resid 365 through 383 Processing helix chain 'Z' and resid 5 through 19 Processing helix chain 'Z' and resid 27 through 30 Processing helix chain 'Z' and resid 31 through 39 removed outlier: 3.689A pdb=" N LYS Z 35 " --> pdb=" O MET Z 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 68 Processing helix chain 'a' and resid 125 through 135 Processing helix chain 'a' and resid 189 through 195 Processing helix chain 'a' and resid 216 through 226 Processing helix chain 'a' and resid 237 through 241 Processing helix chain 'a' and resid 245 through 255 removed outlier: 4.031A pdb=" N GLU a 249 " --> pdb=" O SER a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 315 through 327 removed outlier: 3.517A pdb=" N LEU a 319 " --> pdb=" O ASP a 315 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA a 327 " --> pdb=" O LEU a 323 " (cutoff:3.500A) Processing helix chain 'a' and resid 344 through 360 Processing helix chain 'a' and resid 363 through 368 removed outlier: 3.807A pdb=" N VAL a 368 " --> pdb=" O PRO a 365 " (cutoff:3.500A) Processing helix chain 'a' and resid 393 through 402 Processing helix chain 'a' and resid 405 through 423 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: 6.260A pdb=" N ILE 0 117 " --> pdb=" O LEU 0 97 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU 0 97 " --> pdb=" O ILE 0 117 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR 0 119 " --> pdb=" O TRP 0 95 " (cutoff:3.500A) removed outlier: 5.293A 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: 3.684A pdb=" N VAL 1 204 " --> pdb=" O CYS 1 199 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG H 75 " --> pdb=" O THR H 175 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU H 177 " --> pdb=" O TYR H 73 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR H 73 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU H 72 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR H 149 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.456A 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: 4.208A 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 64 removed outlier: 5.502A pdb=" N GLU H 68 " --> pdb=" O LYS 4 62 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N THR 4 64 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER H 66 " --> pdb=" O THR 4 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 105 through 109 removed outlier: 3.701A pdb=" N GLN 5 171 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE 5 210 " --> pdb=" O VAL 5 227 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS 5 229 " --> pdb=" O HIS 5 208 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N HIS 5 208 " --> pdb=" O HIS 5 229 " (cutoff:3.500A) removed outlier: 7.393A 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 '7' and resid 36 through 37 Processing sheet with id=AA9, first strand: chain '7' and resid 61 through 62 removed outlier: 6.709A pdb=" N VAL 7 61 " --> pdb=" O HIS 7 354 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS 7 290 " --> pdb=" O ARG 7 376 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE 7 259 " --> pdb=" O GLY 7 289 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N PHE 7 291 " --> pdb=" O PHE 7 259 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL 7 261 " --> pdb=" O PHE 7 291 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL 7 293 " --> pdb=" O VAL 7 261 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL 7 263 " --> pdb=" O VAL 7 293 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL 7 295 " --> pdb=" O VAL 7 263 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA 7 265 " --> pdb=" O VAL 7 295 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASN 7 297 " --> pdb=" O ALA 7 265 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET 7 190 " --> pdb=" O VAL 7 263 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA 7 265 " --> pdb=" O MET 7 190 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE 7 192 " --> pdb=" O ALA 7 265 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU 7 189 " --> pdb=" O MET 7 215 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N VAL 7 217 " --> pdb=" O LEU 7 189 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP 7 191 " --> pdb=" O VAL 7 217 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR 7 214 " --> pdb=" O PHE 7 246 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG 7 248 " --> pdb=" O TYR 7 214 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS 7 216 " --> pdb=" O ARG 7 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '7' and resid 61 through 62 removed outlier: 6.709A pdb=" N VAL 7 61 " --> pdb=" O HIS 7 354 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA 7 375 " --> pdb=" O VAL 7 329 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL 7 329 " --> pdb=" O ALA 7 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '7' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain '7' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain '8' and resid 296 through 298 removed outlier: 6.957A pdb=" N VAL 8 147 " --> pdb=" O SER 8 296 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TYR 8 298 " --> pdb=" O VAL 8 147 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA 8 149 " --> pdb=" O TYR 8 298 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N SER 8 63 " --> pdb=" O CYS 8 146 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA 8 148 " --> pdb=" O SER 8 63 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR 8 345 " --> pdb=" O SER 8 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '8' and resid 257 through 262 removed outlier: 3.518A pdb=" N ARG 8 259 " --> pdb=" O LEU 8 197 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N CYS 8 235 " --> pdb=" O TYR 8 230 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR 8 230 " --> pdb=" O CYS 8 235 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL 8 237 " --> pdb=" O SER 8 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '9' and resid 195 through 196 Processing sheet with id=AB7, first strand: chain '9' and resid 278 through 279 removed outlier: 6.894A pdb=" N LEU 9 278 " --> pdb=" O VAL 9 310 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP 9 312 " --> pdb=" O LEU 9 278 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU 9 243 " --> pdb=" O ASP 9 312 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ARG 9 314 " --> pdb=" O LEU 9 243 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL 9 245 " --> pdb=" O ARG 9 314 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN 9 242 " --> pdb=" O SER 9 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '9' and resid 376 through 379 Processing sheet with id=AB9, first strand: chain '9' and resid 527 through 531 removed outlier: 3.746A pdb=" N ALA 9 621 " --> pdb=" O VAL 9 633 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '9' and resid 566 through 570 Processing sheet with id=AC2, first strand: chain 'B' and resid 91 through 94 removed outlier: 5.873A pdb=" N LEU B 91 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE B 116 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N HIS B 93 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 108 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.254A pdb=" N ILE B 142 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS B 167 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE B 144 " --> pdb=" O HIS B 167 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 143 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR B 219 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 236 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLY B 221 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AC5, first strand: chain 'C' and resid 70 through 71 removed outlier: 6.068A pdb=" N LEU C 117 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.384A pdb=" N VAL C 123 " --> pdb=" O VAL C 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 219 through 228 removed outlier: 6.408A pdb=" N LEU D 244 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL D 225 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG D 242 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN D 227 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER D 240 " --> pdb=" O ASN D 227 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 294 through 298 removed outlier: 6.678A pdb=" N ARG D 315 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL D 336 " --> pdb=" O ARG D 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 382 through 385 removed outlier: 6.803A pdb=" N VAL D 370 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 35 through 53 removed outlier: 7.181A pdb=" N ARG E 37 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N TYR E 69 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU E 39 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP E 67 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASN E 41 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU E 65 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY E 43 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN E 59 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N TYR E 49 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 9.836A pdb=" N GLN E 57 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS E 11 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL E 88 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 156 through 163 removed outlier: 3.897A pdb=" N LYS F 163 " --> pdb=" O ARG F 166 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 197 through 199 Processing sheet with id=AD4, first strand: chain 'G' and resid 261 through 262 removed outlier: 6.178A pdb=" N LYS G 294 " --> pdb=" O CYS G 330 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL G 332 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 57 through 68 removed outlier: 6.763A pdb=" N ARG J 82 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N THR J 65 " --> pdb=" O CYS J 80 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS J 80 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR J 67 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N LEU J 123 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL J 92 " --> pdb=" O LEU J 123 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL J 125 " --> pdb=" O VAL J 92 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE J 94 " --> pdb=" O VAL J 125 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 82 through 83 removed outlier: 6.800A pdb=" N TYR M 32 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER M 53 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE M 34 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS M 64 " --> pdb=" O VAL R 157 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR R 159 " --> pdb=" O LYS M 64 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL M 66 " --> pdb=" O THR R 159 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU R 181 " --> pdb=" O LEU R 142 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 12 through 22 removed outlier: 15.570A pdb=" N TRP N 12 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N LEU N 33 " --> pdb=" O TRP N 12 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL N 14 " --> pdb=" O THR N 31 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR N 31 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS N 27 " --> pdb=" O ILE N 18 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR N 20 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR N 25 " --> pdb=" O THR N 20 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N VAL N 77 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE N 50 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS N 79 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU N 65 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ILE N 84 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE N 63 " --> pdb=" O ILE N 84 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 100 through 101 Processing sheet with id=AD9, first strand: chain 'T' and resid 63 through 68 removed outlier: 6.731A pdb=" N TYR T 79 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET T 30 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG T 77 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL T 32 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE T 75 " --> pdb=" O VAL T 32 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 190 through 191 Processing sheet with id=AE2, first strand: chain 'V' and resid 275 through 276 removed outlier: 6.275A pdb=" N LEU V 275 " --> pdb=" O GLU V 348 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'W' and resid 122 through 125 removed outlier: 6.559A pdb=" N ASP W 111 " --> pdb=" O ILE W 107 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE W 107 " --> pdb=" O ASP W 111 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR W 113 " --> pdb=" O PHE W 105 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS W 98 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL W 140 " --> pdb=" O ILE W 172 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE W 172 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU W 142 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU W 170 " --> pdb=" O LEU W 142 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU W 144 " --> pdb=" O VAL W 168 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL W 168 " --> pdb=" O LEU W 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 150 through 151 Processing sheet with id=AE5, first strand: chain 'X' and resid 67 through 70 removed outlier: 4.496A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 151 through 155 removed outlier: 6.812A pdb=" N ARG X 123 " --> pdb=" O ILE X 341 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE X 343 " --> pdb=" O ARG X 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU X 125 " --> pdb=" O ILE X 343 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL X 345 " --> pdb=" O LEU X 125 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR X 127 " --> pdb=" O VAL X 345 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 169 through 170 Processing sheet with id=AE8, first strand: chain 'X' and resid 208 through 209 Processing sheet with id=AE9, first strand: chain 'a' and resid 154 through 158 removed outlier: 6.617A pdb=" N ARG a 112 " --> pdb=" O GLN a 162 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE a 164 " --> pdb=" O ARG a 112 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU a 114 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU a 166 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL a 116 " --> pdb=" O LEU a 166 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N LEU a 199 " --> pdb=" O VAL a 113 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG a 115 " --> pdb=" O LEU a 199 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL a 201 " --> pdb=" O ARG a 115 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL a 117 " --> pdb=" O VAL a 201 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU a 203 " --> pdb=" O VAL a 117 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU a 119 " --> pdb=" O LEU a 203 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ASP a 205 " --> pdb=" O LEU a 119 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL a 200 " --> pdb=" O VAL a 232 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL a 234 " --> pdb=" O VAL a 200 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL a 202 " --> pdb=" O VAL a 234 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASN a 236 " --> pdb=" O VAL a 202 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL a 204 " --> pdb=" O ASN a 236 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER a 231 " --> pdb=" O LYS a 303 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE a 305 " --> pdb=" O SER a 231 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU a 233 " --> pdb=" O ILE a 305 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N MET a 307 " --> pdb=" O LEU a 233 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET a 235 " --> pdb=" O MET a 307 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'a' and resid 154 through 158 removed outlier: 6.617A pdb=" N ARG a 112 " --> pdb=" O GLN a 162 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE a 164 " --> pdb=" O ARG a 112 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU a 114 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU a 166 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL a 116 " --> pdb=" O LEU a 166 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 258 through 259 Processing sheet with id=AF3, first strand: chain 'a' and resid 369 through 377 removed outlier: 6.334A pdb=" N GLN a 386 " --> pdb=" O ALA a 373 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP a 375 " --> pdb=" O VAL a 384 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL a 384 " --> pdb=" O TRP a 375 " (cutoff:3.500A) 2630 hydrogen bonds defined for protein. 7443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 521 hydrogen bonds 942 hydrogen bond angles 0 basepair planarities 211 basepair parallelities 363 stacking parallelities Total time for adding SS restraints: 46.04 Time building geometry restraints manager: 16.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 32970 1.43 - 1.65: 38923 1.65 - 1.87: 409 1.87 - 2.09: 0 2.09 - 2.31: 20 Bond restraints: 72322 Sorted by residual: bond pdb=" N1 GDP X 503 " pdb=" C2 GDP X 503 " ideal model delta sigma weight residual 1.337 1.556 -0.219 2.00e-02 2.50e+03 1.20e+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 6.95e+01 bond pdb=" C5 GDP X 503 " pdb=" C4 GDP X 503 " ideal model delta sigma weight residual 1.490 1.350 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C2 GDP X 503 " pdb=" N3 GDP X 503 " ideal model delta sigma weight residual 1.350 1.454 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C2 GDP X 503 " pdb=" N2 GDP X 503 " ideal model delta sigma weight residual 1.355 1.458 -0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 72317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 99807 2.12 - 4.24: 1315 4.24 - 6.36: 176 6.36 - 8.49: 14 8.49 - 10.61: 2 Bond angle restraints: 101314 Sorted by residual: angle pdb=" CA PRO V 270 " pdb=" N PRO V 270 " pdb=" CD PRO V 270 " ideal model delta sigma weight residual 112.00 105.61 6.39 1.40e+00 5.10e-01 2.08e+01 angle pdb=" C HIS 9 584 " pdb=" CA HIS 9 584 " pdb=" CB HIS 9 584 " ideal model delta sigma weight residual 116.34 111.27 5.07 1.40e+00 5.10e-01 1.31e+01 angle pdb=" C3' C A1330 " pdb=" O3' C A1330 " pdb=" P A A1331 " ideal model delta sigma weight residual 120.20 125.55 -5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" N GLY X 82 " pdb=" CA GLY X 82 " pdb=" C GLY X 82 " ideal model delta sigma weight residual 112.77 117.21 -4.44 1.28e+00 6.10e-01 1.21e+01 angle pdb=" N GLN V 402 " pdb=" CA GLN V 402 " pdb=" CB