Starting phenix.real_space_refine on Sun Mar 24 15:09:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae3_11738/03_2024/7ae3_11738_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae3_11738/03_2024/7ae3_11738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae3_11738/03_2024/7ae3_11738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae3_11738/03_2024/7ae3_11738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae3_11738/03_2024/7ae3_11738_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ae3_11738/03_2024/7ae3_11738_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 7 6.06 5 P 44 5.49 5 Mg 1 5.21 5 S 286 5.16 5 C 26757 2.51 5 N 7380 2.21 5 O 8046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 582": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 618": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ARG 769": "NH1" <-> "NH2" Residue "A ARG 874": "NH1" <-> "NH2" Residue "A ARG 923": "NH1" <-> "NH2" Residue "A ARG 998": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A ARG 1150": "NH1" <-> "NH2" Residue "A ARG 1159": "NH1" <-> "NH2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A ARG 1284": "NH1" <-> "NH2" Residue "A ARG 1375": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 702": "NH1" <-> "NH2" Residue "B PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 805": "NH1" <-> "NH2" Residue "B ARG 957": "NH1" <-> "NH2" Residue "B ARG 978": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1041": "NH1" <-> "NH2" Residue "B ARG 1105": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "M TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 152": "NH1" <-> "NH2" Residue "M ARG 188": "NH1" <-> "NH2" Residue "M ARG 189": "NH1" <-> "NH2" Residue "M ARG 353": "NH1" <-> "NH2" Residue "M PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 156": "NH1" <-> "NH2" Residue "N ARG 332": "NH1" <-> "NH2" Residue "N ARG 336": "NH1" <-> "NH2" Residue "O ARG 202": "NH1" <-> "NH2" Residue "O ARG 449": "NH1" <-> "NH2" Residue "O ARG 459": "NH1" <-> "NH2" Residue "O ARG 496": "NH1" <-> "NH2" Residue "P ARG 196": "NH1" <-> "NH2" Residue "P ARG 271": "NH1" <-> "NH2" Residue "Q ARG 113": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42525 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 10765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1370, 10765 Classifications: {'peptide': 1370} Link IDs: {'PTRANS': 65, 'TRANS': 1304} Chain breaks: 2 Chain: "B" Number of atoms: 8680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8680 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 2 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1001 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1509 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 1 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 849 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3211 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 23, 'TRANS': 376} Chain breaks: 1 Chain: "N" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1448 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "Q" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 883 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 12, 'TRANS': 91} Chain: "R" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "S" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "T" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 477 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 100.390 68.265 120.892 1.00123.46 S ATOM 565 SG CYS A 72 98.286 64.284 120.898 1.00119.00 S ATOM 613 SG CYS A 79 96.753 67.087 119.058 1.00114.39 S ATOM 854 SG CYS A 109 68.039 95.745 145.709 1.00134.61 S ATOM 876 SG CYS A 112 68.208 92.652 148.185 1.00137.99 S ATOM 1245 SG CYS A 156 64.286 93.750 147.420 1.00147.45 S ATOM 1271 SG CYS A 159 67.020 95.855 149.251 1.00148.32 S ATOM 19032 SG CYS B1080 84.051 62.012 130.311 1.00112.41 S ATOM 19051 SG CYS B1083 83.773 65.669 130.511 1.00110.35 S ATOM 19117 SG CYS B1092 87.128 64.186 130.276 1.00113.94 S ATOM 19145 SG CYS B1095 84.940 64.186 133.985 1.00115.16 S ATOM 28260 SG CYS I 5 56.575 148.198 110.415 1.00114.52 S ATOM 28277 SG CYS I 8 60.056 146.253 111.693 1.00114.88 S ATOM 28408 SG CYS I 25 57.316 144.935 113.573 1.00122.98 S ATOM 28429 SG CYS I 28 57.666 148.620 113.767 1.00124.29 S ATOM 29123 SG CYS J 7 88.990 75.449 49.431 1.00 69.10 S ATOM 29147 SG CYS J 10 88.217 72.441 46.598 1.00 67.05 S ATOM 29411 SG CYS J 44 85.751 75.258 47.181 1.00 75.17 S ATOM 29417 SG CYS J 45 89.196 75.520 45.132 1.00 73.81 S ATOM 30506 SG CYS L 19 122.273 91.738 71.855 1.00 96.02 S ATOM 30525 SG CYS L 22 124.259 92.470 68.953 1.00104.23 S ATOM 30642 SG CYS L 36 125.830 92.379 72.354 1.00107.96 S Time building chain proxies: 20.59, per 1000 atoms: 0.48 Number of scatterers: 42525 At special positions: 0 Unit cell: (141.75, 183.75, 206.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 7 29.99 Fe 4 26.01 S 286 16.00 P 44 15.00 Mg 1 11.99 O 8046 8.00 N 7380 7.00 C 26757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.75 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 296 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " Number of angles added : 24 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 48 sheets defined 33.8% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.53 Creating SS restraints... Processing helix chain 'A' and resid 28 through 31 No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.579A pdb=" N GLY A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 130 removed outlier: 3.674A pdb=" N LYS A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 150 removed outlier: 3.534A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.821A pdb=" N PHE A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.788A pdb=" N HIS A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 removed outlier: 5.258A pdb=" N GLY A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ARG A 213 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 3.968A pdb=" N ARG A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 278 through 299 removed outlier: 3.514A pdb=" N GLU A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.578A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.616A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.665A pdb=" N GLN A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 490 through 496 removed outlier: 4.104A pdb=" N THR A 494 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Proline residue: A 495 - end of helix Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'A' and resid 547 through 552 Processing helix chain 'A' and resid 561 through 571 removed outlier: 3.911A pdb=" N SER A 570 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 597 through 605 removed outlier: 4.184A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 655 No H-bonds generated for 'chain 'A' and resid 652 through 655' Processing helix chain 'A' and resid 663 through 671 Processing helix chain 'A' and resid 673 through 694 removed outlier: 3.588A pdb=" N ALA A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Proline residue: A 688 - end of helix removed outlier: 3.751A pdb=" N ASN A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 732 removed outlier: 3.630A pdb=" N LYS A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 767 removed outlier: 3.580A pdb=" N LEU A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 760 " --> pdb=" O LEU A 756 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 782 Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 844 through 879 removed outlier: 3.658A pdb=" N GLU A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 857 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR A 870 " --> pdb=" O ALA A 866 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N MET A 871 " --> pdb=" O GLU A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 921 through 931 Processing helix chain 'A' and resid 942 through 954 removed outlier: 3.813A pdb=" N LYS A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 3.983A pdb=" N CYS A 960 " --> pdb=" O GLU A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 963 through 986 removed outlier: 3.758A pdb=" N LYS A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1008 through 1025 Processing helix chain 'A' and resid 1033 through 1046 Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1095 through 1103 removed outlier: 4.076A pdb=" N LEU A1100 " --> pdb=" O ASP A1096 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1140 Processing helix chain 'A' and resid 1146 through 1152 Processing helix chain 'A' and resid 1186 through 1198 removed outlier: 3.971A pdb=" N LEU A1189 " --> pdb=" O TYR A1186 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A1195 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU A1196 " --> pdb=" O LYS A1193 " (cutoff:3.500A) Proline