Starting phenix.real_space_refine on Mon May 13 21:06:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/05_2024/8xcg_38242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/05_2024/8xcg_38242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/05_2024/8xcg_38242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/05_2024/8xcg_38242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/05_2024/8xcg_38242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xcg_38242/05_2024/8xcg_38242_updated.pdb" } resolution = 3.46 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= 0.004 sd= 0.067 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: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 138 5.16 5 C 16228 2.51 5 N 4523 2.21 5 O 5040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 99": "OE1" <-> "OE2" Residue "F ASP 40": "OD1" <-> "OD2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 180": "OD1" <-> "OD2" Residue "J ASP 16": "OD1" <-> "OD2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 362": "OD1" <-> "OD2" Residue "J PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 560": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "L ASP 3": "OD1" <-> "OD2" Residue "L ASP 27": "OD1" <-> "OD2" Residue "L PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 126": "OD1" <-> "OD2" Residue "L ASP 203": "OD1" <-> "OD2" Residue "M ASP 27": "OD1" <-> "OD2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M GLU 99": "OE1" <-> "OE2" Residue "N ASP 180": "OD1" <-> "OD2" Residue "Y TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 99": "OE1" <-> "OE2" Residue "Y GLU 103": "OE1" <-> "OE2" Residue "Z ASP 16": "OD1" <-> "OD2" Residue "Z PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 278": "OD1" <-> "OD2" Residue "Z TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 314": "OD1" <-> "OD2" Residue "Z TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 463": "OD1" <-> "OD2" Residue "Z PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 59": "OE1" <-> "OE2" Residue "e GLU 103": "OE1" <-> "OE2" Residue "f TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 211": "OD1" <-> "OD2" Residue "m PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 78": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 25941 Number of models: 1 Model: "" Number of chains: 18 Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4627 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 29, 'TRANS': 564} Chain: "I" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 412 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "J" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4657 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 30, 'TRANS': 567} Chain: "K" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "P" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 436 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "Y" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "Z" Number of atoms: 4650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4650 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 29, 'TRANS': 567} Chain: "e" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "f" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "h" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 428 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "m" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12891 SG CYS L 182 91.577 90.470 69.286 1.00 27.16 S ATOM 13062 SG CYS L 205 85.408 91.943 69.478 1.00 51.17 S ATOM 12813 SG CYS L 173 86.791 86.108 68.475 1.00 33.95 S ATOM 13107 SG CYS L 212 87.012 90.562 63.982 1.00 30.13 S ATOM 15576 SG CYS N 182 19.092 62.735 71.304 1.00 53.53 S ATOM 15747 SG CYS N 205 20.398 56.107 71.928 1.00 52.32 S ATOM 15498 SG CYS N 173 24.752 60.179 70.357 1.00 53.47 S ATOM 15792 SG CYS N 212 20.597 58.204 66.112 1.00 40.06 S ATOM 24231 SG CYS f 182 79.850 13.948 75.535 1.00 68.04 S ATOM 24402 SG CYS f 205 84.408 18.820 75.651 1.00 77.47 S ATOM 24153 SG CYS f 173 78.655 20.090 73.384 1.00 75.88 S ATOM 24447 SG CYS f 212 82.450 17.327 69.805 1.00 69.39 S Time building chain proxies: 13.96, per 1000 atoms: 0.54 Number of scatterers: 25941 At special positions: 0 Unit cell: (129.978, 127.83, 166.501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 138 16.00 O 5040 8.00 N 4523 7.00 C 16228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 343 " - pdb=" SG CYS F 348 " distance=2.16 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 348 " distance=2.09 Simple disulfide: pdb=" SG CYS Z 343 " - pdb=" SG CYS Z 348 " distance=2.11 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: 10.39 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 L 301 " pdb="FE1 SF4 L 301 " - pdb=" SG CYS L 182 " pdb="FE4 SF4 L 301 " - pdb=" SG CYS L 212 " pdb="FE2 SF4 L 301 " - pdb=" SG CYS L 205 " pdb="FE3 SF4 L 301 " - pdb=" SG CYS L 173 " pdb=" SF4 N 301 " pdb="FE2 SF4 N 301 " - pdb=" SG CYS N 205 " pdb="FE3 SF4 N 301 " - pdb=" SG CYS N 173 " pdb="FE1 SF4 N 301 " - pdb=" SG CYS N 182 " pdb="FE4 SF4 N 301 " - pdb=" SG CYS N 212 " pdb=" SF4 f 301 " pdb="FE2 SF4 f 301 " - pdb=" SG CYS f 205 " pdb="FE3 SF4 f 301 " - pdb=" SG CYS f 173 " pdb="FE1 SF4 f 301 " - pdb=" SG CYS f 182 " pdb="FE4 SF4 f 301 " - pdb=" SG CYS f 212 " Number of angles added : 36 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 56 sheets defined 12.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'F' and resid 42 through 44 No H-bonds generated for 'chain 'F' and resid 42 through 44' Processing helix chain 'F' and resid 224 through 226 No H-bonds generated for 'chain 'F' and resid 224 through 226' Processing helix chain 'F' and resid 272 through 281 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 420 through 426 removed outlier: 3.958A pdb=" N ARG F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 457 Processing helix chain 'F' and resid 468 through 472 removed outlier: 3.636A pdb=" N LEU F 471 " --> pdb=" O ALA F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 487 No H-bonds generated for 'chain 'F' and resid 484 through 487' Processing helix chain 'F' and resid 593 through 600 removed outlier: 3.884A pdb=" N GLU F 596 " --> pdb=" O PRO F 593 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP F 600 " --> pdb=" O ALA F 597 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 43 No H-bonds generated for 'chain 'J' and resid 41 through 43' Processing helix chain 'J' and resid 272 through 281 Processing helix chain 'J' and resid 298 through 308 Processing helix chain 'J' and resid 335 through 345 Processing helix chain 'J' and resid 392 through 394 No H-bonds generated for 'chain 'J' and resid 392 through 394' Processing helix chain 'J' and resid 420 through 423 No H-bonds generated for 'chain 'J' and resid 420 through 423' Processing helix chain 'J' and resid 441 through 457 Processing helix chain 'J' and resid 468 through 472 removed outlier: 3.834A pdb=" N LEU J 471 " --> pdb=" O ALA J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 484 through 487 No H-bonds generated for 'chain 'J' and resid 484 through 487' Processing helix chain 'J' and resid 593 through 599 removed outlier: 3.572A pdb=" N GLU J 596 " --> pdb=" O PRO J 593 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 63 Processing helix chain 'L' and resid 6 through 13 Processing helix chain 'L' and resid 84 through 92 removed outlier: 3.817A pdb=" N MET L 87 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL L 88 " --> pdb=" O TYR L 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA L 92 " --> pdb=" O THR L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 112 No H-bonds generated for 'chain 'L' and resid 110 through 112' Processing helix chain 'L' and resid 115 through 117 No H-bonds generated for 'chain 'L' and resid 115 through 117' Processing helix chain 'L' and resid 209 through 215 removed outlier: 3.881A pdb=" N ARG L 215 " --> pdb=" O GLY L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 218 through 220 No H-bonds generated for 'chain 'L' and resid 218 through 220' Processing helix chain 'M' and resid 52 through 65 removed outlier: 4.323A pdb=" N THR M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL M 57 " --> pdb=" O GLU M 53 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU M 58 " --> pdb=" O GLU M 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS M 65 " --> pdb=" O PHE M 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 13 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 84 through 92 removed outlier: 3.969A pdb=" N MET N 87 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL N 88 " --> pdb=" O TYR N 85 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR N 89 " --> pdb=" O GLY N 86 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA N 92 " --> pdb=" O THR N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 112 No H-bonds generated for 'chain 'N' and resid 110 through 112' Processing helix chain 'N' and resid 115 through 117 No H-bonds generated for 'chain 'N' and resid 115 through 117' Processing helix chain 'N' and resid 209 through 215 Processing helix chain 'N' and resid 218 through 220 No H-bonds generated for 'chain 'N' and resid 218 through 220' Processing helix chain 'Y' and resid 55 through 65 removed outlier: 3.860A pdb=" N HIS Y 65 " --> pdb=" O PHE Y 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 44 No H-bonds generated for 'chain 'Z' and resid 42 through 44' Processing helix chain 'Z' and resid 272 through 280 Processing helix chain 'Z' and resid 298 through 308 Processing helix chain 'Z' and resid 335 through 345 Processing helix chain 'Z' and resid 392 through 394 No H-bonds generated for 'chain 'Z' and resid 392 through 394' Processing helix chain 'Z' and resid 420 through 425 removed outlier: 3.681A pdb=" N ARG Z 425 " --> pdb=" O GLN Z 421 " (cutoff:3.500A) Processing