GLN V 402 " ideal model delta sigma weight residual 110.16 115.25 -5.09 1.48e+00 4.57e-01 1.18e+01 ... (remaining 101309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 42271 35.56 - 71.13: 2023 71.13 - 106.69: 310 106.69 - 142.26: 6 142.26 - 177.82: 8 Dihedral angle restraints: 44618 sinusoidal: 25199 harmonic: 19419 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 180.00 122.87 57.13 0 5.00e+00 4.00e-02 1.31e+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 28.95 171.05 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' C A 739 " pdb=" C1' C A 739 " pdb=" N1 C A 739 " pdb=" C2 C A 739 " ideal model delta sinusoidal sigma weight residual 200.00 45.83 154.17 1 1.50e+01 4.44e-03 8.11e+01 ... (remaining 44615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.192: 11779 4.192 - 8.385: 0 8.385 - 12.577: 0 12.577 - 16.769: 0 16.769 - 20.961: 4 Chirality restraints: 11783 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 10.41 -20.96 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE2 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S3 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.36 20.92 2.00e-01 2.50e+01 1.09e+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 10.32 -20.88 2.00e-01 2.50e+01 1.09e+04 ... (remaining 11780 not shown) Planarity restraints: 10261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER V 269 " 0.080 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO V 270 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO V 270 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO V 270 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG 0 195 " -0.316 9.50e-02 1.11e+02 1.42e-01 1.29e+01 pdb=" NE ARG 0 195 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG 0 195 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG 0 195 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG 0 195 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 47 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO E 48 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 48 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO E 48 " 0.049 5.00e-02 4.00e+02 ... (remaining 10258 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.59: 574 2.59 - 3.23: 64029 3.23 - 3.87: 143987 3.87 - 4.50: 197942 4.50 - 5.14: 292310 Nonbonded interactions: 698842 Sorted by model distance: nonbonded pdb=" OH TYR 1 198 " pdb=" OD1 ASP 1 203 " model vdw 1.957 3.040 nonbonded pdb=" OG1 THR 5 17 " pdb=" OE1 GLU 5 20 " model vdw 1.963 3.040 nonbonded pdb=" OP1 C A 828 " pdb="MG MG A1714 " model vdw 1.968 2.170 nonbonded pdb=" OP1 A A 801 " pdb="MG MG A1710 " model vdw 1.968 2.170 nonbonded pdb=" OP2 A A 940 " pdb="MG MG A1707 " model vdw 1.982 2.170 ... (remaining 698837 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.000 Check model and map are aligned: 0.400 Set scattering table: 0.470 Process input model: 180.770 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.270 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: 0.030 Load rotamer database and sin/cos tables:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 202.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 0.219 72322 Z= 0.261 Angle : 0.646 10.608 101314 Z= 0.343 Chirality : 0.387 20.961 11783 Planarity : 0.006 0.142 10261 Dihedral : 18.402 177.822 32018 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 6541 helix: 1.20 (0.09), residues: 3020 sheet: -0.23 (0.18), residues: 730 loop : 0.04 (0.12), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Y 375 HIS 0.014 0.001 HIS X 81 PHE 0.025 0.002 PHE 8 232 TYR 0.032 0.002 TYR 4 486 ARG 0.037 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1062 time to evaluate : 5.103 Fit side-chains REVERT: 8 363 MET cc_start: 0.7015 (tpp) cc_final: 0.6812 (mmm) REVERT: D 342 MET cc_start: 0.8422 (tpp) cc_final: 0.7753 (tpp) REVERT: D 360 GLN cc_start: 0.8719 (tp40) cc_final: 0.8488 (tp40) REVERT: G 200 LEU cc_start: 0.7590 (tp) cc_final: 0.7028 (tp) REVERT: G 314 MET cc_start: 0.8911 (ttp) cc_final: 0.8700 (ttm) REVERT: G 348 MET cc_start: 0.8478 (mtm) cc_final: 0.8231 (mtm) REVERT: J 68 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7047 (mtt180) REVERT: J 116 GLN cc_start: 0.7182 (mp10) cc_final: 0.6648 (mp10) REVERT: N 36 ASP cc_start: 0.8529 (t0) cc_final: 0.8148 (t0) REVERT: O 65 GLN cc_start: 0.7133 (mm110) cc_final: 0.6751 (mm-40) REVERT: R 271 MET cc_start: 0.8521 (ttp) cc_final: 0.8276 (ttm) REVERT: S 123 LYS cc_start: 0.7579 (ttpp) cc_final: 0.7330 (ttpt) REVERT: T 3 MET cc_start: 0.7892 (mtp) cc_final: 0.7468 (mtt) REVERT: T 57 TYR cc_start: 0.8499 (t80) cc_final: 0.8180 (t80) REVERT: T 132 ARG cc_start: 0.7342 (tpp-160) cc_final: 0.6797 (tpt90) REVERT: T 138 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7164 (mp0) REVERT: V 169 MET cc_start: 0.8529 (mmm) cc_final: 0.8120 (mmt) REVERT: X 167 ASP cc_start: 0.7135 (p0) cc_final: 0.6916 (t0) REVERT: X 296 MET cc_start: 0.8537 (mmm) cc_final: 0.8166 (mmm) REVERT: Y 378 ASN cc_start: 0.6307 (m110) cc_final: 0.5925 (m-40) REVERT: Z 17 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7406 (ttt180) outliers start: 0 outliers final: 2 residues processed: 1062 average time/residue: 1.7508 time to fit residues: 2350.5344 Evaluate side-chains 711 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 709 time to evaluate : 5.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain Y residue 249 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 610 optimal weight: 0.9990 chunk 548 optimal weight: 0.9990 chunk 304 optimal weight: 10.9990 chunk 187 optimal weight: 10.0000 chunk 369 optimal weight: 3.9990 chunk 292 optimal weight: 20.0000 chunk 566 optimal weight: 0.0470 chunk 219 optimal weight: 0.8980 chunk 344 optimal weight: 9.9990 chunk 421 optimal weight: 0.8980 chunk 656 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 231 HIS 4 346 HIS 4 545 GLN ** 4 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 229 HIS 5 272 GLN 7 69 ASN 7 85 ASN 7 98 HIS 7 398 HIS 7 400 HIS 8 121 GLN 8 145 ASN 8 222 ASN 8 249 GLN 8 313 HIS 9 92 GLN 9 188 HIS 9 283 HIS 9 551 ASN 9 584 HIS B 167 HIS C 57 HIS C 130 HIS D 280 HIS D 341 ASN D 369 HIS E 92 ASN F 72 GLN F 147 GLN G 90 ASN J 35 GLN J 106 GLN K 55 ASN O 98 ASN P 78 GLN R 214 ASN R 247 HIS R 277 ASN R 299 ASN S 47 GLN S 61 GLN U 62 HIS U 110 GLN X 81 HIS X 159 HIS Y 290 ASN Y 329 HIS a 268 GLN ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 301 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.245 72322 Z= 0.249 Angle : 0.795 50.988 101314 Z= 0.476 Chirality : 0.122 6.343 11783 Planarity : 0.005 0.075 10261 Dihedral : 19.429 177.192 18472 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.85 % Allowed : 8.64 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % 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: 1.30 (0.10), residues: 6541 helix: 1.74 (0.09), residues: 3045 sheet: 0.06 (0.18), residues: 761 loop : 0.22 (0.12), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 9 183 HIS 0.019 0.001 HIS 9 187 PHE 0.030 0.001 PHE 8 232 TYR 0.024 0.001 TYR a 322 ARG 0.013 0.001 ARG 9 573 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 769 time to evaluate : 5.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 166 MET cc_start: 0.7885 (mtp) cc_final: 0.7649 (mtp) REVERT: 9 549 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: 9 637 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6700 (m-80) REVERT: D 342 MET cc_start: 0.8505 (tpp) cc_final: 0.8146 (tpp) REVERT: D 361 GLN cc_start: 0.8356 (mt0) cc_final: 0.8105 (mt0) REVERT: E 13 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6347 (mtm) REVERT: E 21 THR cc_start: 0.7980 (m) cc_final: 0.7526 (m) REVERT: F 53 LYS cc_start: 0.7039 (mmmm) cc_final: 0.6774 (tptt) REVERT: F 176 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.6024 (t0) REVERT: G 358 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6367 (pt0) REVERT: J 116 GLN cc_start: 0.7063 (mp10) cc_final: 0.6633 (mp10) REVERT: L 148 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7024 (pttm) REVERT: N 36 ASP cc_start: 0.8195 (t0) cc_final: 0.7868 (t0) REVERT: N 67 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7998 (ttp80) REVERT: N 83 GLU cc_start: 0.7173 (pt0) cc_final: 0.6832 (pt0) REVERT: O 65 GLN cc_start: 0.7100 (mm110) cc_final: 0.6775 (mm-40) REVERT: O 233 GLU cc_start: 0.6874 (tt0) cc_final: 0.6477 (tt0) REVERT: R 214 ASN cc_start: 0.8907 (m110) cc_final: 0.8640 (m-40) REVERT: S 7 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: T 3 MET cc_start: 0.7903 (mtp) cc_final: 0.7422 (mtt) REVERT: T 57 TYR cc_start: 0.8502 (t80) cc_final: 0.8126 (t80) REVERT: T 132 ARG cc_start: 0.7367 (tpp-160) cc_final: 0.6948 (tpt90) REVERT: U 114 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5392 (mtp180) REVERT: V 169 MET cc_start: 0.8532 (mmm) cc_final: 0.8151 (mmt) REVERT: V 392 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7270 (ttp80) REVERT: W 111 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7015 (t0) REVERT: X 167 ASP cc_start: 0.7257 (p0) cc_final: 0.6856 (t0) REVERT: X 296 MET cc_start: 0.8421 (mmm) cc_final: 0.8102 (mmm) REVERT: Y 351 MET cc_start: 0.7692 (mpp) cc_final: 0.7455 (tpp) REVERT: Y 378 ASN cc_start: 0.6422 (m110) cc_final: 0.6007 (m-40) REVERT: Z 17 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7372 (ttt180) REVERT: Z 32 LYS cc_start: 0.5609 (OUTLIER) cc_final: 0.5111 (ttpp) REVERT: a 205 ASP cc_start: 0.6197 (t0) cc_final: 0.5511 (t0) outliers start: 107 outliers final: 26 residues processed: 827 average time/residue: 1.6287 time to fit residues: 1736.8243 Evaluate side-chains 710 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 674 time to evaluate : 5.