residue: A1197 - end of helix Processing helix chain 'A' and resid 1232 through 1237 Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1251 through 1258 Processing helix chain 'A' and resid 1260 through 1277 Processing helix chain 'A' and resid 1284 through 1294 Processing helix chain 'A' and resid 1305 through 1311 removed outlier: 3.777A pdb=" N LYS A1310 " --> pdb=" O PHE A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1319 Processing helix chain 'A' and resid 1324 through 1333 removed outlier: 4.031A pdb=" N LEU A1328 " --> pdb=" O THR A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1349 Processing helix chain 'A' and resid 1356 through 1358 No H-bonds generated for 'chain 'A' and resid 1356 through 1358' Processing helix chain 'A' and resid 1382 through 1384 No H-bonds generated for 'chain 'A' and resid 1382 through 1384' Processing helix chain 'B' and resid 24 through 33 removed outlier: 4.453A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 41 through 61 removed outlier: 3.645A pdb=" N TYR B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 259 through 274 Proline residue: B 267 - end of helix removed outlier: 3.507A pdb=" N GLU B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 removed outlier: 3.567A pdb=" N ASN B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 315 removed outlier: 3.767A pdb=" N LEU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 347 removed outlier: 3.946A pdb=" N TYR B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 365 through 391 removed outlier: 4.046A pdb=" N LEU B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 408 through 420 removed outlier: 4.604A pdb=" N THR B 412 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN B 413 " --> pdb=" O GLN B 410 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 416 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN B 417 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 420 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.820A pdb=" N MET B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.787A pdb=" N ASN B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 552 through 565 Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 661 through 664 Processing helix chain 'B' and resid 669 through 671 No H-bonds generated for 'chain 'B' and resid 669 through 671' Processing helix chain 'B' and resid 680 through 692 removed outlier: 3.685A pdb=" N THR B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 727 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 759 through 762 No H-bonds generated for 'chain 'B' and resid 759 through 762' Processing helix chain 'B' and resid 804 through 806 No H-bonds generated for 'chain 'B' and resid 804 through 806' Processing helix chain 'B' and resid 913 through 915 No H-bonds generated for 'chain 'B' and resid 913 through 915' Processing helix chain 'B' and resid 931 through 937 Proline residue: B 935 - end of helix Processing helix chain 'B' and resid 940 through 953 removed outlier: 3.760A pdb=" N LEU B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 978 removed outlier: 4.209A pdb=" N GLU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 975 " --> pdb=" O ASP B 971 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 976 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 977 " --> pdb=" O CYS B 973 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 978 " --> pdb=" O GLU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1018 No H-bonds generated for 'chain 'B' and resid 1016 through 1018' Processing helix chain 'B' and resid 1039 through 1041 No H-bonds generated for 'chain 'B' and resid 1039 through 1041' Processing helix chain 'B' and resid 1049 through 1057 removed outlier: 3.625A pdb=" N ASP B1053 " --> pdb=" O GLU B1049 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B1055 " --> pdb=" O GLU B1051 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B1057 " --> pdb=" O ASP B1053 " (cutoff:3.500A) Processing helix chain 'B' and resid 1062 through 1068 removed outlier: 3.688A pdb=" N LEU B1068 " --> pdb=" O LEU B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1116 Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 42 through 48 Processing helix chain 'C' and resid 70 through 82 removed outlier: 4.183A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 159 through 162 No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.617A pdb=" N GLU C 252 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 318 through 343 removed outlier: 3.528A pdb=" N VAL C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 26 removed outlier: 3.933A pdb=" N GLN D 26 " --> pdb=" O ASP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 55 removed outlier: 3.647A pdb=" N ILE D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 72 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.559A pdb=" N GLN D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 100 No H-bonds generated for 'chain 'D' and resid 97 through 100' Processing helix chain 'D' and resid 104 through 107 No H-bonds generated for 'chain 'D' and resid 104 through 107' Processing helix chain 'D' and resid 110 through 123 removed outlier: 3.503A pdb=" N LEU D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 23 removed outlier: 3.722A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 43 removed outlier: 3.903A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 removed outlier: 4.024A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP E 120 " --> pdb=" O GLN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 removed outlier: 3.874A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.542A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 98 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 removed outlier: 3.771A pdb=" N ALA G 27 " --> pdb=" O ASN G 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'I' and resid 56 through 59 No H-bonds generated for 'chain 'I' and resid 56 through 59' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 removed outlier: 3.720A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.940A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 4.413A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 removed outlier: 3.753A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 127 Processing helix chain 'M' and resid 71 through 81 removed outlier: 3.617A pdb=" N GLN M 76 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 153 removed outlier: 3.617A pdb=" N GLU M 153 " --> pdb=" O HIS M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 200 Processing helix chain 'M' and resid 216 through 225 removed outlier: 3.668A pdb=" N ARG M 222 " --> pdb=" O SER M 218 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU M 225 " --> pdb=" O GLU M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 278 through 288 Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'M' and resid 309 through 316 removed outlier: 4.543A pdb=" N GLN M 315 " --> pdb=" O ARG M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 329 through 332 No H-bonds generated for 'chain 'M' and resid 329 through 332' Processing helix chain 'M' and resid 350 through 362 removed outlier: 4.404A pdb=" N VAL M 356 " --> pdb=" O GLY M 352 " (cutoff:3.500A) Processing helix chain 'M' and resid 371 through 374 No H-bonds generated for 'chain 'M' and resid 371 through 374' Processing helix chain 'M' and resid 379 through 388 removed outlier: 3.996A pdb=" N ASP M 384 " --> pdb=" O GLU M 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU M 387 " --> pdb=" O LYS M 383 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS M 388 " --> pdb=" O ASP M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 414 through 432 removed outlier: 4.520A pdb=" N GLN M 419 " --> pdb=" O VAL M 416 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP M 423 " --> pdb=" O HIS M 420 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 123 removed outlier: 3.810A pdb=" N TRP N 123 " --> pdb=" O LYS N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 150 No H-bonds generated for 'chain 'N' and resid 148 through 150' Processing helix chain 'N' and resid 250 through 258 removed outlier: 3.540A pdb=" N GLU N 257 " --> pdb=" O GLU N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 389 through 395 removed outlier: 3.559A pdb=" N HIS N 395 " --> pdb=" O SER N 391 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 removed outlier: 3.662A pdb=" N GLN O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 31 removed outlier: 3.604A pdb=" N HIS O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 43 removed outlier: 3.856A pdb=" N ALA O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS O 41 " --> pdb=" O ARG O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 57 Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 79 through 97 removed outlier: 