helix chain 'Z' and resid 441 through 457 Processing helix chain 'Z' and resid 468 through 471 removed outlier: 3.848A pdb=" N LEU Z 471 " --> pdb=" O ALA Z 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 468 through 471' Processing helix chain 'Z' and resid 596 through 600 Processing helix chain 'e' and resid 55 through 65 removed outlier: 3.744A pdb=" N HIS e 65 " --> pdb=" O PHE e 61 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 12 Processing helix chain 'f' and resid 29 through 31 No H-bonds generated for 'chain 'f' and resid 29 through 31' Processing helix chain 'f' and resid 84 through 86 No H-bonds generated for 'chain 'f' and resid 84 through 86' Processing helix chain 'f' and resid 89 through 91 No H-bonds generated for 'chain 'f' and resid 89 through 91' Processing helix chain 'f' and resid 95 through 98 Processing helix chain 'f' and resid 110 through 112 No H-bonds generated for 'chain 'f' and resid 110 through 112' Processing helix chain 'f' and resid 115 through 117 No H-bonds generated for 'chain 'f' and resid 115 through 117' Processing helix chain 'f' and resid 200 through 202 No H-bonds generated for 'chain 'f' and resid 200 through 202' Processing helix chain 'f' and resid 209 through 215 Processing helix chain 'f' and resid 218 through 220 No H-bonds generated for 'chain 'f' and resid 218 through 220' Processing helix chain 'm' and resid 52 through 65 removed outlier: 4.077A pdb=" N THR m 56 " --> pdb=" O ARG m 52 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL m 57 " --> pdb=" O GLU m 53 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 21 through 24 Processing sheet with id= B, first strand: chain 'E' and resid 44 through 51 Processing sheet with id= C, first strand: chain 'E' and resid 90 through 93 Processing sheet with id= D, first strand: chain 'F' and resid 23 through 26 Processing sheet with id= E, first strand: chain 'F' and resid 85 through 89 removed outlier: 7.099A pdb=" N THR F 115 " --> pdb=" O SER F 200 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR F 202 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG F 113 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU F 204 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG F 111 " --> pdb=" O GLU F 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 92 through 94 removed outlier: 3.594A pdb=" N THR F 92 " --> pdb=" O TRP F 199 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR F 197 " --> pdb=" O VAL F 94 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 179 through 183 removed outlier: 6.337A pdb=" N ILE F 141 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR F 149 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 243 through 246 Processing sheet with id= I, first strand: chain 'F' and resid 311 through 313 Processing sheet with id= J, first strand: chain 'F' and resid 349 through 353 Processing sheet with id= K, first strand: chain 'F' and resid 368 through 372 removed outlier: 7.016A pdb=" N VAL F 478 " --> pdb=" O TRP F 369 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TYR F 371 " --> pdb=" O VAL F 478 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU F 480 " --> pdb=" O TYR F 371 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR F 587 " --> pdb=" O VAL F 574 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE F 576 " --> pdb=" O ALA F 585 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA F 585 " --> pdb=" O ILE F 576 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN F 460 " --> pdb=" O GLN F 590 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 411 through 418 removed outlier: 3.821A pdb=" N GLU F 411 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 495 through 499 removed outlier: 6.834A pdb=" N THR F 506 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL F 498 " --> pdb=" O THR F 504 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR F 504 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER F 537 " --> pdb=" O LYS F 545 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 530 through 534 Processing sheet with id= O, first strand: chain 'J' and resid 86 through 89 removed outlier: 7.171A pdb=" N THR J 115 " --> pdb=" O SER J 200 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR J 202 " --> pdb=" O ARG J 113 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG J 113 " --> pdb=" O TYR J 202 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU J 204 " --> pdb=" O ARG J 111 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARG J 111 " --> pdb=" O GLU J 204 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 92 through 94 removed outlier: 4.651A pdb=" N THR J 197 " --> pdb=" O VAL J 94 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 179 through 183 removed outlier: 6.852A pdb=" N ILE J 141 " --> pdb=" O THR J 149 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR J 149 " --> pdb=" O ILE J 141 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 311 through 313 Processing sheet with id= S, first strand: chain 'J' and resid 348 through 352 Processing sheet with id= T, first strand: chain 'J' and resid 369 through 371 removed outlier: 6.939A pdb=" N THR J 587 " --> pdb=" O VAL J 574 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN J 460 " --> pdb=" O GLN J 590 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 411 through 418 removed outlier: 3.848A pdb=" N GLU J 411 " --> pdb=" O ASP J 405 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 492 through 494 removed outlier: 6.624A pdb=" N VAL J 558 " --> pdb=" O VAL J 524 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL J 524 " --> pdb=" O VAL J 558 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 495 through 499 removed outlier: 6.571A pdb=" N THR J 506 " --> pdb=" O LEU J 496 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL J 498 " --> pdb=" O THR J 504 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR J 504 " --> pdb=" O VAL J 498 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 535 through 539 removed outlier: 7.013A pdb=" N LYS J 545 " --> pdb=" O GLN J 536 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL J 538 " --> pdb=" O LYS J 543 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS J 543 " --> pdb=" O VAL J 538 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 13 through 15 removed outlier: 3.598A pdb=" N ASP K 13 " --> pdb=" O SER K 45 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 21 through 23 Processing sheet with id= AA, first strand: chain 'K' and resid 90 through 93 Processing sheet with id= AB, first strand: chain 'L' and resid 36 through 39 removed outlier: 6.822A pdb=" N VAL L 151 " --> pdb=" O GLU L 138 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N CYS L 140 " --> pdb=" O SER L 149 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER L 149 " --> pdb=" O CYS L 140 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 49 through 51 Processing sheet with id= AD, first strand: chain 'M' and resid 21 through 24 Processing sheet with id= AE, first strand: chain 'M' and resid 43 through 51 Processing sheet with id= AF, first strand: chain 'M' and resid 90 through 93 Processing sheet with id= AG, first strand: chain 'N' and resid 35 through 39 Processing sheet with id= AH, first strand: chain 'N' and resid 49 through 51 Processing sheet with id= AI, first strand: chain 'N' and resid 61 through 63 removed outlier: 3.589A pdb=" N GLU N 142 " --> pdb=" O SER N 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL N 151 " --> pdb=" O CYS N 140 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N CYS N 140 " --> pdb=" O VAL N 151 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Y' and resid 13 through 15 removed outlier: 3.825A pdb=" N ASP Y 13 " --> pdb=" O SER Y 45 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Y' and resid 21 through 24 Processing sheet with id= AL, first strand: chain 'Y' and resid 90 through 93 Processing sheet with id= AM, first strand: chain 'Z' and resid 23 through 30 Processing sheet with id= AN, first strand: chain 'Z' and resid 84 through 89 removed outlier: 7.031A pdb=" N THR Z 115 " --> pdb=" O SER Z 200 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR Z 202 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG Z 113 " --> pdb=" O TYR Z 202 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU Z 204 " --> pdb=" O ARG Z 111 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG Z 111 " --> pdb=" O GLU Z 204 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Z' and resid 92 through 94 removed outlier: 4.648A pdb=" N THR Z 197 " --> pdb=" O VAL Z 94 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Z' and resid 179 through 183 removed outlier: 6.234A pdb=" N ILE Z 141 " --> pdb=" O THR Z 149 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR Z 149 " --> pdb=" O ILE Z 141 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG Z 143 " --> pdb=" O TRP Z 147 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP Z 147 " --> pdb=" O ARG Z 143 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Z' and resid 243 through 246 Processing sheet with id= AR, first strand: chain 'Z' and resid 311 through 313 Processing sheet with id= AS, first strand: chain 'Z' and resid 349 through 352 Processing sheet with id= AT, first strand: chain 'Z' and resid 369 through 371 removed outlier: 6.987A pdb=" N THR Z 587 " --> pdb=" O VAL Z 574 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE Z 576 " --> pdb=" O ALA Z 585 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA Z 585 " --> pdb=" O ILE Z 576 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN Z 460 " --> pdb=" O GLN Z 590 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Z' and resid 411 through 418 removed outlier: 3.604A pdb=" N GLU Z 411 " --> pdb=" O ASP Z 405 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Z' and resid 492 through 494 Processing sheet with id= AW, first strand: chain 'Z' and resid 495 through 499 removed outlier: 6.867A pdb=" N THR Z 506 " --> pdb=" O LEU Z 496 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL Z 498 " --> pdb=" O THR Z 504 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR Z 504 " --> pdb=" O VAL Z 498 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER Z 537 " --> pdb=" O LYS Z 545 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'e' and resid 12 through 15 Processing sheet with id= AY, first strand: chain 'e' and resid 21 through 24 Processing sheet with id= AZ, first strand: chain 'e' and resid 90 through 93 Processing sheet with id= BA, first strand: chain 'f' and resid 35 through 39 removed outlier: 6.636A pdb=" N VAL f 151 " --> pdb=" O GLU f 138 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N CYS f 140 " --> pdb=" O SER f 149 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER f 149 " --> pdb=" O CYS f 140 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'f' and resid 49 through 51 Processing sheet with id= BC, first strand: chain 'm' and resid 13 through 15 Processing sheet with id= BD, first strand: chain 'm' and resid 90 through 93 659 hydrogen bonds defined for protein. 