Starting phenix.real_space_refine on Tue Aug 26 17:50:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b0x_44061/08_2025/9b0x_44061_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b0x_44061/08_2025/9b0x_44061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b0x_44061/08_2025/9b0x_44061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b0x_44061/08_2025/9b0x_44061.map" model { file = "/net/cci-nas-00/data/ceres_data/9b0x_44061/08_2025/9b0x_44061_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b0x_44061/08_2025/9b0x_44061_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.010 sd= 1.010 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 5 5.21 5 S 169 5.16 5 C 25399 2.51 5 N 6753 2.21 5 O 7486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39830 Number of models: 1 Model: "" Number of chains: 34 Chain: "1" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "A" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3844 Classifications: {'peptide': 504} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 482} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3842 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain: "C" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3828 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 479} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3525 Classifications: {'peptide': 465} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 439} Chain: "E" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3554 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 443} Chain: "F" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3554 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 443} Chain: "G" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2013 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain breaks: 1 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 984 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 292 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1686 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "M" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1309 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 14, 'TRANS': 146} Chain: "N" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1716 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 206} Chain: "O" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1451 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 220 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'UNK:plan-1': 44} Unresolved non-hydrogen planarities: 44 Chain: "Q" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 390 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "R" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "S" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 596 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "T" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 167 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Time building chain proxies: 8.26, per 1000 atoms: 0.21 Number of scatterers: 39830 At special positions: 0 Unit cell: (140.976, 151.656, 249.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 169 16.00 P 18 15.00 Mg 5 11.99 O 7486 8.00 N 6753 7.00 C 25399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9460 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 24 sheets defined 60.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain '1' and resid 1 through 15 Processing helix chain '1' and resid 18 through 38 Processing helix chain '1' and resid 39 through 41 No H-bonds generated for 'chain '1' and resid 39 through 41' Processing helix chain '1' and resid 42 through 74 removed outlier: 3.570A pdb=" N LEU 1 56 " --> pdb=" O LEU 1 52 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA 1 59 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET 1 60 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY 1 61 " --> pdb=" O SER 1 57 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS 1 64 " --> pdb=" O MET 1 60 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE 1 73 " --> pdb=" O PHE 1 69 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 13 Processing helix chain '2' and resid 14 through 16 No H-bonds generated for 'chain '2' and resid 14 through 16' Processing helix chain '2' and resid 17 through 38 removed outlier: 3.636A pdb=" N ARG 2 38 " --> pdb=" O ILE 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 74 removed outlier: 3.578A pdb=" N LEU 2 46 " --> pdb=" O LEU 2 42 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR 2 49 " --> pdb=" O GLN 2 45 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET 2 67 " --> pdb=" O PHE 2 63 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 15 Processing helix chain '3' and resid 16 through 38 removed outlier: 4.205A pdb=" N GLY 3 20 " --> pdb=" O VAL 3 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER 3 21 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE 3 34 " --> pdb=" O GLY 3 30 " (cutoff:3.500A) Processing helix chain '3' and resid 39 through 41 No H-bonds generated for 'chain '3' and resid 39 through 41' Processing helix chain '3' and resid 42 through 71 removed outlier: 4.180A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS 3 64 " --> pdb=" O MET 3 60 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 13 Processing helix chain '4' and resid 14 through 16 No H-bonds generated for 'chain '4' and resid 14 through 16' Processing helix chain '4' and resid 17 through 38 removed outlier: 3.630A pdb=" N SER 4 21 " --> pdb=" O GLY 4 17 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG 4 38 " --> pdb=" O ILE 4 34 " (cutoff:3.500A) Processing helix chain '4' and resid 39 through 43 removed outlier: 3.841A pdb=" N LEU 4 42 " --> pdb=" O ASN 4 39 " (cutoff:3.500A) Processing helix chain '4' and resid 44 through 71 removed outlier: 3.614A pdb=" N GLY 4 61 " --> pdb=" O SER 4 57 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 15 Processing helix chain '5' and resid 17 through 38 removed outlier: 4.051A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 39 through 41 No H-bonds generated for 