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 4 residue 328 VAL Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 549 GLN Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 160 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 364 optimal weight: 2.9990 chunk 203 optimal weight: 0.0170 chunk 546 optimal weight: 9.9990 chunk 447 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 657 optimal weight: 0.0040 chunk 710 optimal weight: 8.9990 chunk 585 optimal weight: 6.9990 chunk 652 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 527 optimal weight: 2.9990 overall best weight: 2.0036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 111 HIS 0 181 ASN 4 346 HIS 7 85 ASN 7 107 GLN 7 181 ASN 7 282 GLN 8 145 ASN 8 222 ASN 8 249 GLN 8 313 HIS 9 96 GLN B 201 ASN ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN J 106 GLN K 55 ASN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN O 98 ASN O 204 ASN R 299 ASN S 47 GLN S 61 GLN U 110 GLN W 135 GLN X 67 HIS X 81 HIS Y 290 ASN a 295 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 72322 Z= 0.312 Angle : 0.795 50.577 101314 Z= 0.475 Chirality : 0.123 6.406 11783 Planarity : 0.005 0.058 10261 Dihedral : 19.333 177.364 18468 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.99 % Allowed : 10.86 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % 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: 1.33 (0.10), residues: 6541 helix: 1.76 (0.09), residues: 3070 sheet: 0.16 (0.18), residues: 752 loop : 0.18 (0.12), residues: 2719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 9 183 HIS 0.019 0.001 HIS 9 187 PHE 0.027 0.002 PHE 8 232 TYR 0.021 0.002 TYR a 226 ARG 0.008 0.001 ARG a 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 702 time to evaluate : 5.204 Fit side-chains revert: symmetry clash REVERT: 0 70 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7544 (mtt180) REVERT: 4 172 MET cc_start: 0.7759 (tpp) cc_final: 0.7533 (tpt) REVERT: 7 307 MET cc_start: 0.8519 (mmp) cc_final: 0.8232 (mmp) REVERT: 8 166 MET cc_start: 0.8033 (mtp) cc_final: 0.7754 (mtp) REVERT: 9 549 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: 9 637 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: C 161 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7345 (mptt) REVERT: D 342 MET cc_start: 0.8568 (tpp) cc_final: 0.8244 (tpp) REVERT: D 361 GLN cc_start: 0.8374 (mt0) cc_final: 0.8133 (mt0) REVERT: F 72 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: F 234 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5693 (ttm-80) REVERT: G 273 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: G 358 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6373 (pt0) REVERT: J 116 GLN cc_start: 0.7093 (mp10) cc_final: 0.6778 (mp10) REVERT: L 148 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6944 (pttm) REVERT: N 36 ASP cc_start: 0.8222 (t0) cc_final: 0.7875 (t0) REVERT: N 67 ARG cc_start: 0.8261 (ttm110) cc_final: 0.8014 (ttp80) REVERT: N 83 GLU cc_start: 0.7283 (pt0) cc_final: 0.6924 (pt0) REVERT: O 65 GLN cc_start: 0.7240 (mm110) cc_final: 0.6853 (mm-40) REVERT: O 109 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.6636 (ptm160) REVERT: O 233 GLU cc_start: 0.6867 (tt0) cc_final: 0.6477 (tt0) REVERT: R 337 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6637 (mm-40) REVERT: S 7 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: T 3 MET cc_start: 0.7970 (mtp) cc_final: 0.7431 (mtt) REVERT: T 57 TYR cc_start: 0.8529 (t80) cc_final: 0.8167 (t80) REVERT: T 122 GLN cc_start: 0.7506 (tt0) cc_final: 0.7299 (tt0) REVERT: T 132 ARG cc_start: 0.7510 (tpp-160) cc_final: 0.7150 (tpt170) REVERT: U 114 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5387 (mtp180) REVERT: U 116 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7857 (mp) REVERT: U 165 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7079 (ttmt) REVERT: V 169 MET cc_start: 0.8529 (mmm) cc_final: 0.7975 (mmt) REVERT: V 394 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6792 (tp40) REVERT: W 111 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7101 (t0) REVERT: W 130 ASP cc_start: 0.7098 (t0) cc_final: 0.6860 (t0) REVERT: W 139 ARG cc_start: 0.7458 (mpt180) cc_final: 0.7204 (mmt90) REVERT: X 81 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.6872 (p90) REVERT: X 217 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: Y 351 MET cc_start: 0.7780 (mpp) cc_final: 0.7513 (tpp) REVERT: Y 367 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7158 (mtpp) REVERT: Z 32 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5337 (ttpp) outliers start: 115 outliers final: 41 residues processed: 771 average time/residue: 1.6540 time to fit residues: 1644.2504 Evaluate side-chains 717 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 656 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 4 residue 101 LEU Chi-restraints excluded: chain 4 residue 319 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 223 MET Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 220 ILE Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 549 GLN Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain 9 residue 654 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 358 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 165 LYS Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 111 ASP Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain a residue 156 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 649 optimal weight: 2.9990 chunk 494 optimal weight: 9.9990 chunk 341 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 chunk 441 optimal weight: 4.9990 chunk 660 optimal weight: 0.3980 chunk 698 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 625 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 107 GLN 0 181 ASN 4 346 HIS 7 85 ASN 7 107 GLN 8 145 ASN 8 222 ASN 8 229 ASN 8 249 GLN 8 251 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN G 90 ASN J 106 GLN K 55 ASN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 HIS R 299 ASN S 47 GLN S 61 GLN U 110 GLN V 399 GLN ** X 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 290 ASN a 295 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 72322 Z= 0.402 Angle : 0.836 50.648 101314 Z= 0.493 Chirality : 0.125 6.447 11783 Planarity : 0.005 0.058 10261 Dihedral : 19.337 176.415 18468 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.74 % Allowed : 11.68 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % 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: 1.07 (0.10), residues: 6541 helix: 1.54 (0.09), residues: 3077 sheet: 0.05 (0.18), residues: 719 loop : 0.05 (0.12), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 375 HIS 0.035 0.002 HIS X 81 PHE 0.028 0.002 PHE 8 232 TYR 0.022 0.002 TYR W 134 ARG 0.007 0.001 ARG U 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 687 time to evaluate : 5.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7764 (mtt90) REVERT: 0 70 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7548 (mtt180) REVERT: 7 307 MET cc_start: 0.8609 (mmp) cc_final: 0.8077 (mmp) REVERT: 9 549 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: 9 637 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: B 102 MET cc_start: 0.8505 (mmm) cc_final: 0.8253 (mmm) REVERT: C 118 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6801 (mt-10) REVERT: D 361 GLN cc_start: 0.8405 (mt0) cc_final: 0.8164 (mt0) REVERT: F 72 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: F 234 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5709 (ttm-80) REVERT: G 82 ASN cc_start: 0.7712 (m-40) cc_final: 0.7399 (m-40) REVERT: G 273 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: H 182 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: J 116 GLN cc_start: 0.7123 (mp10) cc_final: 0.6772 (mp10) REVERT: N 36 ASP cc_start: 0.8330 (t0) cc_final: 0.8027 (t0) REVERT: O 65 GLN cc_start: 0.7301 (mm110) cc_final: 0.7033 (mm-40) REVERT: O 109 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7014 (ptm160) REVERT: O 233 GLU cc_start: 0.6882 (tt0) cc_final: 0.6492 (tt0) REVERT: R 337 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6723 (mm-40) REVERT: S 7 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: S 102 LYS cc_start: 0.8203 (tppt) cc_final: 0.7869 (tppt) REVERT: S 106 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7791 (mp) REVERT: T 3 MET cc_start: 0.8107 (mtp) cc_final: 0.7602 (mtt) REVERT: T 57 TYR cc_start: 0.8577 (t80) cc_final: 0.8220 (t80) REVERT: T 66 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8105 (mmt) REVERT: T 111 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6095 (tm-30) REVERT: T 115 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: T 132 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7213 (tpt170) REVERT: U 112 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: U 114 ARG cc_start: 0.6334 (OUTLIER) cc_final: 0.5404 (mtp180) REVERT: U 116 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7820 (mp) REVERT: U 146 VAL cc_start: 0.8350 (t) cc_final: 0.8097 (m) REVERT: U 165 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7184 (ttmt) REVERT: V 169 MET cc_start: 0.8516 (mmm) cc_final: 0.8077 (mmt) REVERT: V 394 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6773 (tp40) REVERT: X 103 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7682 (mtpp) REVERT: X 217 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: Y 367 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7198 (mtpp) REVERT: Z 32 LYS cc_start: 0.6069 (OUTLIER) cc_final: 0.5572 (ttpp) REVERT: Z 39 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: a 164 ILE cc_start: 0.5783 (mp) cc_final: 0.5510 (mp) outliers start: 158 outliers final: 63 residues processed: 779 average time/residue: 1.6797 time to fit residues: 1679.6901 Evaluate side-chains 744 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 656 time to evaluate : 5.