1731 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: 8.87 Time building geometry restraints manager: 11.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.41: 10936 1.41 - 1.67: 15337 1.67 - 1.93: 195 1.93 - 2.19: 6 2.19 - 2.45: 30 Bond restraints: 26504 Sorted by residual: bond pdb=" C PRO F 475 " pdb=" O PRO F 475 " ideal model delta sigma weight residual 1.233 1.154 0.079 1.21e-02 6.83e+03 4.24e+01 bond pdb=" C ALA F 293 " pdb=" O ALA F 293 " ideal model delta sigma weight residual 1.233 1.309 -0.077 1.21e-02 6.83e+03 4.00e+01 bond pdb=" C LEU F 357 " pdb=" O LEU F 357 " ideal model delta sigma weight residual 1.235 1.159 0.076 1.22e-02 6.72e+03 3.93e+01 bond pdb=" C ILE J 205 " pdb=" O ILE J 205 " ideal model delta sigma weight residual 1.238 1.170 0.067 1.10e-02 8.26e+03 3.73e+01 bond pdb=" C PRO N 77 " pdb=" O PRO N 77 " ideal model delta sigma weight residual 1.235 1.157 0.079 1.30e-02 5.92e+03 3.65e+01 ... (remaining 26499 not shown) Histogram of bond angle deviations from ideal: 67.38 - 80.85: 36 80.85 - 94.31: 1 94.31 - 107.77: 1911 107.77 - 121.24: 25697 121.24 - 134.70: 8377 Bond angle restraints: 36022 Sorted by residual: angle pdb=" C PHE J 177 " pdb=" CA PHE J 177 " pdb=" CB PHE J 177 " ideal model delta sigma weight residual 110.42 87.21 23.21 1.99e+00 2.53e-01 1.36e+02 angle pdb=" CA TYR F 268 " pdb=" C TYR F 268 " pdb=" O TYR F 268 " ideal model delta sigma weight residual 120.69 110.12 10.57 1.14e+00 7.69e-01 8.60e+01 angle pdb=" CA TRP N 175 " pdb=" C TRP N 175 " pdb=" O TRP N 175 " ideal model delta sigma weight residual 121.44 112.22 9.22 1.08e+00 8.57e-01 7.29e+01 angle pdb=" CA ARG F 241 " pdb=" C ARG F 241 " pdb=" O ARG F 241 " ideal model delta sigma weight residual 121.87 112.57 9.30 1.10e+00 8.26e-01 7.15e+01 angle pdb=" C ASN J 235 " pdb=" CA ASN J 235 " pdb=" CB ASN J 235 " ideal model delta sigma weight residual 110.79 99.11 11.68 1.39e+00 5.18e-01 7.06e+01 ... (remaining 36017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 13334 17.56 - 35.12: 1760 35.12 - 52.68: 557 52.68 - 70.24: 113 70.24 - 87.80: 37 Dihedral angle restraints: 15801 sinusoidal: 6313 harmonic: 9488 Sorted by residual: dihedral pdb=" CA PHE f 163 " pdb=" C PHE f 163 " pdb=" N PRO f 164 " pdb=" CA PRO f 164 " ideal model delta harmonic sigma weight residual -180.00 -99.50 -80.50 0 5.00e+00 4.00e-02 2.59e+02 dihedral pdb=" CA PHE L 163 " pdb=" C PHE L 163 " pdb=" N PRO L 164 " pdb=" CA PRO L 164 " ideal model delta harmonic sigma weight residual -180.00 -115.46 -64.54 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CA ARG J 175 " pdb=" C ARG J 175 " pdb=" N PRO J 176 " pdb=" CA PRO J 176 " ideal model delta harmonic sigma weight residual 180.00 121.74 58.26 0 5.00e+00 4.00e-02 1.36e+02 ... (remaining 15798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2304 0.092 - 0.184: 1448 0.184 - 0.277: 213 0.277 - 0.369: 18 0.369 - 0.461: 3 Chirality restraints: 3986 Sorted by residual: chirality pdb="FE1 SF4 L 301 " pdb=" S2 SF4 L 301 " pdb=" S3 SF4 L 301 " pdb=" S4 SF4 L 301 " both_signs ideal model delta sigma weight residual False -10.55 -11.02 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA CYS F 348 " pdb=" N CYS F 348 " pdb=" C CYS F 348 " pdb=" CB CYS F 348 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CA PHE N 163 " pdb=" N PHE N 163 " pdb=" C PHE N 163 " pdb=" CB PHE N 163 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 3983 not shown) Planarity restraints: 4690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 274 " -0.050 2.00e-02 2.50e+03 2.94e-02 2.17e+01 pdb=" CG TRP J 274 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP J 274 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP J 274 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP J 274 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J 274 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP J 274 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 274 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 274 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP J 274 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Z 274 " 0.045 2.00e-02 2.50e+03 2.82e-02 1.98e+01 pdb=" CG TRP Z 274 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP Z 274 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP Z 274 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP Z 274 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP Z 274 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP Z 274 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP Z 274 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP Z 274 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP Z 274 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 163 " -0.046 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE N 163 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE N 163 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE N 163 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE N 163 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE N 163 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE N 163 " -0.029 2.00e-02 2.50e+03 ... (remaining 4687 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 72 2.40 - 3.03: 15331 3.03 - 3.65: 36831 3.65 - 4.28: 58376 4.28 - 4.90: 97511 Nonbonded interactions: 208121 Sorted by model distance: nonbonded pdb=" O THR J 105 " pdb=" OG1 THR J 105 " model vdw 1.777 2.440 nonbonded pdb=" OG SER F 31 " pdb=" N GLU F 32 " model vdw 1.895 2.520 nonbonded pdb=" OG SER Z 224 " pdb=" O THR h 174 " model vdw 1.989 2.440 nonbonded pdb=" O ASP L 203 " pdb=" OD1 ASP L 203 " model vdw 2.082 3.040 nonbonded pdb=" O GLU Z 32 " pdb=" O GLY Z 33 " model vdw 2.095 3.040 ... (remaining 208116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'M' selection = chain 'Y' selection = chain 'e' selection = chain 'm' } ncs_group { reference = chain 'F' selection = (chain 'J' and resid 11 through 604) selection = (chain 'Z' and resid 11 through 604) } ncs_group { reference = chain 'I' selection = (chain 'P' and resid 167 through 222) selection = (chain 'h' and resid 167 through 222) } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.920 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: 0.020 Extract box with map and model: 8.320 Check model and map are aligned: 0.180 Set scattering table: 0.260 Process input model: 74.720 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.190 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.015 0.179 26504 Z= 1.022 Angle : 1.991 23.213 36022 Z= 1.402 Chirality : 0.105 0.461 3986 Planarity : 0.007 0.070 4690 Dihedral : 18.167 87.803 9706 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 2.71 % Allowed : 13.56 % Favored : 83.73 % Rotamer: Outliers : 8.53 % Allowed : 21.19 % Favored : 70.28 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.12), residues: 3282 helix: -1.91 (0.22), residues: 381 sheet: -1.94 (0.16), residues: 894 loop : -3.11 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.006 TRP J 274 HIS 0.019 0.004 HIS J 396 PHE 0.055 0.007 PHE J 177 TYR 0.051 0.007 TYR F 328 ARG 0.013 0.001 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 380 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8782 (tm-30) REVERT: E 78 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8669 (mt-10) REVERT: E 99 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7777 (mm-30) REVERT: F 17 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8265 (p0) REVERT: F 144 ASN cc_start: 0.9370 (t0) cc_final: 0.8400 (m110) REVERT: F 162 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8610 (tp40) REVERT: F 221 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8076 (mt0) REVERT: F 261 ASP cc_start: 0.9624 (OUTLIER) cc_final: 0.9187 (p0) REVERT: F 489 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7768 (tt) REVERT: F 496 LEU cc_start: 0.8000 (mt) cc_final: 0.7638 (mt) REVERT: I 171 LYS cc_start: 0.5495 (OUTLIER) cc_final: 0.5185 (tptm) REVERT: I 172 GLN cc_start: 0.7009 (tp-100) cc_final: 0.6627 (tp40) REVERT: J 32 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.8786 (tt0) REVERT: J 47 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8564 (mt) REVERT: J 134 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7961 (tm-30) REVERT: J 175 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8033 (mtm-85) REVERT: J 187 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7441 (t70) REVERT: J 272 MET cc_start: 0.8987 (ttm) cc_final: 0.8594 (ttt) REVERT: J 483 ASP cc_start: 0.8637 (t70) cc_final: 0.8351 (t0) REVERT: J 523 