'chain '5' and resid 39 through 41' Processing helix chain '5' and resid 42 through 74 removed outlier: 4.297A pdb=" N ALA 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET 5 60 " --> pdb=" O LEU 5 56 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 15 Processing helix chain '6' and resid 18 through 38 removed outlier: 3.535A pdb=" N ILE 6 33 " --> pdb=" O PHE 6 29 " (cutoff:3.500A) Processing helix chain '6' and resid 39 through 41 No H-bonds generated for 'chain '6' and resid 39 through 41' Processing helix chain '6' and resid 42 through 71 removed outlier: 4.012A pdb=" N ALA 6 59 " --> pdb=" O ALA 6 55 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 15 Processing helix chain '7' and resid 18 through 38 removed outlier: 3.503A pdb=" N ARG 7 38 " --> pdb=" O ILE 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 39 through 41 No H-bonds generated for 'chain '7' and resid 39 through 41' Processing helix chain '7' and resid 42 through 71 removed outlier: 3.631A pdb=" N ALA 7 59 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 15 Processing helix chain '8' and resid 17 through 38 removed outlier: 3.824A pdb=" N ARG 8 38 " --> pdb=" O ILE 8 34 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 41 No H-bonds generated for 'chain '8' and resid 39 through 41' Processing helix chain '8' and resid 42 through 73 removed outlier: 3.528A pdb=" N MET 8 60 " --> pdb=" O LEU 8 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY 8 61 " --> pdb=" O SER 8 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE 8 73 " --> pdb=" O PHE 8 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.635A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 104 " --> pdb=" O GLU A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 104' Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.848A pdb=" N GLN A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 4.053A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 295 through 296 No H-bonds generated for 'chain 'A' and resid 295 through 296' Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.665A pdb=" N HIS A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.769A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 378 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 380 through 400 removed outlier: 4.028A pdb=" N SER A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.777A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 476 removed outlier: 3.557A pdb=" N SER A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.921A pdb=" N LEU A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.877A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 removed outlier: 3.586A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.673A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 3.890A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 295 through 296 No H-bonds generated for 'chain 'B' and resid 295 through 296' Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.679A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.644A pdb=" N GLY B 317 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.598A pdb=" N ALA B 377 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 401 removed outlier: 3.836A pdb=" N SER B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 405 Processing helix chain 'B' and resid 411 through 429 removed outlier: 3.617A pdb=" N LYS B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.989A pdb=" N SER B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 475 " --> pdb=" O HIS B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 490 through 508 Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.695A pdb=" N ALA C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 20 " --> pdb=" O ILE C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.681A pdb=" N HIS C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.598A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.655A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 260 Proline residue: C 247 - end of helix removed outlier: 3.991A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.681A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.639A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.520A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 378 " --> pdb=" O GLY C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 4.225A pdb=" N SER C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.634A pdb=" N GLN C 405 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 406 " --> pdb=" O PHE C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 402 through 406' Processing helix chain 'C' and resid 411 through 428 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 474 removed outlier: 3.676A pdb=" N SER C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.808A pdb=" N LEU C 480 " --> pdb=" O HIS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 234 through 249 Processing helix chain 'D' and resid 261 through 275 removed outlier: 3.748A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 339 through 345 Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 367 through 394 removed outlier: 4.556A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 418 removed outlier: 3.781A pdb=" N SER D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 436 through 449 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 465 through 476 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 164 through 176 Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.993A pdb=" N HIS E 180 " --> pdb=" O ALA E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 234 through 249 Processing helix chain 'E' and resid 261 through 273 removed outlier: 3.892A pdb=" N THR E 265 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA E 273 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 316 through 319 Processing helix chain 'E' and resid 322 through 330 removed outlier: 4.305A pdb=" N ALA E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 345 Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 367 through 394 removed outlier: 