3.638A pdb=" N LEU O 83 " --> pdb=" O CYS O 79 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG O 84 " --> pdb=" O SER O 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU O 86 " --> pdb=" O VAL O 82 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix removed outlier: 3.548A pdb=" N LYS O 96 " --> pdb=" O ILE O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'O' and resid 118 through 130 removed outlier: 3.624A pdb=" N LYS O 123 " --> pdb=" O SER O 119 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA O 126 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 154 removed outlier: 3.559A pdb=" N ARG O 150 " --> pdb=" O ASN O 146 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 258 removed outlier: 3.511A pdb=" N ILE O 251 " --> pdb=" O ARG O 247 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA O 254 " --> pdb=" O ALA O 250 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN O 257 " --> pdb=" O SER O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 261 through 273 removed outlier: 3.589A pdb=" N ILE O 266 " --> pdb=" O THR O 262 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL O 267 " --> pdb=" O SER O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 296 removed outlier: 3.688A pdb=" N PHE O 294 " --> pdb=" O SER O 290 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG O 295 " --> pdb=" O ASN O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 314 Processing helix chain 'O' and resid 339 through 358 removed outlier: 3.919A pdb=" N VAL O 353 " --> pdb=" O THR O 349 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL O 354 " --> pdb=" O LEU O 350 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN O 355 " --> pdb=" O GLU O 351 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU O 356 " --> pdb=" O SER O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 371 removed outlier: 4.031A pdb=" N ILE O 365 " --> pdb=" O ARG O 361 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU O 370 " --> pdb=" O PHE O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 377 through 383 Processing helix chain 'O' and resid 391 through 399 removed outlier: 4.347A pdb=" N MET O 398 " --> pdb=" O MET O 394 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU O 399 " --> pdb=" O LEU O 395 " (cutoff:3.500A) Processing helix chain 'O' and resid 417 through 419 No H-bonds generated for 'chain 'O' and resid 417 through 419' Processing helix chain 'O' and resid 428 through 456 removed outlier: 3.794A pdb=" N LYS O 441 " --> pdb=" O HIS O 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 458 through 472 removed outlier: 3.625A pdb=" N GLU O 462 " --> pdb=" O LYS O 458 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 481 through 483 No H-bonds generated for 'chain 'O' and resid 481 through 483' Processing helix chain 'O' and resid 491 through 493 No H-bonds generated for 'chain 'O' and resid 491 through 493' Processing helix chain 'O' and resid 495 through 529 removed outlier: 3.529A pdb=" N LEU O 499 " --> pdb=" O ARG O 496 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU O 500 " --> pdb=" O GLN O 497 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG O 504 " --> pdb=" O THR O 501 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL O 506 " --> pdb=" O LYS O 503 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN O 507 " --> pdb=" O ARG O 504 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP O 510 " --> pdb=" O ASN O 507 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER O 512 " --> pdb=" O LEU O 509 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN O 515 " --> pdb=" O SER O 512 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL O 516 " --> pdb=" O GLU O 513 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE O 521 " --> pdb=" O GLU O 518 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU O 524 " --> pdb=" O PHE O 521 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER O 525 " --> pdb=" O LEU O 522 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU O 528 " --> pdb=" O SER O 525 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS O 529 " --> pdb=" O TYR O 526 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 196 removed outlier: 3.649A pdb=" N GLU P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU P 180 " --> pdb=" O PHE P 176 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN P 182 " --> pdb=" O GLU P 178 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE P 185 " --> pdb=" O ASN P 181 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS P 186 " --> pdb=" O GLN P 182 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE P 187 " --> pdb=" O GLN P 183 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS P 191 " --> pdb=" O PHE P 187 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA P 192 " --> pdb=" O LEU P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 209 removed outlier: 3.516A pdb=" N ASN P 207 " --> pdb=" O MET P 203 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 223 removed outlier: 3.509A pdb=" N ILE P 220 " --> pdb=" O VAL P 216 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS P 221 " --> pdb=" O TRP P 217 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU P 222 " --> pdb=" O LYS P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 244 removed outlier: 4.063A pdb=" N THR P 237 " --> pdb=" O GLU P 233 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN P 240 " --> pdb=" O GLU P 236 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR P 241 " --> pdb=" O THR P 237 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU P 242 " --> pdb=" O ILE P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 289 Processing helix chain 'P' and resid 293 through 295 No H-bonds generated for 'chain 'P' and resid 293 through 295' Processing helix chain 'P' and resid 304 through 306 No H-bonds generated for 'chain 'P' and resid 304 through 306' Processing helix chain 'P' and resid 308 through 313 removed outlier: 3.506A pdb=" N TRP P 313 " --> pdb=" O TYR P 309 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 19 No H-bonds generated for 'chain 'Q' and resid 16 through 19' Processing helix chain 'Q' and resid 54 through 68 removed outlier: 3.632A pdb=" N LEU Q 58 " --> pdb=" O GLU Q 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG Q 65 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU Q 66 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 89 No H-bonds generated for 'chain 'Q' and resid 87 through 89' Processing helix chain 'Q' and resid 108 through 110 No H-bonds generated for 'chain 'Q' and resid 108 through 110' Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.613A pdb=" N GLY A 84 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.505A pdb=" N LYS A 167 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 174 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 364 through 368 Processing sheet with id= E, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.055A pdb=" N PHE A 486 " --> pdb=" O SER A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.122A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 617 through 620 Processing sheet with id= H, first strand: chain 'A' and resid 1085 through 1087 removed outlier: 3.650A pdb=" N ARG A1209 " --> pdb=" O GLU A1228 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1172 through 1175 removed outlier: 3.941A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 64 through 66 removed outlier: 6.982A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.736A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'B' and resid 181 through 184 Processing sheet with id= N, first strand: chain 'B' and resid 190 through 193 removed outlier: 3.531A pdb=" N THR B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 212 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 573 through 577 removed outlier: 6.355A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 547 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 593 through 597 Processing sheet with id= Q, first strand: chain 'B' and resid 709 through 712 removed outlier: 3.958A pdb=" N LYS B 868 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 886 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE B 866 " --> pdb=" O ARG B 886 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 737 through 743 removed outlier: 4.423A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 831 through 833 Processing sheet with id= T, first strand: chain 'B' and resid 1074 through 1080 Processing sheet with id= U, first strand: chain 'B' and resid 110 through 115 removed outlier: 3.709A pdb=" N GLY B 134 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 115 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 755 through 758 removed outlier: 7.495A pdb=" N LEU B 757 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ILE B 