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8253 (mt) REVERT: J 568 GLN cc_start: 0.7536 (tp40) cc_final: 0.7215 (tp40) REVERT: J 601 ASN cc_start: 0.6967 (OUTLIER) cc_final: 0.6599 (m110) REVERT: K 9 LYS cc_start: 0.7809 (mmtp) cc_final: 0.7309 (mmtp) REVERT: K 31 GLN cc_start: 0.8879 (mt0) cc_final: 0.8050 (mt0) REVERT: K 40 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.7017 (t0) REVERT: K 63 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8130 (mm-30) REVERT: K 64 GLU cc_start: 0.8877 (mp0) cc_final: 0.8417 (mp0) REVERT: K 97 ARG cc_start: 0.7241 (mmp-170) cc_final: 0.6517 (mmp-170) REVERT: L 1 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7905 (mmm) REVERT: L 59 TYR cc_start: 0.9202 (t80) cc_final: 0.8855 (t80) REVERT: L 69 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8854 (m-40) REVERT: M 9 LYS cc_start: 0.2275 (OUTLIER) cc_final: 0.0769 (mmmm) REVERT: M 52 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7881 (mtp-110) REVERT: M 63 GLU cc_start: 0.8281 (tp30) cc_final: 0.8045 (tp30) REVERT: M 79 TRP cc_start: 0.8075 (m100) cc_final: 0.7788 (m100) REVERT: P 180 ASP cc_start: 0.8942 (t0) cc_final: 0.8672 (t0) REVERT: Y 2 LYS cc_start: 0.6322 (tptt) cc_final: 0.6027 (tptp) REVERT: Y 24 ARG cc_start: 0.9343 (ttp-110) cc_final: 0.8954 (ttp80) REVERT: Y 40 ASN cc_start: 0.7577 (p0) cc_final: 0.7308 (p0) REVERT: Y 63 GLU cc_start: 0.8666 (pp20) cc_final: 0.8406 (pp20) REVERT: Y 69 LYS cc_start: 0.7857 (tmtt) cc_final: 0.7266 (tmtt) REVERT: Y 72 LEU cc_start: 0.8995 (mp) cc_final: 0.8771 (mp) REVERT: Z 346 MET cc_start: 0.9385 (ptm) cc_final: 0.9177 (ptt) REVERT: Z 425 ARG cc_start: 0.9181 (ptt-90) cc_final: 0.8821 (ptm160) REVERT: e 12 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7484 (ttt) REVERT: e 95 MET cc_start: 0.7282 (tpp) cc_final: 0.6785 (tpp) REVERT: e 103 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8536 (mm-30) REVERT: f 2 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8702 (tm-30) REVERT: f 111 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7877 (ptp-170) REVERT: f 149 SER cc_start: 0.9334 (OUTLIER) cc_final: 0.9027 (p) REVERT: f 213 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8530 (mtpp) REVERT: h 182 MET cc_start: 0.9150 (mmm) cc_final: 0.8832 (mmm) REVERT: h 196 MET cc_start: 0.9060 (tpp) cc_final: 0.8689 (tpp) REVERT: m 9 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7499 (mtmm) REVERT: m 59 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7697 (tm-30) outliers start: 244 outliers final: 126 residues processed: 579 average time/residue: 0.4447 time to fit residues: 388.5315 Evaluate side-chains 475 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 328 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 162 GLN Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 211 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 592 VAL Chi-restraints excluded: chain F residue 599 VAL Chi-restraints excluded: chain F residue 604 HIS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 175 ARG Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain J residue 280 LEU Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 407 ASN Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 463 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 601 ASN Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 9 LYS Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 133 SER Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain N residue 162 VAL Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 103 THR Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 181 MET Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 215 THR Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 248 ASN Chi-restraints excluded: chain Z residue 339 LEU Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 461 THR Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 12 MET Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain f residue 2 GLN Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 74 SER Chi-restraints excluded: chain f residue 111 ARG Chi-restraints excluded: chain f residue 149 SER Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 213 LYS Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 181 ASN Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 205 GLN Chi-restraints excluded: chain h residue 214 ASP Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 251 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 291 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 443 GLN F 460 GLN I 172 GLN I 185 GLN I 205 GLN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 GLN J 119 GLN ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN N 6 GLN N 42 GLN ** Z 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 332 GLN e 40 ASN e 106 GLN f 6 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26504 Z= 0.202 Angle : 0.684 10.779 36022 Z= 0.363 Chirality : 0.046 0.192 3986 Planarity : 0.005 0.097 4690 Dihedral : 9.313 83.267 3858 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 1.04 % Allowed : 9.81 % Favored : 89.15 % Rotamer: Outliers : 5.84 % Allowed : 23.39 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.03 % 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: -2.63 (0.14), residues: 3282 helix: 0.12 (0.26), residues: 374 sheet: -1.37 (0.16), residues: 1033 loop : -2.44 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP M 89 HIS 0.005 0.001 HIS F 445 PHE 0.023 0.001 PHE N 163 TYR 0.019 0.001 TYR Z 212 ARG 0.006 0.001 ARG e 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 357 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8695 (mt-10) REVERT: F 17 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.8005 (p0) REVERT: F 40 ASP cc_start: 0.8684 (t0) cc_final: 0.8440 (t0) REVERT: F 72 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8747 (mm-30) REVERT: F 182 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8015 (ptm160) REVERT: F 264 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: F 287 MET cc_start: 0.9180 (tpp) cc_final: 0.8828 (tpp) REVERT: F 489 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7578 (tt) REVERT: F 507 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8174 (pp) REVERT: F 516 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8112 (p) REVERT: J 22 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8109 (pt0) REVERT: J 27 ILE cc_start: 0.9129 (mt) cc_final: 0.8799 (tt) REVERT: J 96 TYR cc_start: 0.7936 (t80) cc_final: 0.7356 (t80) REVERT: J 134 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8136 (tm-30) REVERT: K 9 LYS cc_start: 0.7759 (mmtp) cc_final: 0.7297 (mmtp) REVERT: K 22 LYS cc_start: 0.9062 (ttpp) cc_final: 0.8835 (ptmt) REVERT: K 31 GLN cc_start: 0.8616 (mt0) cc_final: 0.8004 (mt0) REVERT: K 40 ASN cc_start: 0.7310 (OUTLIER) cc_final: 0.6929 (t0) REVERT: K 64 GLU cc_start: 0.8740 (mp0) cc_final: 0.8294 (pt0) REVERT: K 97 ARG cc_start: 0.7136 (mmp-170) cc_final: 0.6635 (mmp-170) REVERT: L 59 TYR cc_start: 0.9059 (t80) cc_final: 0.8704 (t80) REVERT: L 69 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8291 (m-40) REVERT: L 87 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8226 (tpp) REVERT: L 214 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8354 (t80) REVERT: M 13 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8116 (t0) REVERT: M 64 GLU cc_start: 0.9027 (tp30) cc_final: 0.8511 (tm-30) REVERT: M 78 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8032 (tm-30) REVERT: M 92 ARG cc_start: 0.8264 (tpp80) cc_final: 0.8000 (tpp80) REVERT: N 3 ASP cc_start: 0.8253 (p0) cc_final: 0.8044 (p0) REVERT: N 128 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: N 181 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: P 172 GLN cc_start: 0.7854 (mp10) cc_final: 0.7050 (tp40) REVERT: P 180 ASP cc_start: 0.8957 (t0) cc_final: 0.8631 (t0) REVERT: Y 5 ARG cc_start: 0.7569 (mpt-90) cc_final: 0.7242 (mmt-90) REVERT: Y 24 ARG cc_start: 0.9343 (ttp-110) cc_final: 0.9004 (ttp80) REVERT: Y 27 ASP cc_start: 0.8773 (m-30) cc_final: 0.8232 (m-30) REVERT: Y 69 LYS cc_start: 0.7874 (tmtt) cc_final: 0.7483 (tmtt) REVERT: Z 179 ILE cc_start: 0.9120 (pp) cc_final: 0.8702 (pt) REVERT: Z 272 MET cc_start: 0.9003 (tpp) cc_final: 0.8657 (tpt) REVERT: Z 332 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8452 (tp40) REVERT: Z 373 ARG cc_start: 0.8656 (ttt90) cc_final: 0.8348 (mtp85) REVERT: Z 425 ARG cc_start: 0.9090 (ptt-90) cc_final: 0.8682 (ptm160) REVERT: e 12 MET cc_start: 0.7673 (ttt) cc_final: 0.7132 (ttt) REVERT: e 95 MET cc_start: 0.7267 (tpp) cc_final: 0.6869 (tpp) REVERT: f 159 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8675 (m-30) REVERT: h 171 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7625 (mptt) REVERT: h 182 MET cc_start: 0.8480 (mmm) cc_final: 0.8034 (mmm) REVERT: m 5 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6895 (mtm110) outliers start: 167 outliers final: 99 residues processed: 486 average time/residue: 0.4514 time to fit residues: 337.6581 Evaluate side-chains 446 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 330 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 211 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 507 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 604 HIS Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 280 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 339 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 439 THR Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain K residue 40 ASN Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain N residue 181 GLU Chi-restraints excluded: chain P residue 177 SER Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 27 ILE Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 215 THR Chi-restraints excluded: chain Z residue 332 GLN