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 319 LEU Chi-restraints excluded: chain 4 residue 328 VAL Chi-restraints excluded: chain 4 residue 392 ILE Chi-restraints excluded: chain 4 residue 502 VAL Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 228 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 223 MET Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 549 GLN Chi-restraints excluded: chain 9 residue 588 GLN Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain 9 residue 654 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 182 GLU Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 165 LYS Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 103 LYS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain a residue 160 GLU Chi-restraints excluded: chain a residue 326 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 582 optimal weight: 4.9990 chunk 396 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 520 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 596 optimal weight: 7.9990 chunk 483 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 chunk 627 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 ASN 4 346 HIS 7 85 ASN 7 107 GLN 7 144 HIS 8 145 ASN 8 222 ASN 8 249 GLN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 HIS B 265 GLN H 147 HIS J 106 GLN K 55 ASN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN R 299 ASN S 47 GLN S 61 GLN T 101 HIS U 110 GLN W 135 GLN Y 381 ASN ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 72322 Z= 0.351 Angle : 0.814 50.682 101314 Z= 0.483 Chirality : 0.124 6.432 11783 Planarity : 0.005 0.057 10261 Dihedral : 19.291 176.584 18468 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.56 % Allowed : 13.18 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % 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: 1.09 (0.10), residues: 6541 helix: 1.57 (0.09), residues: 3078 sheet: 0.08 (0.18), residues: 722 loop : 0.03 (0.12), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 375 HIS 0.020 0.001 HIS 9 187 PHE 0.039 0.002 PHE 8 206 TYR 0.022 0.002 TYR F 50 ARG 0.007 0.001 ARG N 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 687 time to evaluate : 5.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7734 (mtt90) REVERT: 0 70 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7594 (mtt180) REVERT: 5 116 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7248 (mtmt) REVERT: 7 307 MET cc_start: 0.8612 (mmp) cc_final: 0.8091 (mmp) REVERT: 8 166 MET cc_start: 0.8056 (mtp) cc_final: 0.7651 (mtp) REVERT: 9 637 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: B 64 ASN cc_start: 0.7671 (m110) cc_final: 0.7344 (m110) REVERT: B 102 MET cc_start: 0.8514 (mmm) cc_final: 0.8232 (mmm) REVERT: C 19 ARG cc_start: 0.5396 (OUTLIER) cc_final: 0.4344 (mmp80) REVERT: C 118 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: D 361 GLN cc_start: 0.8412 (mt0) cc_final: 0.8165 (mt0) REVERT: F 72 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: F 234 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5684 (ttm-80) REVERT: G 82 ASN cc_start: 0.7725 (m-40) cc_final: 0.7448 (m-40) REVERT: G 273 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: J 116 GLN cc_start: 0.7106 (mp10) cc_final: 0.6710 (mp10) REVERT: L 148 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7190 (pttt) REVERT: N 36 ASP cc_start: 0.8291 (t0) cc_final: 0.8010 (t0) REVERT: N 67 ARG cc_start: 0.8348 (ttm110) cc_final: 0.8136 (ttp80) REVERT: O 65 GLN cc_start: 0.7282 (mm110) cc_final: 0.7015 (mm-40) REVERT: O 197 ASP cc_start: 0.7866 (m-30) cc_final: 0.7607 (m-30) REVERT: O 233 GLU cc_start: 0.6835 (tt0) cc_final: 0.6457 (tt0) REVERT: R 337 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6639 (mm-40) REVERT: S 7 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: S 106 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7785 (mp) REVERT: T 3 MET cc_start: 0.8115 (mtp) cc_final: 0.7644 (mtt) REVERT: T 57 TYR cc_start: 0.8544 (t80) cc_final: 0.8176 (t80) REVERT: T 111 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5991 (tm-30) REVERT: T 115 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.5972 (mp0) REVERT: T 122 GLN cc_start: 0.7619 (tt0) cc_final: 0.7406 (tt0) REVERT: T 132 ARG cc_start: 0.7646 (tpp-160) cc_final: 0.7251 (tpt170) REVERT: U 112 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7219 (tp30) REVERT: U 114 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5396 (mtp180) REVERT: U 116 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7828 (mp) REVERT: U 146 VAL cc_start: 0.8371 (t) cc_final: 0.8132 (m) REVERT: U 165 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7172 (ttmt) REVERT: V 169 MET cc_start: 0.8519 (mmm) cc_final: 0.8085 (mmt) REVERT: V 394 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6779 (tp40) REVERT: V 403 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: X 103 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7793 (mtpp) REVERT: X 217 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: Y 291 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5945 (mt-10) REVERT: Y 367 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7318 (mtpp) REVERT: Z 13 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6917 (ttm170) REVERT: Z 21 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: Z 32 LYS cc_start: 0.6132 (ttpt) cc_final: 0.5643 (ttpp) REVERT: a 267 ARG cc_start: 0.5379 (OUTLIER) cc_final: 0.4638 (ttt-90) outliers start: 148 outliers final: 63 residues processed: 775 average time/residue: 1.6981 time to fit residues: 1698.3989 Evaluate side-chains 742 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 652 time to evaluate : 5.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 328 VAL Chi-restraints excluded: chain 4 residue 392 ILE Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 25 LEU Chi-restraints excluded: chain 5 residue 116 LYS Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 223 MET Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 535 MET Chi-restraints excluded: chain 9 residue 588 GLN Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain 9 residue 654 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain S residue 105 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 115 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 165 LYS Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 96 LYS Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 103 LYS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain Y residue 291 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Z residue 13 ARG Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain a residue 160 GLU Chi-restraints excluded: chain a residue 267 ARG Chi-restraints excluded: chain a residue 326 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 235 optimal weight: 4.9990 chunk 629 optimal weight: 3.9990 chunk 138 optimal weight: 0.3980 chunk 410 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 699 optimal weight: 0.0870 chunk 580 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 367 optimal weight: 6.9990 overall best weight: 2.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 ASN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 85 ASN 7 107 GLN 7 112 HIS 8 145 ASN 8 222 ASN 8 249 GLN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 GLN B 265 GLN J 106 GLN K 55 ASN K 113 HIS O 152 GLN R 299 ASN S 47 GLN S 61 GLN T 101 HIS U 110 GLN X 81 HIS Y 381 ASN a 123 ASN ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 72322 Z= 0.310 Angle : 0.798 50.658 101314 Z= 0.476 Chirality : 0.123 6.398 11783 Planarity : 0.004 0.054 10261 Dihedral : 19.234 176.848 18468 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.65 % Allowed : 13.67 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % 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: 6541 helix: 1.69 (0.09), residues: 3071 sheet: 0.22 (0.18), residues: 729 loop : 0.05 (0.12), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 1 239 HIS 0.021 0.001 HIS 9 187 PHE 0.035 0.002 PHE 8 206 TYR 0.022 0.002 TYR F 50 ARG 0.008 0.000 ARG 0 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 684 time to evaluate : 5.