910 " --> pdb=" O LEU B 757 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 50 through 57 removed outlier: 6.869A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 232 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 230 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= Y, first strand: chain 'C' and resid 143 through 145 Processing sheet with id= Z, first strand: chain 'C' and resid 262 through 266 Processing sheet with id= AA, first strand: chain 'C' and resid 86 through 94 removed outlier: 6.600A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 72 through 75 removed outlier: 7.145A pdb=" N ARG E 101 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N PHE E 75 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU E 103 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 126 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE E 104 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU E 128 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL E 106 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE E 130 " --> pdb=" O VAL E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.938A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 105 through 109 Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 13 Processing sheet with id= AF, first strand: chain 'G' and resid 37 through 39 removed outlier: 4.031A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 84 through 87 removed outlier: 6.771A pdb=" N VAL G 187 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU G 155 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR G 185 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE G 107 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY G 91 " --> pdb=" O HIS G 98 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER G 100 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE G 89 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.893A pdb=" N HIS G 71 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 25 through 31 removed outlier: 3.511A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 13 through 16 Processing sheet with id= AK, first strand: chain 'I' and resid 77 through 82 removed outlier: 3.558A pdb=" N TYR I 95 " --> pdb=" O TRP I 106 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP I 106 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS I 97 " --> pdb=" O HIS I 104 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS I 104 " --> pdb=" O CYS I 97 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 27 through 31 Processing sheet with id= AM, first strand: chain 'L' and resid 17 through 19 Processing sheet with id= AN, first strand: chain 'M' and resid 14 through 17 Processing sheet with id= AO, first strand: chain 'M' and resid 26 through 29 removed outlier: 7.184A pdb=" N GLY M 131 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLN M 29 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU M 133 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL M 56 " --> pdb=" O SER M 104 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS M 55 " --> pdb=" O LYS M 50 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER M 46 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA M 47 " --> pdb=" O LEU M 208 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 318 through 321 Processing sheet with id= AQ, first strand: chain 'M' and resid 390 through 392 Processing sheet with id= AR, first strand: chain 'N' and resid 328 through 331 removed outlier: 5.245A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N LEU N 266 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS N 382 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE N 268 " --> pdb=" O LYS N 382 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL N 384 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN N 270 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N SER N 386 " --> pdb=" O GLN N 270 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'N' and resid 359 through 364 removed outlier: 3.665A pdb=" N GLY N 377 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER N 362 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL N 375 " --> pdb=" O SER N 362 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY N 364 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N MET N 373 " --> pdb=" O GLY N 364 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'O' and resid 63 through 67 removed outlier: 3.561A pdb=" N GLU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'O' and resid 157 through 159 Processing sheet with id= AV, first strand: chain 'P' and resid 251 through 254 1170 hydrogen bonds defined for protein. 3231 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.83 Time building geometry restraints manager: 16.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 17702 1.43 - 1.64: 25250 1.64 - 1.85: 446 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 43410 Sorted by residual: bond pdb=" CA TYR A1187 " pdb=" C TYR A1187 " ideal model delta sigma weight residual 1.523 1.619 -0.096 1.34e-02 5.57e+03 5.13e+01 bond pdb=" C ILE B 392 " pdb=" N PRO B 393 " ideal model delta sigma weight residual 1.337 1.391 -0.055 1.06e-02 8.90e+03 2.65e+01 bond pdb=" C LYS D 55 " pdb=" N THR D 56 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.48e-02 4.57e+03 7.71e+00 bond pdb=" C GLN G 116 " pdb=" N PRO G 117 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.11e-02 8.12e+03 7.54e+00 bond pdb=" C GLN B 716 " pdb=" N LYS B 717 " ideal model delta sigma weight residual 1.329 1.283 0.046 1.86e-02 2.89e+03 6.03e+00 ... (remaining 43405 not shown) Histogram of bond angle deviations from ideal: 73.55 - 86.27: 12 86.27 - 98.98: 15 98.98 - 111.70: 20559 111.70 - 124.42: 37324 124.42 - 137.13: 892 Bond angle restraints: 58802 Sorted by residual: angle pdb=" C LEU B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta sigma weight residual 121.97 137.13 -15.16 1.80e+00 3.09e-01 7.10e+01 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 109.34 120.01 -10.67 2.08e+00 2.31e-01 2.63e+01 angle pdb=" N ILE A1153 " pdb=" CA ILE A1153 " pdb=" C ILE A1153 " ideal model delta sigma weight residual 110.05 104.60 5.45 1.09e+00 8.42e-01 2.50e+01 angle pdb=" C ASN B 52 " pdb=" N VAL B 53 " pdb=" CA VAL B 53 " ideal model delta sigma weight residual 122.77 117.70 5.07 1.05e+00 9.07e-01 2.34e+01 angle pdb=" C ILE A1153 " pdb=" N CYS A1154 " pdb=" CA CYS A1154 " ideal model delta sigma weight residual 122.74 129.52 -6.78 1.44e+00 4.82e-01 2.21e+01 ... (remaining 58797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.35: 26098 30.35 - 60.69: 456 60.69 - 91.04: 36 91.04 - 121.38: 0 121.38 - 151.73: 2 Dihedral angle restraints: 26592 sinusoidal: 11359 harmonic: 15233 Sorted by residual: dihedral pdb=" CA LEU B 39 " pdb=" C LEU B 39 " pdb=" N VAL B 40 " pdb=" CA VAL B 40 " ideal model delta harmonic sigma weight residual 180.00 -128.50 -51.50 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA ARG A 464 " pdb=" C ARG A 464 " pdb=" N GLN A 465 " pdb=" CA GLN A 465 " ideal model delta harmonic sigma weight residual 180.00 -150.19 -29.81 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ARG E 52 " pdb=" C ARG E 52 " pdb=" N PRO E 53 " pdb=" CA PRO E 53 " ideal model delta harmonic sigma weight residual 180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 26589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5533 0.075 - 0.150: 985 0.150 - 0.225: 77 0.225 - 0.301: 11 0.301 - 0.376: 2 Chirality restraints: 6608 Sorted by residual: chirality pdb=" CA ALA G 137 " pdb=" N ALA G 137 " pdb=" C ALA G 137 " pdb=" CB ALA G 137 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE A 473 " pdb=" CA ILE A 473 " pdb=" CG1 ILE A 473 " pdb=" CG2 ILE A 473 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C3' A R 14 " pdb=" C4' A R 14 " pdb=" O3' A R 14 " pdb=" C2' A R 14 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 6605 not shown) Planarity restraints: 7427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN M 281 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLN M 281 " -0.057 2.00e-02 2.50e+03 pdb=" O GLN M 281 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE M 282 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1003 " -0.027 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR B1003 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B1003 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B1003 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B1003 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B1003 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B1003 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1003 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 467 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO B 468 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 468 