4.353A pdb=" N ASP E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 417 removed outlier: 4.046A pdb=" N ASP E 403 " --> pdb=" O LEU E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 436 through 450 Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 466 through 480 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 180 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.782A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.600A pdb=" N MET F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 319 Processing helix chain 'F' and resid 322 through 330 removed outlier: 3.706A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 345 removed outlier: 3.567A pdb=" N LEU F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 394 removed outlier: 4.503A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 removed outlier: 3.803A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 424 through 429 Processing helix chain 'F' and resid 436 through 449 Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 465 through 480 removed outlier: 3.545A pdb=" N VAL F 469 " --> pdb=" O PRO F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 56 removed outlier: 4.062A pdb=" N VAL G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) Proline residue: G 43 - end of helix removed outlier: 4.130A pdb=" N PHE G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 94 Processing helix chain 'G' and resid 105 through 117 removed outlier: 3.756A pdb=" N ARG G 109 " --> pdb=" O GLY G 105 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG G 114 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU G 115 " --> pdb=" O ILE G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 147 Processing helix chain 'G' and resid 176 through 182 Processing helix chain 'G' and resid 184 through 189 removed outlier: 4.010A pdb=" N ALA G 187 " --> pdb=" O ASP G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 267 removed outlier: 4.026A pdb=" N ALA G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 121 Processing helix chain 'H' and resid 125 through 147 Processing helix chain 'I' and resid 12 through 16 Processing helix chain 'I' and resid 19 through 33 Processing helix chain 'I' and resid 38 through 44 removed outlier: 4.460A pdb=" N GLU I 42 " --> pdb=" O GLU I 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 26 Processing helix chain 'J' and resid 28 through 45 Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'K' and resid 31 through 48 removed outlier: 4.583A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 120 removed outlier: 4.214A pdb=" N TYR K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR K 59 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LYS K 76 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 184 Processing helix chain 'K' and resid 186 through 207 Processing helix chain 'L' and resid 5 through 25 Processing helix chain 'L' and resid 33 through 52 Processing helix chain 'M' and resid 11 through 19 removed outlier: 3.616A pdb=" N MET M 15 " --> pdb=" O ASP M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 24 Processing helix chain 'M' and resid 25 through 43 removed outlier: 3.583A pdb=" N ALA M 32 " --> pdb=" O ASN M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 60 removed outlier: 3.999A pdb=" N TYR M 56 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 124 Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'N' and resid 17 through 23 removed outlier: 3.556A pdb=" N LEU N 20 " --> pdb=" O SER N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.726A pdb=" N PHE N 28 " --> pdb=" O ILE N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 56 Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 66 through 82 Processing helix chain 'N' and resid 95 through 118 removed outlier: 3.691A pdb=" N THR N 99 " --> pdb=" O HIS N 95 " (cutoff:3.500A) Proline residue: N 105 - end of helix Processing helix chain 'N' and resid 118 through 126 removed outlier: 3.524A pdb=" N LEU N 126 " --> pdb=" O ALA N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 175 removed outlier: 4.191A pdb=" N MET N 139 " --> pdb=" O LEU N 135 " (cutoff:3.500A) Proline residue: N 151 - end of helix removed outlier: 4.099A pdb=" N MET N 162 " --> pdb=" O LEU N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 219 removed outlier: 3.615A pdb=" N GLU N 219 " --> pdb=" O LEU N 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 29 Processing helix chain 'O' and resid 31 through 49 Processing helix chain 'O' and resid 49 through 58 removed outlier: 3.767A pdb=" N GLY O 53 " --> pdb=" O PHE O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 76 removed outlier: 4.244A pdb=" N GLU O 76 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 93 Processing helix chain 'O' and resid 95 through 97 No H-bonds generated for 'chain 'O' and resid 95 through 97' Processing helix chain 'O' and resid 98 through 114 Processing helix chain 'O' and resid 129 through 141 removed outlier: 3.510A pdb=" N ASP O 134 " --> pdb=" O ALA O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 160 Processing helix chain 'O' and resid 175 through 189 Processing helix chain 'P' and resid 4 through 9 Processing helix chain 'P' and resid 13 through 20 removed outlier: 3.619A pdb=" N UNK P 20 " --> pdb=" O UNK P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 44 Processing helix chain 'Q' and resid 9 through 29 Processing helix chain 'Q' and resid 40 through 45 Processing helix chain 'R' and resid 29 through 33 removed outlier: 3.596A pdb=" N GLN R 32 " --> pdb=" O PRO R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 45 Processing helix chain 'R' and resid 48 through 68 Processing helix chain 'R' and resid 75 through 93 removed outlier: 3.632A pdb=" N ILE R 82 " --> pdb=" O TYR R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 99 Processing helix chain 'S' and resid 27 through 36 Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 44 through 60 removed outlier: 3.750A pdb=" N GLY S 51 " --> pdb=" O LYS S 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS S 60 " --> pdb=" O