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7724 (mtt90) REVERT: 0 70 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7590 (mtt180) REVERT: 5 20 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6128 (mp0) REVERT: 5 116 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7256 (mtmt) REVERT: 7 307 MET cc_start: 0.8599 (mmp) cc_final: 0.8006 (mmp) REVERT: 8 166 MET cc_start: 0.8067 (mtp) cc_final: 0.7631 (mtp) REVERT: 9 637 PHE cc_start: 0.6944 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: B 102 MET cc_start: 0.8539 (mmm) cc_final: 0.8248 (mmm) REVERT: C 19 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.4402 (mmp80) REVERT: C 118 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: C 153 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8367 (tt) REVERT: D 361 GLN cc_start: 0.8407 (mt0) cc_final: 0.8163 (mt0) REVERT: E 56 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7116 (tm-30) REVERT: F 72 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: F 234 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.5696 (ttm-80) REVERT: G 273 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7103 (pm20) REVERT: J 116 GLN cc_start: 0.7075 (mp10) cc_final: 0.6659 (mp10) REVERT: L 148 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7215 (pttt) REVERT: N 36 ASP cc_start: 0.8338 (t0) cc_final: 0.8027 (t0) REVERT: N 67 ARG cc_start: 0.8333 (ttm110) cc_final: 0.8108 (ttp80) REVERT: O 65 GLN cc_start: 0.7266 (mm110) cc_final: 0.6998 (mm-40) REVERT: O 109 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.6947 (ptm160) REVERT: O 197 ASP cc_start: 0.7875 (m-30) cc_final: 0.7615 (m-30) REVERT: O 233 GLU cc_start: 0.6831 (tt0) cc_final: 0.6421 (tt0) REVERT: P 88 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7471 (m) REVERT: R 337 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6755 (mm-40) REVERT: S 7 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: S 102 LYS cc_start: 0.8215 (tppt) cc_final: 0.7839 (tppt) REVERT: S 106 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7758 (mp) REVERT: T 3 MET cc_start: 0.8079 (mtp) cc_final: 0.7606 (mtt) REVERT: T 57 TYR cc_start: 0.8536 (t80) cc_final: 0.8150 (t80) REVERT: T 132 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.7286 (tpt170) REVERT: U 112 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: U 114 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5375 (mtp180) REVERT: U 116 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7864 (mp) REVERT: U 146 VAL cc_start: 0.8369 (t) cc_final: 0.8142 (m) REVERT: U 165 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7171 (ttmt) REVERT: V 169 MET cc_start: 0.8517 (mmm) cc_final: 0.8150 (mmt) REVERT: V 394 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6829 (tp40) REVERT: X 217 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: Y 367 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7171 (mtpp) REVERT: Z 13 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6875 (ttm170) REVERT: Z 21 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: Z 32 LYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5686 (ttpp) REVERT: Z 39 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7060 (pt0) outliers start: 153 outliers final: 66 residues processed: 777 average time/residue: 1.6483 time to fit residues: 1657.9684 Evaluate side-chains 746 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 653 time to evaluate : 5.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 319 LEU Chi-restraints excluded: chain 4 residue 392 ILE Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 20 GLU Chi-restraints excluded: chain 5 residue 25 LEU Chi-restraints excluded: chain 5 residue 116 LYS Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 5 residue 228 VAL Chi-restraints excluded: chain 7 residue 74 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 223 MET Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 535 MET Chi-restraints excluded: chain 9 residue 588 GLN Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain 9 residue 654 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 234 ARG Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 105 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 165 LYS Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Z residue 13 ARG Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain Z residue 39 GLU Chi-restraints excluded: chain a residue 255 THR Chi-restraints excluded: chain a residue 326 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 674 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 398 optimal weight: 1.9990 chunk 510 optimal weight: 4.9990 chunk 395 optimal weight: 2.9990 chunk 588 optimal weight: 4.9990 chunk 390 optimal weight: 4.9990 chunk 696 optimal weight: 0.9990 chunk 436 optimal weight: 0.7980 chunk 424 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 ASN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 85 ASN 7 107 GLN 7 112 HIS 8 70 GLN 8 145 ASN 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 GLN 9 665 ASN B 265 GLN J 106 GLN K 55 ASN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN R 299 ASN S 47 GLN S 61 GLN T 122 GLN U 110 GLN W 135 GLN X 81 HIS Y 381 ASN ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 72322 Z= 0.288 Angle : 0.790 50.650 101314 Z= 0.472 Chirality : 0.123 6.388 11783 Planarity : 0.004 0.055 10261 Dihedral : 19.173 177.052 18468 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.46 % Allowed : 14.29 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.10), residues: 6541 helix: 1.77 (0.09), residues: 3065 sheet: 0.26 (0.19), residues: 727 loop : 0.07 (0.12), residues: 2749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 1 239 HIS 0.008 0.001 HIS 9 187 PHE 0.031 0.001 PHE 8 206 TYR 0.022 0.001 TYR F 50 ARG 0.007 0.000 ARG W 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 693 time to evaluate : 5.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7723 (mtt90) REVERT: 0 70 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7598 (mtt180) REVERT: 1 97 MET cc_start: 0.7209 (mtm) cc_final: 0.6952 (mtp) REVERT: 4 154 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5895 (tt0) REVERT: 4 172 MET cc_start: 0.7822 (tpp) cc_final: 0.7505 (tpt) REVERT: 4 594 LYS cc_start: 0.7560 (mtmt) cc_final: 0.7355 (mtpt) REVERT: 5 20 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: 7 307 MET cc_start: 0.8594 (mmp) cc_final: 0.8018 (mmp) REVERT: 8 166 MET cc_start: 0.8031 (mtp) cc_final: 0.7589 (mtp) REVERT: 9 637 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: B 102 MET cc_start: 0.8550 (mmm) cc_final: 0.8330 (mmm) REVERT: C 19 ARG cc_start: 0.5436 (OUTLIER) cc_final: 0.4479 (mmp80) REVERT: C 118 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: C 153 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8336 (tt) REVERT: D 361 GLN cc_start: 0.8410 (mt0) cc_final: 0.8166 (mt0) REVERT: E 21 THR cc_start: 0.8014 (m) cc_final: 0.7584 (m) REVERT: F 72 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: G 273 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: H 185 LYS cc_start: 0.7657 (mmmm) cc_final: 0.7423 (mmmt) REVERT: J 116 GLN cc_start: 0.7042 (mp10) cc_final: 0.6738 (mp10) REVERT: L 148 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7210 (pttt) REVERT: N 36 ASP cc_start: 0.8318 (t0) cc_final: 0.7997 (t0) REVERT: N 67 ARG cc_start: 0.8326 (ttm110) cc_final: 0.8108 (ttp80) REVERT: N 83 GLU cc_start: 0.7258 (pt0) cc_final: 0.6963 (pt0) REVERT: O 65 GLN cc_start: 0.7268 (mm110) cc_final: 0.6998 (mm-40) REVERT: O 197 ASP cc_start: 0.7872 (m-30) cc_final: 0.7609 (m-30) REVERT: O 233 GLU cc_start: 0.6861 (tt0) cc_final: 0.6460 (tt0) REVERT: P 88 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7471 (m) REVERT: R 255 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7948 (ttpp) REVERT: R 337 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6762 (mm-40) REVERT: S 7 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: S 106 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7762 (mp) REVERT: T 3 MET cc_start: 0.8072 (mtp) cc_final: 0.7602 (mtt) REVERT: T 57 TYR cc_start: 0.8551 (t80) cc_final: 0.8233 (t80) REVERT: T 132 ARG cc_start: 0.7635 (tpp-160) cc_final: 0.7282 (tpt170) REVERT: U 112 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7203 (tp30) REVERT: U 114 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5361 (mtp180) REVERT: U 116 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7880 (mp) REVERT: U 165 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7148 (ttmt) REVERT: V 169 MET cc_start: 0.8536 (mmm) cc_final: 0.8185 (mmt) REVERT: V 376 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: V 394 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6830 (tp40) REVERT: X 103 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7622 (mtpp) REVERT: X 217 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: Y 291 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.5858 (mt-10) REVERT: Z 13 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6862 (ttm170) REVERT: Z 21 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: Z 32 LYS cc_start: 0.6062 (OUTLIER) cc_final: 0.5621 (ttpp) outliers start: 142 outliers final: 72 residues processed: 786 average time/residue: 1.6828 time to fit residues: 1736.5511 Evaluate side-chains 748 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 650 time to evaluate : 5.