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 468 " 0.041 5.00e-02 4.00e+02 ... (remaining 7424 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 19 2.33 - 2.97: 18419 2.97 - 3.62: 59905 3.62 - 4.26: 96338 4.26 - 4.90: 158508 Nonbonded interactions: 333189 Sorted by model distance: nonbonded pdb=" O3' G R 19 " pdb="MG MG R 101 " model vdw 1.688 2.170 nonbonded pdb=" OD1 ASP A 501 " pdb="MG MG R 101 " model vdw 1.851 2.170 nonbonded pdb=" OD2 ASP A 499 " pdb="MG MG R 101 " model vdw 1.980 2.170 nonbonded pdb=" O TYR B 618 " pdb=" OG SER M 269 " model vdw 2.252 2.440 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG R 101 " model vdw 2.264 2.170 ... (remaining 333184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 10.380 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 111.230 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.008 0.112 43410 Z= 0.527 Angle : 0.971 15.163 58802 Z= 0.548 Chirality : 0.057 0.376 6608 Planarity : 0.007 0.075 7427 Dihedral : 11.227 151.727 16742 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 0.37 % Allowed : 2.75 % Favored : 96.88 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.09), residues: 5180 helix: -3.46 (0.08), residues: 1758 sheet: -2.02 (0.17), residues: 704 loop : -2.22 (0.10), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP N 123 HIS 0.013 0.003 HIS A 415 PHE 0.034 0.003 PHE M 400 TYR 0.054 0.003 TYR B1003 ARG 0.026 0.001 ARG M 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 668 time to evaluate : 4.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 ILE cc_start: 0.8321 (mt) cc_final: 0.8110 (mm) REVERT: D 5 ASP cc_start: 0.8354 (t0) cc_final: 0.7991 (t0) REVERT: D 17 PHE cc_start: 0.8812 (t80) cc_final: 0.8607 (t80) REVERT: D 18 GLN cc_start: 0.8976 (tt0) cc_final: 0.8613 (pt0) REVERT: D 47 TYR cc_start: 0.8719 (t80) cc_final: 0.8488 (t80) REVERT: D 76 HIS cc_start: 0.7927 (m-70) cc_final: 0.7706 (m-70) REVERT: E 36 THR cc_start: 0.7783 (m) cc_final: 0.7579 (p) REVERT: F 121 ASP cc_start: 0.8017 (p0) cc_final: 0.7791 (m-30) REVERT: G 90 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8409 (mtpt) REVERT: I 39 THR cc_start: 0.4789 (p) cc_final: 0.4421 (m) REVERT: K 119 LYS cc_start: 0.9304 (ttpt) cc_final: 0.9025 (ttpp) REVERT: L 37 ARG cc_start: 0.8204 (tmm160) cc_final: 0.7959 (ptt90) REVERT: M 139 PHE cc_start: 0.7407 (m-80) cc_final: 0.7128 (m-10) REVERT: M 338 SER cc_start: -0.0613 (OUTLIER) cc_final: -0.0909 (p) REVERT: N 375 VAL cc_start: 0.8452 (t) cc_final: 0.8194 (m) REVERT: Q 87 TYR cc_start: 0.7433 (t80) cc_final: 0.6354 (t80) REVERT: Q 91 TYR cc_start: 0.6964 (m-10) cc_final: 0.6632 (m-80) outliers start: 17 outliers final: 3 residues processed: 683 average time/residue: 0.5801 time to fit residues: 632.9750 Evaluate side-chains 345 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 341 time to evaluate : 4.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain M residue 338 SER Chi-restraints excluded: chain M residue 341 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 436 optimal weight: 10.0000 chunk 391 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 264 optimal weight: 0.7980 chunk 209 optimal weight: 0.7980 chunk 405 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 301 optimal weight: 4.9990 chunk 469 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 82 HIS A 158 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 316 GLN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS A 599 GLN A 616 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN A1180 ASN A1202 GLN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 ASN B 320 HIS B 346 GLN B 501 HIS B 602 GLN B 677 HIS B 683 ASN B 758 ASN B 901 HIS B 903 GLN B1100 HIS ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS E 148 HIS H 44 ASN H 76 ASN I 10 ASN ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS M 76 GLN M 125 HIS ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 HIS N 111 GLN N 395 HIS O 146 ASN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 GLN O 339 HIS O 377 GLN P 200 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 43410 Z= 0.263 Angle : 0.662 12.336 58802 Z= 0.341 Chirality : 0.045 0.333 6608 Planarity : 0.005 0.063 7427 Dihedral : 10.048 153.458 6185 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.56 % Rotamer: Outliers : 1.82 % Allowed : 7.03 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.10), residues: 5180 helix: -1.70 (0.11), residues: 1770 sheet: -1.30 (0.18), residues: 699 loop : -1.55 (0.11), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 123 HIS 0.010 0.001 HIS I 21 PHE 0.034 0.002 PHE A 312 TYR 0.037 0.002 TYR P 270 ARG 0.008 0.001 ARG Q 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 362 time to evaluate : 5.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.8713 (mtp) cc_final: 0.8434 (mtm) REVERT: A 912 MET cc_start: 0.7582 (mmm) cc_final: 0.6952 (mmm) REVERT: A 1048 MET cc_start: 0.8238 (ptt) cc_final: 0.7806 (ptt) REVERT: A 1101 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8068 (p) REVERT: A 1308 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8754 (tt) REVERT: B 653 ASP cc_start: 0.6858 (m-30) cc_final: 0.6569 (p0) REVERT: B 689 MET cc_start: 0.7656 (mmp) cc_final: 0.7351 (mmp) REVERT: B 1020 MET cc_start: 0.8721 (ttp) cc_final: 0.8519 (ttp) REVERT: B 1069 MET cc_start: 0.8402 (tpp) cc_final: 0.8183 (tpt) REVERT: C 98 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8848 (p) REVERT: D 5 ASP cc_start: 0.8419 (t0) cc_final: 0.8066 (t0) REVERT: D 112 GLN cc_start: 0.8865 (mt0) cc_final: 0.8544 (mt0) REVERT: E 36 THR cc_start: 0.8022 (m) cc_final: 0.7787 (p) REVERT: E 55 ARG cc_start: 0.7542 (mpt90) cc_final: 0.6711 (tmm160) REVERT: G 90 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8732 (mtpt) REVERT: G 142 MET cc_start: 0.8498 (tpp) cc_final: 0.7968 (tpp) REVERT: L 27 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7654 (tm-30) REVERT: N 116 MET cc_start: 0.8655 (tmm) cc_final: 0.8170 (tmm) REVERT: P 244 TYR cc_start: 0.7692 (m-80) cc_final: 0.7462 (m-80) REVERT: Q 69 LYS cc_start: 0.9443 (mtmt) cc_final: 0.9103 (mttp) REVERT: Q 82 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7489 (tm-30) REVERT: Q 87 TYR cc_start: 0.7008 (t80) cc_final: 0.6469 (t80) REVERT: Q 104 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.8151 (mtm-85) outliers start: 84 outliers final: 49 residues processed: 428 average time/residue: 0.5348 time to fit residues: 380.4814 Evaluate side-chains 359 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 307 time to evaluate : 5.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 321 LEU Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 187 MET Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain Q residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 260 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 390 optimal weight: 2.9990 chunk 319 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 chunk 508 optimal weight: 6.9990 chunk 418 optimal weight: 20.0000 chunk 466 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 377 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 ASN A 314 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 ASN A 836 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 932 HIS ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS ** I 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 412 HIS N 122 ASN N 338 GLN N 395 HIS O 155 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 515 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 43410 Z= 0.487 Angle : 0.795 11.891 58802 Z= 0.406 Chirality : 0.049 0.258 6608 Planarity : 0.006 0.069 7427 Dihedral : 10.140 152.362 6184 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.79 % Favored : 95.17 % Rotamer: Outliers : 2.77 % Allowed : 8.50 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5180 helix: -0.65 (0.12), residues: 1789 sheet: -1.12 (0.18), residues: 718 loop : -1.18 (0.11), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 423 HIS 0.019 0.002 HIS I 21 PHE 0.032 0.003 PHE B 326 TYR 0.042 0.003 TYR B 357 ARG 0.011 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 284 time to evaluate : 5.