Chi-restraints excluded: chain Z residue 343 CYS Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 463 ASP Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain h residue 169 ASN Chi-restraints excluded: chain h residue 173 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 292 optimal weight: 0.0870 chunk 315 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 289 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 187 ASN J 22 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN P 185 GLN ** Z 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 195 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 270 ASN f 228 ASN ** h 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26504 Z= 0.171 Angle : 0.619 10.563 36022 Z= 0.324 Chirality : 0.045 0.181 3986 Planarity : 0.004 0.084 4690 Dihedral : 6.989 69.696 3709 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.98 % Allowed : 10.27 % Favored : 88.76 % Rotamer: Outliers : 4.86 % Allowed : 24.83 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.03 % 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: -2.19 (0.14), residues: 3282 helix: 0.67 (0.28), residues: 374 sheet: -1.00 (0.16), residues: 1057 loop : -2.27 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 89 HIS 0.005 0.001 HIS K 65 PHE 0.017 0.001 PHE F 68 TYR 0.017 0.001 TYR Z 212 ARG 0.007 0.000 ARG e 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 346 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7555 (mm-30) REVERT: F 264 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: F 489 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7656 (tt) REVERT: F 507 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8012 (pp) REVERT: J 16 ASP cc_start: 0.6706 (t0) cc_final: 0.4968 (p0) REVERT: J 96 TYR cc_start: 0.7988 (t80) cc_final: 0.7416 (t80) REVERT: J 134 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8054 (tm-30) REVERT: J 503 ARG cc_start: 0.7629 (ptt-90) cc_final: 0.7151 (ptp90) REVERT: J 600 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7650 (p0) REVERT: K 9 LYS cc_start: 0.7555 (mmtp) cc_final: 0.7258 (mmtp) REVERT: K 22 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8824 (ptmt) REVERT: K 31 GLN cc_start: 0.8639 (mt0) cc_final: 0.8118 (mt0) REVERT: K 63 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7755 (mm-30) REVERT: K 97 ARG cc_start: 0.7416 (mmp-170) cc_final: 0.6715 (mmp-170) REVERT: L 1 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7762 (tmm) REVERT: L 59 TYR cc_start: 0.9036 (t80) cc_final: 0.8615 (t80) REVERT: L 69 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7787 (m-40) REVERT: M 13 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8130 (t0) REVERT: M 64 GLU cc_start: 0.8991 (tp30) cc_final: 0.8471 (tm-30) REVERT: N 3 ASP cc_start: 0.8294 (p0) cc_final: 0.8006 (p0) REVERT: N 128 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: P 172 GLN cc_start: 0.7754 (mp10) cc_final: 0.7089 (tp40) REVERT: P 180 ASP cc_start: 0.8952 (t0) cc_final: 0.8610 (t0) REVERT: Y 27 ASP cc_start: 0.8713 (m-30) cc_final: 0.8281 (m-30) REVERT: Y 69 LYS cc_start: 0.7837 (tmtt) cc_final: 0.7372 (tmtt) REVERT: Z 179 ILE cc_start: 0.9126 (pp) cc_final: 0.8678 (pt) REVERT: Z 272 MET cc_start: 0.9004 (tpp) cc_final: 0.8710 (tpt) REVERT: Z 373 ARG cc_start: 0.8646 (ttt90) cc_final: 0.8358 (mtp85) REVERT: e 12 MET cc_start: 0.7618 (ttt) cc_final: 0.7085 (ttt) REVERT: e 22 LYS cc_start: 0.8128 (tptt) cc_final: 0.7702 (tptp) REVERT: e 95 MET cc_start: 0.7259 (tpp) cc_final: 0.6848 (tpp) REVERT: h 171 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7655 (mppt) REVERT: h 197 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8199 (ptp90) REVERT: m 5 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6758 (mtm110) REVERT: m 59 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7493 (tm-30) outliers start: 139 outliers final: 82 residues processed: 447 average time/residue: 0.4500 time to fit residues: 307.1098 Evaluate side-chains 419 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 327 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 507 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 600 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 157 GLU Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain P residue 185 GLN Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 463 ASP Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 228 ASN Chi-restraints excluded: chain h residue 169 ASN Chi-restraints excluded: chain h residue 173 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 310 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 187 ASN J 162 GLN K 40 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 ASN ** Z 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 26504 Z= 0.532 Angle : 0.746 11.384 36022 Z= 0.389 Chirality : 0.050 0.221 3986 Planarity : 0.006 0.096 4690 Dihedral : 6.938 67.524 3656 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 1.13 % Allowed : 12.25 % Favored : 86.62 % Rotamer: Outliers : 6.85 % Allowed : 23.67 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.14), residues: 3282 helix: 0.42 (0.28), residues: 371 sheet: -1.13 (0.16), residues: 1073 loop : -2.38 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP M 89 HIS 0.006 0.002 HIS J 282 PHE 0.018 0.002 PHE Z 68 TYR 0.021 0.002 TYR J 202 ARG 0.006 0.001 ARG e 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 322 time to evaluate : 3.138 Fit side-chains revert: symmetry clash REVERT: F 17 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8095 (p0) REVERT: F 40 ASP cc_start: 0.8775 (t0) cc_final: 0.8438 (t0) REVERT: F 53 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8228 (mt) REVERT: F 182 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8490 (ptm160) REVERT: F 264 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: F 489 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7822 (tt) REVERT: F 507 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8102 (pp) REVERT: F 516 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8531 (p) REVERT: J 36 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: J 134 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7969 (tm-30) REVERT: J 523 LEU cc_start: 0.8460 (mm) cc_final: 0.8233 (mm) REVERT: K 9 LYS cc_start: 0.7369 (mmtp) cc_final: 0.7058 (mmtp) REVERT: K 63 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7833 (mm-30) REVERT: K 64 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8329 (mp0) REVERT: K 79 TRP cc_start: 0.7956 (m100) cc_final: 0.7662 (m100) REVERT: K 97 ARG cc_start: 0.7459 (mmp-170) cc_final: 0.7054 (mmp-170) REVERT: L 1 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7776 (tmm) REVERT: L 69 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8297 (m-40) REVERT: L 87 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: M 52 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7731 (mtp-110) REVERT: M 64 GLU cc_start: 0.8999 (tp30) cc_final: 0.8456 (tm-30) REVERT: N 3 ASP cc_start: 0.8373 (p0) cc_final: 0.8127 (p0) REVERT: N 128 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: P 180 ASP cc_start: 0.8882 (t0) cc_final: 0.8549 (t0) REVERT: Y 27 ASP cc_start: 0.8821 (m-30) cc_final: 0.8511 (m-30) REVERT: Y 69 LYS cc_start: 0.7847 (tmtt) cc_final: 0.7317 (tmtt) REVERT: Z 62 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.7965 (p) REVERT: Z 272 MET cc_start: 0.9192 (tpp) cc_final: 0.8779 (tpt) REVERT: Z 373 ARG cc_start: 0.8632 (ttt90) cc_final: 0.8327 (mtp85) REVERT: e 12 MET cc_start: 0.7625 (ttt) cc_final: 0.7118 (ttt) REVERT: e 22 LYS cc_start: 0.8144 (tptt) cc_final: 0.7725 (tptp) REVERT: e 95 MET cc_start: 0.7201 (tpp) cc_final: 0.6869 (tpp) REVERT: f 159 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8706 (m-30) REVERT: h 171 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7591 (mptt) REVERT: h 197 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8242 (ptp90) REVERT: m 2 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8032 (mtpt) outliers start: 196 outliers final: 145 residues processed: 484 average time/residue: 0.4122 time to fit residues: 304.9330 Evaluate side-chains 473 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 312 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 393 LYS Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 507 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 557 SER Chi-restraints excluded: chain F residue 563 LEU Chi-restraints excluded: chain F residue 587 THR Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 508 ASP Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 173 CYS Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain N residue 120 ASN Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 206 SER Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 40 ASN Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 197 THR Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 290 ARG Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 463 ASP Chi-restraints excluded: chain Z residue 511 ILE Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 72 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain h residue 169 ASN Chi-restraints excluded: chain h residue 173 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 181 ASN Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 2 LYS Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 21 ARG Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 84 VAL Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 172 GLN I 187 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN P 185 GLN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26504 Z= 0.330 Angle : 0.661 9.914 36022 Z= 0.344 Chirality : 0.047 0.184 3986 Planarity : 0.005 0.083 4690 Dihedral : 6.722 66.601 3651 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 