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 154 GLU Chi-restraints excluded: chain 4 residue 319 LEU Chi-restraints excluded: chain 4 residue 328 VAL Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 20 GLU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 5 residue 228 VAL Chi-restraints excluded: chain 5 residue 283 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 223 MET Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 7 residue 276 ASP Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 9 residue 92 GLN Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 535 MET Chi-restraints excluded: chain 9 residue 588 GLN Chi-restraints excluded: chain 9 residue 637 PHE Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain 9 residue 654 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 337 GLN Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 165 LYS Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 376 GLU Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 103 LYS Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 291 GLU Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Z residue 13 ARG Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 255 THR Chi-restraints excluded: chain a residue 326 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 431 optimal weight: 2.9990 chunk 278 optimal weight: 20.0000 chunk 416 optimal weight: 0.0000 chunk 209 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 443 optimal weight: 1.9990 chunk 474 optimal weight: 2.9990 chunk 344 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 547 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 181 ASN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 85 ASN 7 107 GLN 8 145 ASN 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 GLN B 265 GLN J 106 GLN K 55 ASN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN R 299 ASN S 47 GLN S 61 GLN T 122 GLN X 81 HIS Y 381 ASN ** a 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 72322 Z= 0.268 Angle : 0.786 50.613 101314 Z= 0.470 Chirality : 0.122 6.364 11783 Planarity : 0.004 0.077 10261 Dihedral : 19.123 177.186 18468 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.11 % Allowed : 14.93 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.10), residues: 6541 helix: 1.85 (0.09), residues: 3067 sheet: 0.33 (0.19), residues: 726 loop : 0.12 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP 1 239 HIS 0.007 0.001 HIS 7 52 PHE 0.033 0.001 PHE 8 206 TYR 0.022 0.001 TYR F 50 ARG 0.018 0.000 ARG 9 573 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 679 time to evaluate : 5.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7719 (mtt90) REVERT: 0 70 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7603 (mtt180) REVERT: 1 97 MET cc_start: 0.7218 (mtm) cc_final: 0.6962 (mtp) REVERT: 4 154 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5889 (tt0) REVERT: 4 172 MET cc_start: 0.7799 (tpp) cc_final: 0.7503 (tpt) REVERT: 5 20 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6110 (mp0) REVERT: 8 115 ASP cc_start: 0.7355 (m-30) cc_final: 0.7101 (m-30) REVERT: B 102 MET cc_start: 0.8549 (mmm) cc_final: 0.8319 (mmm) REVERT: C 19 ARG cc_start: 0.5404 (OUTLIER) cc_final: 0.4465 (mmp80) REVERT: C 118 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6798 (mt-10) REVERT: C 153 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8245 (tt) REVERT: D 361 GLN cc_start: 0.8419 (mt0) cc_final: 0.8179 (mt0) REVERT: E 21 THR cc_start: 0.7958 (m) cc_final: 0.7757 (m) REVERT: F 72 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: G 273 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7049 (pm20) REVERT: H 185 LYS cc_start: 0.7674 (mmmm) cc_final: 0.7472 (mmmt) REVERT: J 116 GLN cc_start: 0.7032 (mp10) cc_final: 0.6740 (mp10) REVERT: L 148 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7215 (pttt) REVERT: N 36 ASP cc_start: 0.8296 (t0) cc_final: 0.7967 (t0) REVERT: N 67 ARG cc_start: 0.8303 (ttm110) cc_final: 0.8081 (ttp80) REVERT: N 73 ARG cc_start: 0.7991 (ptm-80) cc_final: 0.6938 (ptm-80) REVERT: N 83 GLU cc_start: 0.7314 (pt0) cc_final: 0.7021 (pt0) REVERT: O 65 GLN cc_start: 0.7313 (mm110) cc_final: 0.6925 (mm-40) REVERT: O 109 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.6942 (ptm160) REVERT: O 197 ASP cc_start: 0.7863 (m-30) cc_final: 0.7606 (m-30) REVERT: O 233 GLU cc_start: 0.6884 (tt0) cc_final: 0.6484 (tt0) REVERT: P 88 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7509 (m) REVERT: R 255 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7939 (ttpp) REVERT: S 7 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: S 106 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7804 (mp) REVERT: T 3 MET cc_start: 0.8057 (mtp) cc_final: 0.7595 (mtt) REVERT: T 57 TYR cc_start: 0.8547 (t80) cc_final: 0.8224 (t80) REVERT: T 111 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5972 (tm-30) REVERT: T 132 ARG cc_start: 0.7619 (tpp-160) cc_final: 0.7292 (tpt170) REVERT: U 112 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7216 (tp30) REVERT: U 114 ARG cc_start: 0.6187 (OUTLIER) cc_final: 0.5337 (mtp180) REVERT: U 116 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7872 (mp) REVERT: U 165 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7130 (ttmt) REVERT: V 169 MET cc_start: 0.8522 (mmm) cc_final: 0.8088 (mmt) REVERT: V 394 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6829 (tp40) REVERT: X 103 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7598 (mtpp) REVERT: X 182 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7794 (mm) REVERT: X 217 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: Z 21 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: Z 32 LYS cc_start: 0.6058 (OUTLIER) cc_final: 0.5630 (ttpp) REVERT: Z 39 GLU cc_start: 0.7391 (pt0) cc_final: 0.7161 (pm20) outliers start: 122 outliers final: 59 residues processed: 758 average time/residue: 1.6239 time to fit residues: 1589.9810 Evaluate side-chains 733 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 650 time to evaluate : 5.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 154 GLU Chi-restraints excluded: chain 4 residue 319 LEU Chi-restraints excluded: chain 4 residue 328 VAL Chi-restraints excluded: chain 4 residue 392 ILE Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 5 residue 20 GLU Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 5 residue 283 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 9 residue 92 GLN Chi-restraints excluded: chain 9 residue 205 VAL Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 535 MET Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 148 LYS Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain O residue 226 GLU Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain S residue 7 GLU Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 165 LYS Chi-restraints excluded: chain V residue 64 LYS Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 103 LYS Chi-restraints excluded: chain X residue 108 LEU Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 32 LYS Chi-restraints excluded: chain a residue 255 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 633 optimal weight: 1.9990 chunk 667 optimal weight: 0.7980 chunk 609 optimal weight: 0.9990 chunk 649 optimal weight: 0.4980 chunk 390 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 509 optimal weight: 7.9990 chunk 199 optimal weight: 0.3980 chunk 586 optimal weight: 4.9990 chunk 614 optimal weight: 1.9990 chunk 647 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 148 GLN ** 4 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 141 ASN 7 85 ASN 7 107 GLN 8 145 ASN 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 GLN D 288 HIS J 106 GLN K 55 ASN O 152 GLN R 299 ASN S 47 GLN U 79 GLN V 78 ASN W 135 GLN X 81 HIS Y 381 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 72322 Z= 0.238 Angle : 0.777 50.635 101314 Z= 0.465 Chirality : 0.122 6.352 11783 Planarity : 0.004 0.053 10261 Dihedral : 19.034 177.469 18468 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.54 % Allowed : 15.82 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % 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: 1.62 (0.10), residues: 6541 helix: 2.06 (0.09), residues: 3046 sheet: 0.42 (0.19), residues: 743 loop : 0.23 (0.12), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP 1 239 HIS 0.007 0.001 HIS 7 52 PHE 0.029 0.001 PHE 8 232 TYR 0.024 0.001 TYR F 50 ARG 0.009 0.000 ARG E 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 683 time to evaluate : 5.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7712 (mtt90) REVERT: 0 70 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7603 (mtt180) REVERT: 1 97 MET cc_start: 0.7129 (mtm) cc_final: 0.6866 (mtp) REVERT: 4 172 MET cc_start: 0.7754 (tpp) cc_final: 0.7478 (tpt) REVERT: 8 330 MET cc_start: 0.7981 (mmp) cc_final: 0.7653 (mmp) REVERT: B 102 MET cc_start: 0.8558 (mmm) cc_final: 0.8234 (mmm) REVERT: D 361 GLN cc_start: 0.8410 (mt0) cc_final: 0.8153 (mt0) REVERT: F 72 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7702 (mt0) REVERT: F 156 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8073 (mp) REVERT: G 273 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6957 (pm20) REVERT: H 185 LYS cc_start: 0.7686 (mmmm) cc_final: 0.7445 (mmmt) REVERT: L 75 ASP cc_start: 0.7420 (m-30) cc_final: 0.7110 (m-30) REVERT: N 36 ASP cc_start: 0.8283 (t0) cc_final: 0.7934 (t0) REVERT: N 67 ARG cc_start: 0.8226 (ttm110) cc_final: 0.8013 (ttp80) REVERT: O 65 GLN cc_start: 0.7297 (mm110) cc_final: 0.6944 (mm-40) REVERT: O 109 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.6786 (ptm160) REVERT: O 197 ASP cc_start: 0.7860 (m-30) cc_final: 0.7609 (m-30) REVERT: O 233 GLU cc_start: 0.6909 (tt0) cc_final: 0.6514 (tt0) REVERT: P 88 THR cc_start: 0.7816 (p) cc_final: 0.7490 (m) REVERT: R 337 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6972 (mm-40) REVERT: T 3 MET cc_start: 0.8001 (mtp) cc_final: 0.7560 (mtt) REVERT: T 57 TYR cc_start: 0.8504 (t80) cc_final: 0.8246 (t80) REVERT: T 132 ARG cc_start: 0.7601 (tpp-160) cc_final: 0.7280 (tpt170) REVERT: U 112 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: U 114 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5299 (mtp180) REVERT: U 116 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7855 (mp) REVERT: U 146 VAL cc_start: 0.8434 (t) cc_final: 0.8227 (m) REVERT: U 165 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7141 (ttmt) REVERT: V 169 MET cc_start: 0.8504 (mmm) cc_final: 0.8108 (mmt) REVERT: V 394 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6859 (tp40) REVERT: X 103 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7560 (mtpp) REVERT: X 217 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6875 (tm-30) REVERT: Z 10 ARG cc_start: 0.7175 (ttp-170) cc_final: 0.6850 (ttm-80) REVERT: Z 21 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: Z 32 LYS cc_start: 0.6122 (ttpt) cc_final: 0.5704 (ttpp) REVERT: Z 39 GLU cc_start: 0.7339 (pt0) cc_final: 0.7089 (pm20) REVERT: Z 55 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.6304 (m90) REVERT: a 239 ASP cc_start: 0.6089 (p0) cc_final: 0.5360 (p0) outliers start: 89 outliers final: 44 residues processed: 742 average time/residue: 1.6122 time to fit residues: 1554.3540 Evaluate side-chains 705 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 647 time to evaluate : 5.