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8261 (pm20) REVERT: A 312 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8082 (t80) REVERT: A 332 MET cc_start: 0.6689 (mmp) cc_final: 0.6487 (mmm) REVERT: A 1167 VAL cc_start: 0.8368 (m) cc_final: 0.8018 (t) REVERT: A 1382 ASN cc_start: 0.8607 (t0) cc_final: 0.8038 (p0) REVERT: B 689 MET cc_start: 0.8209 (mmp) cc_final: 0.7816 (mmp) REVERT: B 719 MET cc_start: 0.9021 (mmm) cc_final: 0.8738 (tpp) REVERT: B 755 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9114 (pp) REVERT: B 1069 MET cc_start: 0.8633 (tpp) cc_final: 0.7624 (tpt) REVERT: C 98 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8824 (p) REVERT: D 5 ASP cc_start: 0.8576 (t0) cc_final: 0.8227 (t0) REVERT: E 36 THR cc_start: 0.8671 (m) cc_final: 0.8398 (p) REVERT: E 94 MET cc_start: 0.7641 (ttt) cc_final: 0.7075 (ttt) REVERT: E 152 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8730 (p) REVERT: G 131 TYR cc_start: 0.7269 (t80) cc_final: 0.6950 (t80) REVERT: G 142 MET cc_start: 0.8909 (tpp) cc_final: 0.8659 (tpp) REVERT: G 180 LYS cc_start: 0.7629 (mmmt) cc_final: 0.7353 (tptp) REVERT: H 37 MET cc_start: 0.8835 (mmt) cc_final: 0.8465 (mmt) REVERT: I 82 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8174 (tp) REVERT: L 30 SER cc_start: 0.8872 (m) cc_final: 0.8636 (p) REVERT: M 235 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8266 (m-40) REVERT: N 256 ARG cc_start: 0.7725 (ptp-170) cc_final: 0.7174 (ptt90) REVERT: O 270 MET cc_start: 0.9444 (OUTLIER) cc_final: 0.8974 (mpp) REVERT: O 474 MET cc_start: -0.1078 (tmm) cc_final: -0.1691 (ptt) REVERT: P 310 MET cc_start: 0.8780 (mmt) cc_final: 0.8489 (mmt) REVERT: Q 29 ASP cc_start: 0.7667 (m-30) cc_final: 0.7444 (t0) REVERT: Q 69 LYS cc_start: 0.9512 (mtmt) cc_final: 0.9244 (mttp) REVERT: Q 82 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7882 (tm-30) REVERT: Q 87 TYR cc_start: 0.7545 (t80) cc_final: 0.7028 (t80) outliers start: 128 outliers final: 56 residues processed: 384 average time/residue: 0.5361 time to fit residues: 348.8290 Evaluate side-chains 318 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 254 time to evaluate : 4.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 MET Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 70 CYS Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 397 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 270 MET Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 177 VAL Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 108 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 464 optimal weight: 20.0000 chunk 353 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 472 optimal weight: 4.9990 chunk 499 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 447 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 HIS ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS I 61 ASN ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 43410 Z= 0.164 Angle : 0.547 13.511 58802 Z= 0.277 Chirality : 0.042 0.198 6608 Planarity : 0.004 0.055 7427 Dihedral : 9.784 151.738 6182 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.56 % Allowed : 9.84 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.11), residues: 5180 helix: 0.04 (0.13), residues: 1784 sheet: -0.75 (0.18), residues: 715 loop : -0.98 (0.12), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 123 HIS 0.006 0.001 HIS I 32 PHE 0.016 0.001 PHE A 462 TYR 0.017 0.001 TYR I 30 ARG 0.010 0.000 ARG M 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 278 time to evaluate : 4.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8370 (t80) REVERT: A 332 MET cc_start: 0.7304 (mmp) cc_final: 0.6388 (mmm) REVERT: A 1167 VAL cc_start: 0.8185 (m) cc_final: 0.7904 (t) REVERT: A 1382 ASN cc_start: 0.8561 (t0) cc_final: 0.8067 (p0) REVERT: B 719 MET cc_start: 0.8847 (mmm) cc_final: 0.8553 (tpp) REVERT: B 755 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8987 (pp) REVERT: B 1020 MET cc_start: 0.9000 (ttp) cc_final: 0.8783 (ttp) REVERT: B 1069 MET cc_start: 0.8608 (tpp) cc_final: 0.8024 (tpt) REVERT: C 98 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8879 (p) REVERT: D 5 ASP cc_start: 0.8590 (t0) cc_final: 0.8218 (t0) REVERT: D 14 TYR cc_start: 0.7595 (t80) cc_final: 0.6568 (t80) REVERT: E 36 THR cc_start: 0.8696 (m) cc_final: 0.8396 (p) REVERT: E 94 MET cc_start: 0.7526 (ttt) cc_final: 0.7044 (ttt) REVERT: G 7 MET cc_start: 0.8130 (pmm) cc_final: 0.7805 (pmm) REVERT: I 1 MET cc_start: 0.5496 (pmm) cc_final: 0.4915 (pmm) REVERT: N 139 ASN cc_start: 0.7955 (p0) cc_final: 0.7737 (p0) REVERT: N 256 ARG cc_start: 0.7650 (ptp-170) cc_final: 0.7404 (ptp-170) REVERT: O 531 MET cc_start: 0.7357 (mmp) cc_final: 0.7059 (mmm) REVERT: P 250 MET cc_start: 0.8273 (mmm) cc_final: 0.8070 (mmm) REVERT: P 310 MET cc_start: 0.8686 (mmt) cc_final: 0.7808 (mpp) REVERT: Q 69 LYS cc_start: 0.9494 (mtmt) cc_final: 0.9167 (mttp) REVERT: Q 82 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7887 (tm-30) REVERT: Q 87 TYR cc_start: 0.7338 (t80) cc_final: 0.6675 (t80) outliers start: 72 outliers final: 41 residues processed: 334 average time/residue: 0.5064 time to fit residues: 288.2841 Evaluate side-chains 294 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 250 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain I residue 91 MET Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 416 optimal weight: 2.9990 chunk 283 optimal weight: 0.0270 chunk 7 optimal weight: 8.9990 chunk 372 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 426 optimal weight: 4.9990 chunk 345 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 448 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 43410 Z= 0.269 Angle : 0.578 12.778 58802 Z= 0.292 Chirality : 0.043 0.235 6608 Planarity : 0.004 0.049 7427 Dihedral : 9.647 151.061 6180 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 2.10 % Allowed : 10.08 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.12), residues: 5180 helix: 0.36 (0.13), residues: 1808 sheet: -0.61 (0.19), residues: 728 loop : -0.80 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 123 HIS 0.008 0.001 HIS A 415 PHE 0.019 0.001 PHE B 326 TYR 0.024 0.001 TYR B 357 ARG 0.005 0.000 ARG M 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 255 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 MET cc_start: 0.8311 (mmt) cc_final: 0.8110 (mmt) REVERT: A 953 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8556 (mtt) REVERT: A 1280 MET cc_start: 0.7915 (mpp) cc_final: 0.7607 (mpp) REVERT: A 1382 ASN cc_start: 0.8521 (t0) cc_final: 0.8022 (p0) REVERT: B 719 MET cc_start: 0.8911 (mmm) cc_final: 0.8604 (tpp) REVERT: B 755 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9052 (pp) REVERT: B 1020 MET cc_start: 0.9111 (ttp) cc_final: 0.8897 (ttp) REVERT: C 98 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8902 (p) REVERT: D 5 ASP cc_start: 0.8642 (t0) cc_final: 0.8283 (t0) REVERT: D 67 ARG cc_start: 0.8854 (mmt-90) cc_final: 0.8650 (mmt-90) REVERT: E 94 MET cc_start: 0.7973 (ttt) cc_final: 0.7720 (ttt) REVERT: G 7 MET cc_start: 0.8130 (pmm) cc_final: 0.7773 (pmm) REVERT: I 1 MET cc_start: 0.5591 (pmm) cc_final: 0.5068 (pmm) REVERT: N 256 ARG cc_start: 0.7829 (ptp-170) cc_final: 0.7563 (ptp-170) REVERT: O 187 MET cc_start: 0.8559 (ptm) cc_final: 0.8280 (tmm) REVERT: O 270 MET cc_start: 0.9258 (mpp) cc_final: 0.8948 (mpp) REVERT: O 531 MET cc_start: 0.7709 (mmp) cc_final: 0.7410 (mmm) REVERT: Q 69 LYS cc_start: 0.9505 (mtmt) cc_final: 0.9159 (mttp) REVERT: Q 82 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7929 (tm-30) REVERT: Q 87 TYR cc_start: 0.7283 (t80) cc_final: 0.7009 (t80) REVERT: Q 111 MET cc_start: 0.8460 (mmp) cc_final: 0.7903 (mmp) outliers start: 97 outliers final: 58 residues processed: 324 average time/residue: 0.5183 time to fit residues: 284.6087 Evaluate side-chains 309 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 248 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 953 MET Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1300 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 91 MET Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain P residue 294 ASP Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 108 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 168 optimal weight: 0.9980 chunk 450 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 500 optimal weight: 20.0000 chunk 415 optimal weight: 40.0000 chunk 231 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 165 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 395 ASN N 395 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 534 GLN P 207 ASN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.7201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 43410 Z= 0.319 Angle : 0.601 12.789 58802 Z= 0.304 Chirality : 0.043 0.174 6608 Planarity : 0.004 0.192 7427 Dihedral : 9.701 150.297 6180 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 1.73 % Allowed : 10.82 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 5180 helix: 0.55 (0.13), residues: 1820 sheet: -0.64 (0.19), residues: 731 loop : -0.75 (0.12), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 123 HIS 0.015 0.001 HIS M 207 PHE 0.023 0.001 PHE B 326 TYR 0.025 0.001 TYR B 357 ARG 0.026 0.000 ARG P 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 248 time to evaluate : 5.