1.04 % Allowed : 11.03 % Favored : 87.93 % Rotamer: Outliers : 6.78 % Allowed : 24.79 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.14), residues: 3282 helix: 0.45 (0.29), residues: 365 sheet: -1.09 (0.16), residues: 1082 loop : -2.26 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 89 HIS 0.005 0.001 HIS J 282 PHE 0.014 0.001 PHE Z 68 TYR 0.016 0.001 TYR Z 212 ARG 0.008 0.000 ARG J 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 324 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 17 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8181 (p0) REVERT: F 40 ASP cc_start: 0.8709 (t0) cc_final: 0.8353 (t0) REVERT: F 53 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8143 (mt) REVERT: F 58 ASN cc_start: 0.8205 (p0) cc_final: 0.7890 (p0) REVERT: F 264 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: F 489 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7910 (tt) REVERT: F 516 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8541 (p) REVERT: I 221 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7008 (mt) REVERT: J 36 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: J 100 ILE cc_start: 0.8488 (mm) cc_final: 0.8234 (mm) REVERT: J 503 ARG cc_start: 0.7675 (ptt-90) cc_final: 0.7227 (ptp90) REVERT: J 523 LEU cc_start: 0.8482 (mm) cc_final: 0.8194 (mt) REVERT: K 9 LYS cc_start: 0.7337 (mmtp) cc_final: 0.7020 (mmtp) REVERT: K 63 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7807 (mm-30) REVERT: K 64 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8390 (mp0) REVERT: K 97 ARG cc_start: 0.7526 (mmp-170) cc_final: 0.7086 (mmp-170) REVERT: L 1 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7736 (tmm) REVERT: L 87 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8184 (tpp) REVERT: M 52 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7644 (mtp-110) REVERT: M 64 GLU cc_start: 0.8996 (tp30) cc_final: 0.8452 (tm-30) REVERT: N 3 ASP cc_start: 0.8327 (p0) cc_final: 0.8084 (p0) REVERT: P 172 GLN cc_start: 0.7785 (mp10) cc_final: 0.6890 (tp40) REVERT: P 180 ASP cc_start: 0.8854 (t0) cc_final: 0.8512 (t0) REVERT: Y 69 LYS cc_start: 0.7846 (tmtt) cc_final: 0.7278 (tmtt) REVERT: Z 36 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: Z 62 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.7968 (p) REVERT: Z 179 ILE cc_start: 0.9291 (pp) cc_final: 0.8974 (pt) REVERT: Z 272 MET cc_start: 0.9118 (tpp) cc_final: 0.8717 (tpt) REVERT: Z 373 ARG cc_start: 0.8663 (ttt90) cc_final: 0.8356 (mtp85) REVERT: Z 576 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9024 (mt) REVERT: e 12 MET cc_start: 0.7685 (ttt) cc_final: 0.7227 (ttt) REVERT: e 22 LYS cc_start: 0.8124 (tptt) cc_final: 0.7688 (tptp) REVERT: e 95 MET cc_start: 0.7088 (tpp) cc_final: 0.6753 (tpp) REVERT: f 159 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8703 (m-30) REVERT: h 171 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7614 (mptt) REVERT: h 197 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8199 (ptp90) REVERT: m 2 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7917 (mtpt) outliers start: 194 outliers final: 129 residues processed: 478 average time/residue: 0.4201 time to fit residues: 307.7975 Evaluate side-chains 462 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 318 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 264 PHE Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 416 LEU Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 518 THR Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 221 ILE Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 168 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 508 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 176 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 76 THR Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 281 THR Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 463 ASP Chi-restraints excluded: chain Z residue 511 ILE Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain Z residue 576 ILE Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain h residue 169 ASN Chi-restraints excluded: chain h residue 173 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 181 ASN Chi-restraints excluded: chain h residue 188 VAL Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 2 LYS Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 21 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 6.9990 chunk 279 optimal weight: 0.0980 chunk 61 optimal weight: 7.9990 chunk 182 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 310 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 0.0050 chunk 163 optimal weight: 7.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 187 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 408 ASN K 40 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Y 40 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26504 Z= 0.214 Angle : 0.624 9.148 36022 Z= 0.324 Chirality : 0.045 0.253 3986 Planarity : 0.005 0.082 4690 Dihedral : 6.362 64.326 3648 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.73 % Favored : 88.36 % Rotamer: Outliers : 5.49 % Allowed : 26.26 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3282 helix: 0.65 (0.29), residues: 362 sheet: -0.91 (0.16), residues: 1071 loop : -2.21 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 89 HIS 0.004 0.001 HIS e 65 PHE 0.011 0.001 PHE F 264 TYR 0.016 0.001 TYR Z 212 ARG 0.005 0.000 ARG e 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 328 time to evaluate : 3.075 Fit side-chains revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8538 (tm-30) REVERT: F 17 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8076 (p0) REVERT: F 182 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8020 (ptm160) REVERT: F 489 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7846 (tt) REVERT: F 516 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8469 (p) REVERT: J 36 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: J 100 ILE cc_start: 0.8295 (mm) cc_final: 0.8091 (mm) REVERT: J 183 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6349 (ttt180) REVERT: J 503 ARG cc_start: 0.7722 (ptt-90) cc_final: 0.7282 (ptp90) REVERT: J 523 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8219 (mt) REVERT: K 9 LYS cc_start: 0.7249 (mmtp) cc_final: 0.6920 (mmtp) REVERT: K 31 GLN cc_start: 0.8629 (mt0) cc_final: 0.8002 (mt0) REVERT: K 63 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7807 (mm-30) REVERT: K 64 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8403 (mp0) REVERT: K 79 TRP cc_start: 0.7931 (m100) cc_final: 0.7655 (m100) REVERT: K 97 ARG cc_start: 0.7526 (mmp-170) cc_final: 0.7047 (mmp-170) REVERT: L 1 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7703 (tmm) REVERT: L 214 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8296 (t80) REVERT: M 64 GLU cc_start: 0.8980 (tp30) cc_final: 0.8431 (tm-30) REVERT: N 128 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: P 172 GLN cc_start: 0.7748 (mp10) cc_final: 0.6885 (tp40) REVERT: P 180 ASP cc_start: 0.8864 (t0) cc_final: 0.8516 (t0) REVERT: Y 69 LYS cc_start: 0.7845 (tmtt) cc_final: 0.7257 (tmtt) REVERT: Z 36 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: Z 62 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7909 (p) REVERT: Z 179 ILE cc_start: 0.9274 (pp) cc_final: 0.8961 (pt) REVERT: Z 272 MET cc_start: 0.9007 (tpp) cc_final: 0.8650 (tpt) REVERT: Z 373 ARG cc_start: 0.8655 (ttt90) cc_final: 0.8384 (mtp85) REVERT: e 12 MET cc_start: 0.7682 (ttt) cc_final: 0.7287 (ttt) REVERT: e 95 MET cc_start: 0.7038 (tpp) cc_final: 0.6605 (tpp) REVERT: f 1 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8509 (tmm) REVERT: f 159 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8696 (m-30) REVERT: h 171 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7588 (mptt) REVERT: h 197 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8240 (ptp90) REVERT: m 9 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7544 (mtmm) outliers start: 157 outliers final: 120 residues processed: 452 average time/residue: 0.4209 time to fit residues: 291.0155 Evaluate side-chains 454 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 319 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 36 GLU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 408 ASN Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 508 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 164 LEU Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 461 THR Chi-restraints excluded: chain Z residue 463 ASP Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 27 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain h residue 169 ASN Chi-restraints excluded: chain h residue 173 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 21 ARG Chi-restraints excluded: chain m residue 84 VAL Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 173 optimal weight: 0.2980 chunk 309 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 ASN ** Z 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26504 Z= 0.266 Angle : 0.629 9.082 36022 Z= 0.326 Chirality : 0.046 0.218 3986 Planarity : 0.005 0.083 4690 Dihedral : 6.325 63.300 3648 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.91 % Allowed : 11.15 % Favored : 87.93 % Rotamer: Outliers : 6.22 % Allowed : 25.59 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 3282 helix: 0.64 (0.29), residues: 363 sheet: -0.92 (0.16), residues: 1077 loop : -2.21 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 89 HIS 0.004 0.001 HIS J 282 PHE 0.013 0.001 PHE F 264 TYR 0.015 0.001 TYR m 77 ARG 0.006 0.000 ARG e 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 315 time to evaluate : 2.956 Fit side-chains revert: symmetry clash REVERT: F 17 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7991 (p0) REVERT: F 40 ASP cc_start: 0.8577 (t0) cc_final: 0.8345 (t0) REVERT: F 182 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8017 (ptm160) REVERT: F 489 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7929 (tt) REVERT: F 516 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8490 (p) REVERT: J 183 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6375 (ttt180) REVERT: J 503 ARG cc_start: 0.7735 (ptt-90) cc_final: 0.7276 (ptp90) REVERT: J 523 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8221 (mt) REVERT: K 9 LYS cc_start: 0.7283 (mmtp) cc_final: 0.6952 (mmtp) REVERT: K 31 GLN cc_start: 0.8578 (mt0) cc_final: 0.7917 (mt0) REVERT: K 63 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7788 (mm-30) REVERT: K 64 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8399 (mp0) REVERT: K 97 ARG cc_start: 0.7527 (mmp-170) cc_final: 0.7032 (mmp-170) REVERT: L 1 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7699 (tmm) REVERT: L 87 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8095 (tpp) REVERT: L 192 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8671 (mp0) REVERT: L 214 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8281 (t80) REVERT: M 64 GLU cc_start: 0.8977 (tp30) cc_final: 0.8427 (tm-30) REVERT: P 172 GLN cc_start: 0.7787 (mp10) cc_final: 0.6872 (tp40) REVERT: P 180 ASP cc_start: 0.8879 (t0) cc_final: 0.8519 (t0) REVERT: Y 69 LYS cc_start: 0.7842 (tmtt) cc_final: 0.7266 (tmtt) REVERT: Z 62 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7905 (p) REVERT: Z 179 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8948 (pt) REVERT: Z 373 ARG cc_start: 0.8649 (ttt90) cc_final: 0.8387 (mtp85) REVERT: Z 576 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8898 (mp) REVERT: e 12 MET cc_start: 0.7631 (ttt) cc_final: 0.7246 (ttt) REVERT: e 69 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7667 (ttpp) REVERT: e 95 MET cc_start: 0.7046 (tpp) cc_final: 0.6630 (tpp) REVERT: f 1 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8485 (tmm) REVERT: f 159 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8706 (m-30) REVERT: h 171 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7587 (mptt) REVERT: h 197 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8262 (ptp90) REVERT: m 2 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7795 (mtpt) outliers start: 178 outliers final: 132 residues processed: 459 average time/residue: 0.4180 time to fit residues: 295.8110 Evaluate side-chains 464 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 314 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 248 ASN Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 518 THR Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 551 ASP Chi-restraints excluded: chain F residue 587 THR Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 181 MET Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 358 THR Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 417 VAL Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 508 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 123 SER Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain L residue 218 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 174 THR Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 191 ASP Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 212 TYR Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 281 THR Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 418 GLU Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 452 ILE Chi-restraints excluded: chain Z residue 461 THR Chi-restraints excluded: chain Z residue 463 ASP Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain Z residue 576 ILE Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 27 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 69 LYS Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain h residue 169 ASN Chi-restraints excluded: chain h residue 173 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 198 VAL Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 2 LYS Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 21 ARG Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 84 VAL Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 184 optimal weight: 0.4980 chunk 93 optimal weight: 0.4980 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 210 optimal weight: 0.0470 chunk 152 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 ASN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26504 Z= 0.162 Angle : 0.598 8.095 36022 Z= 0.310 Chirality : 0.044 0.196 3986 Planarity : 0.005 0.081 4690 Dihedral : 5.984 58.864 3648 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.51 % Favored : 89.76 % Rotamer: Outliers : 4.65 % Allowed : 27.20 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.15), residues: 3282 helix: 0.62 (0.29), residues: 368 sheet: -0.72 (0.17), residues: 1035 loop : -2.15 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP e 6 HIS 0.003 0.001 HIS Z 396 PHE 0.015 0.001 PHE F 264 TYR 0.019 0.001 TYR F 202 ARG 0.006 0.000 ARG e 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 349 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8623 (tm-30) REVERT: F 489 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7808 (tt) REVERT: F 516 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8384 (p) REVERT: I 180 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8471 (p0) REVERT: J 96 TYR cc_start: 0.7803 (t80) cc_final: 0.7259 (t80) REVERT: J 134 GLU cc_start: 0.8344 (mp0) cc_final: 0.7302 (tm-30) REVERT: J 503 ARG cc_start: 0.7703 (ptt-90) cc_final: 0.7258 (ptp90) REVERT: J 523 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8195 (mt) REVERT: K 9 LYS cc_start: 0.7218 (mmtp) cc_final: 0.6675 (mmtp) REVERT: K 31 GLN cc_start: 0.8487 (mt0) cc_final: 0.7836 (mt0) REVERT: K 63 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7734 (mm-30) REVERT: K 64 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8455 (mp0) REVERT: K 78 GLU cc_start: 0.8650 (tt0) cc_final: 0.8368 (tt0) REVERT: K 97 ARG cc_start: 0.7610 (mmp-170) cc_final: 0.7177 (mmp-170) REVERT: L 192 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8511 (mp0) REVERT: L 214 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8279 (t80) REVERT: M 13 ASP cc_start: 0.8428 (m-30) cc_final: 0.8075 (t0) REVERT: N 128 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: P 172 GLN cc_start: 0.7739 (mp10) cc_final: 0.6859 (tp40) REVERT: P 180 ASP cc_start: 0.8896 (t0) cc_final: 0.8550 (t0) REVERT: Y 69 LYS cc_start: 0.7811 (tmtt) cc_final: 0.7280 (tmtt) REVERT: Z 62 SER cc_start: 0.8429 (m) cc_final: 0.8099 (p) REVERT: Z 179 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8953 (pt) REVERT: Z 373 ARG cc_start: 0.8597 (ttt90) cc_final: 0.8331 (mtp85) REVERT: e 12 MET cc_start: 0.7652 (ttt) cc_final: 0.7308 (ttt) REVERT: e 95 MET cc_start: 0.7047 (tpp) cc_final: 0.6554 (tpp) REVERT: f 73 THR cc_start: 0.8221 (t) cc_final: 0.7989 (t) REVERT: f 159 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8700 (m-30) REVERT: h 171 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7444 (mptt) REVERT: h 197 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8337 (ptp90) REVERT: m 83 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7771 (ttmm) outliers start: 133 outliers final: 88 residues processed: 451 average time/residue: 0.4488 time to fit residues: 310.3414 Evaluate side-chains 426 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 328 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain J residue 508 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 463 ASP Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain h residue 173 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 21 ARG Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 88 LYS Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 8.9990 chunk 296 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 125 optimal weight: 0.0470 chunk 226 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 260 optimal weight: 0.0000 chunk 272 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 overall best weight: 1.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 187 ASN ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 ASN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26504 Z= 0.213 Angle : 0.609 8.533 36022 Z= 0.314 Chirality : 0.044 0.181 3986 Planarity : 0.005 0.097 4690 Dihedral : 5.900 58.243 3642 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.67 % Allowed : 10.73 % Favored : 88.60 % Rotamer: Outliers : 4.27 % Allowed : 27.73 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 3282 helix: 0.72 (0.30), residues: 363 sheet: -0.74 (0.17), residues: 1057 loop : -2.15 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP K 79 HIS 0.003 0.001 HIS J 282 PHE 0.018 0.001 PHE f 163 TYR 0.017 0.001 TYR h 175 ARG 0.006 0.000 ARG e 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 326 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8571 (tm-30) REVERT: F 17 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7971 (p0) REVERT: F 182 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8057 (ptm160) REVERT: F 516 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8428 (p) REVERT: I 180 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8482 (p0) REVERT: J 96 TYR cc_start: 0.7743 (t80) cc_final: 0.7129 (t80) REVERT: J 183 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6469 (ttt180) REVERT: J 503 ARG cc_start: 0.7720 (ptt-90) cc_final: 0.7270 (ptp90) REVERT: J 523 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8204 (mt) REVERT: K 9 LYS cc_start: 0.7189 (mmtp) cc_final: 0.6841 (mmtp) REVERT: K 31 GLN cc_start: 0.8560 (mt0) cc_final: 0.7932 (mt0) REVERT: K 63 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7743 (mm-30) REVERT: K 64 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8420 (mp0) REVERT: L 1 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7709 (tmm) REVERT: L 192 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: L 214 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8287 (t80) REVERT: M 13 ASP cc_start: 0.8375 (m-30) cc_final: 0.8037 (t0) REVERT: M 98 VAL cc_start: 0.7040 (OUTLIER) cc_final: 0.6787 (m) REVERT: P 172 GLN cc_start: 0.7786 (mp10) cc_final: 0.6893 (tp40) REVERT: P 180 ASP cc_start: 0.8950 (t0) cc_final: 0.8593 (t0) REVERT: Y 1 MET cc_start: 0.5292 (tmm) cc_final: 0.4599 (mmt) REVERT: Y 63 GLU cc_start: 0.8553 (pp20) cc_final: 0.8095 (pp20) REVERT: Y 69 LYS cc_start: 0.7845 (tmtt) cc_final: 0.7293 (tmtt) REVERT: Z 62 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8306 (p) REVERT: Z 179 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8903 (pt) REVERT: Z 272 MET cc_start: 0.8955 (tpp) cc_final: 0.8604 (tpp) REVERT: Z 373 ARG cc_start: 0.8590 (ttt90) cc_final: 0.8335 (mtp85) REVERT: e 12 MET cc_start: 0.7601 (ttt) cc_final: 0.7256 (ttt) REVERT: e 95 MET cc_start: 0.7143 (tpp) cc_final: 0.6692 (tpp) REVERT: f 1 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8482 (tmm) REVERT: f 73 THR cc_start: 0.8202 (t) cc_final: 0.7965 (t) REVERT: f 159 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8685 (m-30) REVERT: h 171 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7442 (mptt) REVERT: h 197 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8397 (ptp-170) REVERT: m 83 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7661 (ttmm) outliers start: 122 outliers final: 92 residues processed: 419 average time/residue: 0.4492 time to fit residues: 287.7261 Evaluate side-chains 429 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 322 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 508 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 281 THR Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 461 THR Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 27 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain h residue 173 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 21 ARG Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 6.9990 chunk 304 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 254 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 ASN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26504 Z= 0.242 Angle : 0.621 8.917 36022 Z= 0.320 Chirality : 0.045 0.170 3986 Planarity : 0.005 0.097 4690 Dihedral : 5.922 59.195 3639 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.79 % Favored : 88.60 % Rotamer: Outliers : 4.27 % Allowed : 27.55 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.15), residues: 3282 helix: 0.73 (0.30), residues: 363 sheet: -0.77 (0.16), residues: 1062 loop : -2.15 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP e 6 HIS 0.004 0.001 HIS J 282 PHE 0.015 0.001 PHE f 163 TYR 0.018 0.001 TYR m 77 ARG 0.006 0.000 ARG e 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6564 Ramachandran restraints generated. 3282 Oldfield, 0 Emsley, 3282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 322 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8564 (tm-30) REVERT: F 17 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7995 (p0) REVERT: F 182 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8058 (ptm160) REVERT: F 516 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8453 (p) REVERT: I 180 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8517 (p0) REVERT: J 56 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: J 96 TYR cc_start: 0.7744 (t80) cc_final: 0.7120 (t80) REVERT: J 183 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6473 (ttt180) REVERT: J 503 ARG cc_start: 0.7729 (ptt-90) cc_final: 0.7277 (ptp90) REVERT: J 523 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8201 (mt) REVERT: K 9 LYS cc_start: 0.7140 (mmtp) cc_final: 0.6595 (mmtp) REVERT: K 31 GLN cc_start: 0.8563 (mt0) cc_final: 0.7933 (mt0) REVERT: K 64 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8457 (mp0) REVERT: K 97 ARG cc_start: 0.7286 (mmp-170) cc_final: 0.6673 (mmp-170) REVERT: L 1 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7676 (tmm) REVERT: L 192 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8634 (mp0) REVERT: L 214 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8242 (t80) REVERT: M 13 ASP cc_start: 0.8378 (m-30) cc_final: 0.8055 (t0) REVERT: M 98 VAL cc_start: 0.7005 (OUTLIER) cc_final: 0.6739 (m) REVERT: P 172 GLN cc_start: 0.7803 (mp10) cc_final: 0.6897 (tp40) REVERT: P 180 ASP cc_start: 0.8944 (t0) cc_final: 0.8601 (t0) REVERT: Y 69 LYS cc_start: 0.7844 (tmtt) cc_final: 0.7286 (tmtt) REVERT: Z 62 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8106 (p) REVERT: Z 179 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8922 (pt) REVERT: Z 272 MET cc_start: 0.8977 (tpp) cc_final: 0.8637 (tpp) REVERT: Z 373 ARG cc_start: 0.8594 (ttt90) cc_final: 0.8339 (mtp85) REVERT: Z 576 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8885 (mp) REVERT: e 12 MET cc_start: 0.7540 (ttt) cc_final: 0.7205 (ttt) REVERT: e 95 MET cc_start: 0.6987 (tpp) cc_final: 0.6529 (tpp) REVERT: f 1 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8488 (tmm) REVERT: f 73 THR cc_start: 0.8196 (t) cc_final: 0.7957 (t) REVERT: f 159 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8685 (m-30) REVERT: h 171 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7444 (mptt) REVERT: h 197 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8286 (ptp90) REVERT: m 83 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7541 (tptm) outliers start: 122 outliers final: 95 residues processed: 417 average time/residue: 0.4186 time to fit residues: 267.7747 Evaluate side-chains 435 residues out of total 2860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 323 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 325 CYS Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 587 THR Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 135 VAL Chi-restraints excluded: chain J residue 177 PHE Chi-restraints excluded: chain J residue 183 ARG Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 222 VAL Chi-restraints excluded: chain J residue 244 GLN Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 325 CYS Chi-restraints excluded: chain J residue 329 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 349 MET Chi-restraints excluded: chain J residue 377 VAL Chi-restraints excluded: chain J residue 508 ASP Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 69 ASN Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 158 THR Chi-restraints excluded: chain L residue 192 GLU Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 214 PHE Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 38 ASN Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 98 VAL Chi-restraints excluded: chain N residue 12 CYS Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain P residue 173 ASN Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 62 SER Chi-restraints excluded: chain Z residue 97 ASP Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 189 THR Chi-restraints excluded: chain Z residue 190 THR Chi-restraints excluded: chain Z residue 193 LEU Chi-restraints excluded: chain Z residue 243 LEU Chi-restraints excluded: chain Z residue 281 THR Chi-restraints excluded: chain Z residue 291 LEU Chi-restraints excluded: chain Z residue 340 SER Chi-restraints excluded: chain Z residue 344 SER Chi-restraints excluded: chain Z residue 368 THR Chi-restraints excluded: chain Z residue 377 VAL Chi-restraints excluded: chain Z residue 381 ASP Chi-restraints excluded: chain Z residue 451 LEU Chi-restraints excluded: chain Z residue 461 THR Chi-restraints excluded: chain Z residue 544 VAL Chi-restraints excluded: chain Z residue 566 LEU Chi-restraints excluded: chain Z residue 576 ILE Chi-restraints excluded: chain Z residue 606 ASP Chi-restraints excluded: chain e residue 3 THR Chi-restraints excluded: chain e residue 27 ASP Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 38 ASN Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 133 SER Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 159 ASP Chi-restraints excluded: chain h residue 173 ASN Chi-restraints excluded: chain h residue 174 THR Chi-restraints excluded: chain h residue 197 ARG Chi-restraints excluded: chain h residue 202 VAL Chi-restraints excluded: chain h residue 218 VAL Chi-restraints excluded: chain h residue 219 VAL Chi-restraints excluded: chain m residue 5 ARG Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 21 ARG Chi-restraints excluded: chain m residue 46 VAL Chi-restraints excluded: chain m residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 234 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 40 ASN Z 48 ASN ** Z 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 205 GLN ** m 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.128347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101333 restraints weight = 46102.283| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.80 r_work: 0.3069 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26504 Z= 0.191 Angle : 0.607 8.583 36022 Z= 0.312 Chirality : 0.044 0.205 3986 Planarity : 0.005 0.093 4690 Dihedral : 5.823 58.604 3639 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.48 % Favored : 88.94 % Rotamer: Outliers : 4.27 % Allowed : 27.59 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 3282 helix: 0.72 (0.30), residues: 363 sheet: -0.74 (0.17), residues: 1050 loop : -2.12 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP e 6 HIS 0.003 0.001 HIS J 282 PHE 0.013 0.001 PHE F 264 TYR 0.019 0.001 TYR m 77 ARG 0.007 0.000 ARG Y 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6487.65 seconds wall clock time: 118 minutes 51.23 seconds (7131.23 seconds total)