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 5 residue 62 VAL Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 220 ILE Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 165 LYS Chi-restraints excluded: chain V residue 64 LYS Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 103 LYS Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 55 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 426 optimal weight: 8.9990 chunk 686 optimal weight: 1.9990 chunk 419 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 chunk 477 optimal weight: 0.5980 chunk 720 optimal weight: 9.9990 chunk 662 optimal weight: 0.6980 chunk 573 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 443 optimal weight: 5.9990 chunk 351 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 85 ASN 7 107 GLN 7 290 HIS 8 145 ASN 8 222 ASN 8 283 GLN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 GLN B 265 GLN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN H 133 GLN J 106 GLN K 55 ASN O 152 GLN R 299 ASN S 47 GLN S 61 GLN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 381 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 72322 Z= 0.261 Angle : 0.784 50.635 101314 Z= 0.469 Chirality : 0.122 6.370 11783 Planarity : 0.004 0.052 10261 Dihedral : 18.996 177.321 18468 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.42 % Allowed : 16.47 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % 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: 1.62 (0.10), residues: 6541 helix: 2.04 (0.09), residues: 3051 sheet: 0.43 (0.19), residues: 743 loop : 0.25 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP 1 239 HIS 0.007 0.001 HIS 7 52 PHE 0.029 0.001 PHE 8 206 TYR 0.024 0.001 TYR F 50 ARG 0.016 0.000 ARG U 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13082 Ramachandran restraints generated. 6541 Oldfield, 0 Emsley, 6541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 664 time to evaluate : 5.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7732 (mtt90) REVERT: 0 70 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7589 (mtt180) REVERT: 1 97 MET cc_start: 0.7155 (mtm) cc_final: 0.6906 (mtp) REVERT: 4 172 MET cc_start: 0.7766 (tpp) cc_final: 0.7521 (tpt) REVERT: B 102 MET cc_start: 0.8545 (mmm) cc_final: 0.8240 (mmm) REVERT: D 361 GLN cc_start: 0.8421 (mt0) cc_final: 0.8156 (mt0) REVERT: G 273 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: H 185 LYS cc_start: 0.7683 (mmmm) cc_final: 0.7443 (mmmt) REVERT: L 75 ASP cc_start: 0.7405 (m-30) cc_final: 0.7096 (m-30) REVERT: N 36 ASP cc_start: 0.8288 (t0) cc_final: 0.7955 (t0) REVERT: N 67 ARG cc_start: 0.8282 (ttm110) cc_final: 0.8072 (ttp80) REVERT: N 83 GLU cc_start: 0.7354 (pt0) cc_final: 0.7086 (pt0) REVERT: O 65 GLN cc_start: 0.7304 (mm110) cc_final: 0.6957 (mm-40) REVERT: O 109 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.6787 (ptm160) REVERT: O 233 GLU cc_start: 0.6882 (tt0) cc_final: 0.6485 (tt0) REVERT: P 88 THR cc_start: 0.7825 (p) cc_final: 0.7509 (m) REVERT: T 3 MET cc_start: 0.8018 (mtp) cc_final: 0.7560 (mtt) REVERT: T 57 TYR cc_start: 0.8526 (t80) cc_final: 0.8265 (t80) REVERT: T 132 ARG cc_start: 0.7615 (tpp-160) cc_final: 0.7290 (tpt170) REVERT: U 112 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7240 (tp30) REVERT: U 114 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5315 (mtp180) REVERT: U 116 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7867 (mp) REVERT: U 146 VAL cc_start: 0.8399 (t) cc_final: 0.8191 (m) REVERT: U 165 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7119 (ttmt) REVERT: V 169 MET cc_start: 0.8496 (mmm) cc_final: 0.8144 (mmt) REVERT: V 394 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6865 (tp40) REVERT: X 103 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7575 (mtpp) REVERT: X 167 ASP cc_start: 0.7225 (p0) cc_final: 0.6805 (t0) REVERT: X 182 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7744 (tp) REVERT: X 217 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6771 (tm-30) REVERT: Z 21 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: Z 32 LYS cc_start: 0.6169 (ttpt) cc_final: 0.5739 (ttpp) REVERT: Z 39 GLU cc_start: 0.7368 (pt0) cc_final: 0.7114 (pt0) REVERT: a 239 ASP cc_start: 0.5948 (p0) cc_final: 0.5226 (p0) outliers start: 82 outliers final: 52 residues processed: 721 average time/residue: 1.5831 time to fit residues: 1489.3842 Evaluate side-chains 708 residues out of total 5858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 644 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 49 ARG Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 88 VAL Chi-restraints excluded: chain 4 residue 328 VAL Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 527 LEU Chi-restraints excluded: chain 4 residue 530 GLU Chi-restraints excluded: chain 5 residue 62 VAL Chi-restraints excluded: chain 5 residue 117 VAL Chi-restraints excluded: chain 5 residue 118 GLU Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 164 ASP Chi-restraints excluded: chain 7 residue 188 THR Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 7 residue 226 LEU Chi-restraints excluded: chain 8 residue 82 LEU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 314 LYS Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 270 GLU Chi-restraints excluded: chain 9 residue 530 VAL Chi-restraints excluded: chain 9 residue 647 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 107 GLN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 272 SER Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 107 GLU Chi-restraints excluded: chain O residue 109 ARG Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 122 VAL Chi-restraints excluded: chain S residue 61 GLN Chi-restraints excluded: chain S residue 76 SER Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain U residue 112 GLU Chi-restraints excluded: chain U residue 114 ARG Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 165 LYS Chi-restraints excluded: chain V residue 64 LYS Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 393 GLU Chi-restraints excluded: chain V residue 394 GLN Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 161 THR Chi-restraints excluded: chain X residue 103 LYS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 200 ASN Chi-restraints excluded: chain X residue 217 GLU Chi-restraints excluded: chain X residue 272 THR Chi-restraints excluded: chain Y residue 339 GLU Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 723 random chunks: chunk 455 optimal weight: 6.9990 chunk 610 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 528 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 574 optimal weight: 7.9990 chunk 240 optimal weight: 1.9990 chunk 589 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 602 HIS 7 85 ASN 7 107 GLN 8 145 ASN 8 222 ASN ** 8 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 92 GLN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN J 106 GLN K 55 ASN O 152 GLN R 299 ASN R 337 GLN S 47 GLN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 135 GLN Y 381 ASN ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.148735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.114853 restraints weight = 106747.797| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.48 r_work: 0.3371 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 72322 Z= 0.268 Angle : 0.820 59.195 101314 Z= 0.492 Chirality : 0.123 6.435 11783 Planarity : 0.004 0.052 10261 Dihedral : 18.996 177.318 18468 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.40 % Allowed : 16.66 % Favored : 81.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.87 % Cis-general : 0.00 % Twisted Proline : 0.27 % 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: 1.62 (0.10), residues: 6541 helix: 2.04 (0.09), residues: 3051 sheet: 0.44 (0.19), residues: 743 loop : 0.25 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP 1 239 HIS 0.008 0.001 HIS a 301 PHE 0.028 0.001 PHE 8 206 TYR 0.022 0.001 TYR F 50 ARG 0.011 0.000 ARG U 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25426.77 seconds wall clock time: 437 minutes 35.22 seconds (26255.22 seconds total)