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8395 (t80) REVERT: A 332 MET cc_start: 0.7730 (mmp) cc_final: 0.6650 (mmm) REVERT: A 737 GLN cc_start: 0.8126 (tp40) cc_final: 0.7376 (pp30) REVERT: A 1275 MET cc_start: 0.8822 (mmm) cc_final: 0.8610 (mmm) REVERT: A 1382 ASN cc_start: 0.8473 (t0) cc_final: 0.8001 (p0) REVERT: B 59 MET cc_start: 0.8509 (tmm) cc_final: 0.8296 (ppp) REVERT: B 719 MET cc_start: 0.8969 (mmm) cc_final: 0.8659 (tpp) REVERT: B 755 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9058 (pp) REVERT: B 1020 MET cc_start: 0.9139 (ttp) cc_final: 0.8904 (ttp) REVERT: C 98 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8855 (p) REVERT: C 173 MET cc_start: 0.8817 (mmm) cc_final: 0.8452 (mtp) REVERT: C 279 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7565 (ttm-80) REVERT: D 1 MET cc_start: 0.8157 (tmm) cc_final: 0.7929 (tmm) REVERT: D 5 ASP cc_start: 0.8663 (t0) cc_final: 0.8286 (t0) REVERT: D 67 ARG cc_start: 0.8816 (mmt-90) cc_final: 0.8603 (mmt-90) REVERT: E 18 MET cc_start: 0.9213 (mmm) cc_final: 0.8952 (mmm) REVERT: E 94 MET cc_start: 0.8171 (ttt) cc_final: 0.7962 (ttt) REVERT: E 121 MET cc_start: 0.8580 (ppp) cc_final: 0.8018 (ppp) REVERT: G 7 MET cc_start: 0.8267 (pmm) cc_final: 0.7987 (pmm) REVERT: I 1 MET cc_start: 0.5543 (pmm) cc_final: 0.5322 (pmm) REVERT: J 31 GLU cc_start: 0.8856 (mp0) cc_final: 0.8608 (mp0) REVERT: L 44 MET cc_start: 0.8999 (mmt) cc_final: 0.8474 (mmt) REVERT: M 286 MET cc_start: 0.3442 (pmm) cc_final: 0.3216 (tpt) REVERT: M 341 HIS cc_start: 0.4846 (OUTLIER) cc_final: 0.4495 (p90) REVERT: N 256 ARG cc_start: 0.7852 (ptp-170) cc_final: 0.7617 (ptp-170) REVERT: O 118 MET cc_start: 0.9086 (tpt) cc_final: 0.8844 (tpt) REVERT: O 270 MET cc_start: 0.9293 (mpp) cc_final: 0.8870 (mpp) REVERT: O 398 MET cc_start: 0.8003 (mmm) cc_final: 0.7613 (mmp) REVERT: O 474 MET cc_start: -0.1299 (tmm) cc_final: -0.2891 (ptt) REVERT: O 531 MET cc_start: 0.8156 (mmp) cc_final: 0.7881 (mmm) REVERT: P 203 MET cc_start: 0.8866 (tpt) cc_final: 0.8651 (mmt) REVERT: Q 69 LYS cc_start: 0.9503 (mtmt) cc_final: 0.9296 (mttp) REVERT: Q 82 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8087 (tm-30) REVERT: Q 87 TYR cc_start: 0.7168 (t80) cc_final: 0.6830 (t80) REVERT: Q 111 MET cc_start: 0.8575 (mmp) cc_final: 0.8071 (mmp) outliers start: 80 outliers final: 58 residues processed: 310 average time/residue: 0.5064 time to fit residues: 268.9400 Evaluate side-chains 300 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 237 time to evaluate : 4.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 MET Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 482 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 283 optimal weight: 0.0980 chunk 421 optimal weight: 6.9990 chunk 279 optimal weight: 4.9990 chunk 498 optimal weight: 0.0470 chunk 311 optimal weight: 5.9990 chunk 303 optimal weight: 8.9990 chunk 230 optimal weight: 5.9990 overall best weight: 2.8284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 395 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 ASN P 240 ASN P 297 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 43410 Z= 0.241 Angle : 0.547 12.876 58802 Z= 0.276 Chirality : 0.042 0.162 6608 Planarity : 0.003 0.054 7427 Dihedral : 9.581 149.718 6180 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 1.88 % Allowed : 10.73 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 5180 helix: 0.76 (0.13), residues: 1814 sheet: -0.48 (0.19), residues: 727 loop : -0.62 (0.12), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 123 HIS 0.006 0.001 HIS A 415 PHE 0.016 0.001 PHE B 326 TYR 0.022 0.001 TYR E 8 ARG 0.007 0.000 ARG P 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 247 time to evaluate : 4.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7710 (m) REVERT: A 912 MET cc_start: 0.9091 (mmp) cc_final: 0.8817 (mmm) REVERT: A 1382 ASN cc_start: 0.8500 (t0) cc_final: 0.8057 (p0) REVERT: B 59 MET cc_start: 0.8575 (tmm) cc_final: 0.8317 (ppp) REVERT: B 719 MET cc_start: 0.8916 (mmm) cc_final: 0.8596 (tpp) REVERT: B 755 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9036 (pp) REVERT: B 1020 MET cc_start: 0.9144 (ttp) cc_final: 0.8907 (ttp) REVERT: C 98 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8873 (p) REVERT: C 173 MET cc_start: 0.8862 (mmm) cc_final: 0.8391 (mtp) REVERT: C 279 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7366 (ttm-80) REVERT: D 5 ASP cc_start: 0.8613 (t0) cc_final: 0.8277 (t0) REVERT: D 67 ARG cc_start: 0.8772 (mmt-90) cc_final: 0.8539 (mmt-90) REVERT: E 121 MET cc_start: 0.8522 (ppp) cc_final: 0.7855 (ppp) REVERT: G 7 MET cc_start: 0.8300 (pmm) cc_final: 0.8016 (pmm) REVERT: I 1 MET cc_start: 0.5509 (pmm) cc_final: 0.5287 (pmm) REVERT: M 289 VAL cc_start: 0.0237 (OUTLIER) cc_final: -0.1995 (p) REVERT: M 341 HIS cc_start: 0.4837 (OUTLIER) cc_final: 0.4591 (p-80) REVERT: N 256 ARG cc_start: 0.7840 (ptp-170) cc_final: 0.7581 (ptp-170) REVERT: O 187 MET cc_start: 0.8872 (ptm) cc_final: 0.8628 (tmm) REVERT: O 270 MET cc_start: 0.9217 (mpp) cc_final: 0.8731 (mpp) REVERT: O 398 MET cc_start: 0.8034 (mmm) cc_final: 0.7664 (mmp) REVERT: O 474 MET cc_start: -0.1300 (tmm) cc_final: -0.2437 (ptt) REVERT: O 531 MET cc_start: 0.8211 (mmp) cc_final: 0.7940 (mmm) REVERT: P 232 MET cc_start: 0.6953 (mmm) cc_final: 0.6219 (mmm) REVERT: Q 69 LYS cc_start: 0.9532 (mtmt) cc_final: 0.9307 (mttp) REVERT: Q 82 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8080 (tm-30) REVERT: Q 87 TYR cc_start: 0.7310 (t80) cc_final: 0.6999 (t80) REVERT: Q 111 MET cc_start: 0.8598 (mmp) cc_final: 0.8096 (mmp) outliers start: 87 outliers final: 62 residues processed: 317 average time/residue: 0.5102 time to fit residues: 274.7116 Evaluate side-chains 304 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 236 time to evaluate : 5.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 MET Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 136 HIS Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 92 MET Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 308 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 297 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 339 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 391 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 ASN A 794 GLN ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 296 ASN N 395 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.7720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 43410 Z= 0.294 Angle : 0.579 12.506 58802 Z= 0.291 Chirality : 0.043 0.163 6608 Planarity : 0.003 0.052 7427 Dihedral : 9.603 149.432 6180 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 1.86 % Allowed : 11.14 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.12), residues: 5180 helix: 0.80 (0.13), residues: 1827 sheet: -0.46 (0.19), residues: 733 loop : -0.62 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 217 HIS 0.008 0.001 HIS A1278 PHE 0.018 0.001 PHE B 326 TYR 0.027 0.001 TYR A 902 ARG 0.004 0.000 ARG M 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 236 time to evaluate : 5.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 VAL cc_start: 0.7935 (OUTLIER) cc_final: 0.7588 (m) REVERT: A 1382 ASN cc_start: 0.8468 (t0) cc_final: 0.8051 (p0) REVERT: B 59 MET cc_start: 0.8596 (tmm) cc_final: 0.8361 (ppp) REVERT: B 229 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9205 (t) REVERT: B 719 MET cc_start: 0.8961 (mmm) cc_final: 0.8641 (tpp) REVERT: B 755 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9021 (pp) REVERT: B 1020 MET cc_start: 0.9119 (ttp) cc_final: 0.8847 (ttp) REVERT: C 98 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 279 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7521 (ttm-80) REVERT: D 5 ASP cc_start: 0.8629 (t0) cc_final: 0.8352 (t0) REVERT: E 94 MET cc_start: 0.8821 (ttt) cc_final: 0.8584 (ttp) REVERT: G 7 MET cc_start: 0.8357 (pmm) cc_final: 0.8055 (pmm) REVERT: K 79 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8694 (mtmm) REVERT: M 341 HIS cc_start: 0.5024 (OUTLIER) cc_final: 0.4683 (p90) REVERT: N 256 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7615 (ptp-170) REVERT: O 270 MET cc_start: 0.9238 (mpp) cc_final: 0.8718 (mpp) REVERT: O 398 MET cc_start: 0.8056 (mmm) cc_final: 0.7719 (mmp) REVERT: O 474 MET cc_start: -0.1197 (tmm) cc_final: -0.2364 (ptt) REVERT: O 531 MET cc_start: 0.8294 (mmp) cc_final: 0.8042 (mmm) REVERT: P 217 TRP cc_start: 0.7804 (t60) cc_final: 0.7386 (t60) REVERT: Q 69 LYS cc_start: 0.9514 (mtmt) cc_final: 0.9294 (mttp) REVERT: Q 82 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8121 (tm-30) REVERT: Q 87 TYR cc_start: 0.7283 (t80) cc_final: 0.6970 (t80) REVERT: Q 111 MET cc_start: 0.8588 (mmp) cc_final: 0.8099 (mmp) outliers start: 86 outliers final: 65 residues processed: 302 average time/residue: 0.5066 time to fit residues: 262.0072 Evaluate side-chains 302 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 230 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 91 MET Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 92 MET Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 453 optimal weight: 10.0000 chunk 477 optimal weight: 9.9990 chunk 435 optimal weight: 4.9990 chunk 464 optimal weight: 20.0000 chunk 279 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 364 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 419 optimal weight: 6.9990 chunk 439 optimal weight: 9.9990 chunk 462 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 903 GLN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 GLN ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 HIS ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.8103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 43410 Z= 0.406 Angle : 0.652 12.108 58802 Z= 0.328 Chirality : 0.045 0.167 6608 Planarity : 0.004 0.051 7427 Dihedral : 9.797 148.560 6180 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.25 % Rotamer: Outliers : 1.86 % Allowed : 11.19 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.12), residues: 5180 helix: 0.71 (0.13), residues: 1837 sheet: -0.64 (0.18), residues: 753 loop : -0.71 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 106 HIS 0.008 0.001 HIS A 415 PHE 0.025 0.002 PHE O 148 TYR 0.027 0.002 TYR B 357 ARG 0.006 0.000 ARG M 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 236 time to evaluate : 4.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7611 (m) REVERT: A 1311 MET cc_start: 0.9104 (mtm) cc_final: 0.8790 (mtp) REVERT: A 1382 ASN cc_start: 0.8466 (t0) cc_final: 0.8129 (p0) REVERT: B 229 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.9222 (t) REVERT: B 719 MET cc_start: 0.9043 (mmm) cc_final: 0.8772 (tpp) REVERT: B 755 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9116 (pp) REVERT: B 1020 MET cc_start: 0.9143 (ttp) cc_final: 0.8869 (ttp) REVERT: C 98 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8804 (p) REVERT: C 279 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7583 (ttm-80) REVERT: D 5 ASP cc_start: 0.8640 (t0) cc_final: 0.8363 (t0) REVERT: D 47 TYR cc_start: 0.8833 (t80) cc_final: 0.8525 (t80) REVERT: E 94 MET cc_start: 0.8698 (ttt) cc_final: 0.8491 (ttp) REVERT: G 7 MET cc_start: 0.8419 (pmm) cc_final: 0.8122 (pmm) REVERT: H 37 MET cc_start: 0.8772 (mmt) cc_final: 0.8366 (mmt) REVERT: M 341 HIS cc_start: 0.5336 (OUTLIER) cc_final: 0.4986 (p90) REVERT: N 256 ARG cc_start: 0.7928 (ptp-170) cc_final: 0.7678 (ptp-170) REVERT: O 187 MET cc_start: 0.8835 (ptm) cc_final: 0.8568 (tmm) REVERT: O 270 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8478 (mpp) REVERT: O 398 MET cc_start: 0.8075 (mmm) cc_final: 0.7775 (mmp) REVERT: O 474 MET cc_start: -0.1066 (tmm) cc_final: -0.2093 (ptt) REVERT: O 531 MET cc_start: 0.8297 (mmp) cc_final: 0.8021 (mmm) REVERT: P 217 TRP cc_start: 0.7802 (t60) cc_final: 0.7432 (t60) REVERT: P 250 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8491 (tmm) REVERT: Q 69 LYS cc_start: 0.9502 (mtmt) cc_final: 0.9291 (mttp) REVERT: Q 82 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8229 (tm-30) REVERT: Q 87 TYR cc_start: 0.7294 (t80) cc_final: 0.6766 (t80) REVERT: Q 111 MET cc_start: 0.8564 (mmp) cc_final: 0.8073 (mmp) outliers start: 86 outliers final: 67 residues processed: 303 average time/residue: 0.5031 time to fit residues: 262.0171 Evaluate side-chains 303 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 228 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 91 MET Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 270 MET Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 250 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 304 optimal weight: 4.9990 chunk 491 optimal weight: 9.9990 chunk 299 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 341 optimal weight: 4.9990 chunk 515 optimal weight: 20.0000 chunk 474 optimal weight: 5.9990 chunk 410 optimal weight: 40.0000 chunk 42 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.8232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 43410 Z= 0.347 Angle : 0.611 13.369 58802 Z= 0.307 Chirality : 0.044 0.166 6608 Planarity : 0.004 0.058 7427 Dihedral : 9.756 148.061 6180 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 1.71 % Allowed : 11.40 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 5180 helix: 0.83 (0.13), residues: 1824 sheet: -0.60 (0.19), residues: 753 loop : -0.68 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 106 HIS 0.007 0.001 HIS A 415 PHE 0.019 0.001 PHE B 326 TYR 0.037 0.001 TYR A 902 ARG 0.009 0.000 ARG P 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10360 Ramachandran restraints generated. 5180 Oldfield, 0 Emsley, 5180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 228 time to evaluate : 5.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7637 (m) REVERT: A 1311 MET cc_start: 0.9072 (mtm) cc_final: 0.8761 (mtp) REVERT: A 1382 ASN cc_start: 0.8471 (t0) cc_final: 0.8115 (p0) REVERT: B 229 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.9256 (t) REVERT: B 719 MET cc_start: 0.9000 (mmm) cc_final: 0.8713 (tpp) REVERT: B 755 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9051 (pp) REVERT: B 1020 MET cc_start: 0.9137 (ttp) cc_final: 0.8832 (ttp) REVERT: C 98 THR cc_start: 0.9183 (OUTLIER) cc_final: 0.8895 (p) REVERT: C 279 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7414 (ttm-80) REVERT: D 5 ASP cc_start: 0.8653 (t0) cc_final: 0.8376 (t0) REVERT: D 47 TYR cc_start: 0.8817 (t80) cc_final: 0.8510 (t80) REVERT: E 94 MET cc_start: 0.8730 (ttt) cc_final: 0.8515 (ttp) REVERT: E 121 MET cc_start: 0.8425 (ppp) cc_final: 0.8085 (ppp) REVERT: G 7 MET cc_start: 0.8373 (pmm) cc_final: 0.8094 (pmm) REVERT: H 37 MET cc_start: 0.8860 (mmt) cc_final: 0.8444 (mmt) REVERT: I 97 CYS cc_start: 0.5190 (OUTLIER) cc_final: 0.4783 (t) REVERT: K 79 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8768 (mtmm) REVERT: M 341 HIS cc_start: 0.5284 (OUTLIER) cc_final: 0.4896 (p90) REVERT: N 256 ARG cc_start: 0.7878 (ptp-170) cc_final: 0.7639 (ptp-170) REVERT: O 139 MET cc_start: 0.7639 (tpp) cc_final: 0.7298 (tpp) REVERT: O 270 MET cc_start: 0.9060 (mpp) cc_final: 0.8393 (mpp) REVERT: O 474 MET cc_start: -0.0891 (tmm) cc_final: -0.2152 (ptt) REVERT: O 531 MET cc_start: 0.8292 (mmp) cc_final: 0.7780 (mmt) REVERT: P 217 TRP cc_start: 0.7765 (t60) cc_final: 0.7403 (t60) REVERT: P 250 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8520 (tmm) REVERT: Q 69 LYS cc_start: 0.9491 (mtmt) cc_final: 0.9253 (mttp) REVERT: Q 82 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8169 (tm-30) REVERT: Q 111 MET cc_start: 0.8581 (mmp) cc_final: 0.8098 (mmp) outliers start: 79 outliers final: 67 residues processed: 290 average time/residue: 0.5106 time to fit residues: 254.4509 Evaluate side-chains 301 residues out of total 4622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 225 time to evaluate : 4.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 91 MET Chi-restraints excluded: chain I residue 97 CYS Chi-restraints excluded: chain K residue 28 GLU Chi-restraints excluded: chain K residue 65 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 339 SER Chi-restraints excluded: chain M residue 341 HIS Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 349 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain O residue 79 CYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 349 THR Chi-restraints excluded: chain P residue 250 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 41 THR Chi-restraints excluded: chain Q residue 108 ARG Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 517 random chunks: chunk 325 optimal weight: 9.9990 chunk 436 optimal weight: 8.9990 chunk 125 optimal weight: 0.0970 chunk 378 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 410 optimal weight: 20.0000 chunk 171 optimal weight: 6.9990 chunk 421 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN ** A1385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.066421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.043682 restraints weight = 177092.957| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.71 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.8288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43410 Z= 0.177 Angle : 0.545 13.711 58802 Z= 0.272 Chirality : 0.042 0.163 6608 Planarity : 0.003 0.055 7427 Dihedral : 9.596 148.166 6180 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 1.41 % Allowed : 11.79 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 5180 helix: 1.07 (0.13), residues: 1822 sheet: -0.37 (0.19), residues: 731 loop : -0.59 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 123 HIS 0.005 0.001 HIS A 415 PHE 0.021 0.001 PHE P 210 TYR 0.044 0.001 TYR Q 87 ARG 0.004 0.000 ARG M 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8285.48 seconds wall clock time: 151 minutes 31.46 seconds (9091.46 seconds total)