ILE S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 94 removed outlier: 3.931A pdb=" N TRP S 85 " --> pdb=" O GLU S 81 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 35 removed outlier: 6.716A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 43 current: chain 'A' and resid 60 through 66 removed outlier: 6.380A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 current: chain 'B' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 5.713A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 75 current: chain 'D' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 23 through 28 current: chain 'D' and resid 49 through 57 removed outlier: 5.612A pdb=" N VAL D 52 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE D 64 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 60 through 65 current: chain 'E' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 23 through 28 current: chain 'E' and resid 49 through 57 removed outlier: 5.655A pdb=" N VAL E 52 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE E 64 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.259A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.391A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASP A 269 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.477A pdb=" N ILE A 159 " --> pdb=" O MET A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.071A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.271A pdb=" N VAL B 108 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.042A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL F 19 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP F 25 " --> pdb=" O THR F 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.219A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.405A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 88 Processing sheet with id=AB2, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.302A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER D 184 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL D 221 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE D 186 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY D 223 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY D 188 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 183 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLY D 153 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLN D 311 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE D 155 " --> pdb=" O GLN D 311 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE D 313 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU D 157 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS D 154 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR D 336 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY D 156 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.213A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 88 Processing sheet with id=AB5, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.202A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N TYR E 314 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE E 313 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU E 157 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LYS E 154 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR E 336 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY E 156 " --> pdb=" O THR E 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.150A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 86 through 88 Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.316A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AC1, first strand: chain 'F' and resid 184 through 191 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 218 through 220 current: chain 'F' and resid 306 through 311 Processing sheet with id=AC2, first strand: chain 'G' and resid 120 through 124 removed outlier: 6.321A pdb=" N VAL G 101 " --> pdb=" O MET G 122 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N CYS G 124 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS G 103 " --> pdb=" O CYS G 124 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE G 68 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL G 104 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA G 70 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU G 67 " --> pdb=" O LYS G 155 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL G 157 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE G 69 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ASN G 159 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N ILE G 71 " --> pdb=" O ASN G 159 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N PHE G 161 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR G 158 " --> pdb=" O THR G 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 17 through 18 removed outlier: 5.987A pdb=" N ALA H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL H 92 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.633A pdb=" N GLY H 61 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AC6, first strand: chain 'O' and resid 148 through 155 2307 hydrogen bonds defined for protein. 6726 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: 7.46 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6917 1.32 - 1.44: 9659 1.44 - 1.57: 23577 1.57 - 1.69: 31 1.69 - 1.81: 314 Bond restraints: 40498 Sorted by residual: bond pdb=" O5' ATP C 601 " pdb=" PA ATP C 601 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.27e+00 bond pdb=" O5' ATP B 601 " pdb=" PA ATP B 601 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.27e+00 bond pdb=" O5' ATP D 601 " pdb=" PA ATP D 601 " ideal model delta sigma weight residual 1.579 1.609 -0.030 1.10e-02 8.26e+03 7.21e+00 bond pdb=" O5' ATP A 601 " pdb=" PA ATP A 601 " ideal model delta sigma weight residual 1.579 1.608 -0.029 1.10e-02 8.26e+03 7.16e+00 bond pdb=" O2B ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 1.529 1.477 0.052 2.20e-02 2.07e+03 5.64e+00 ... (remaining 40493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 54308 2.47 - 4.94: 356 4.94 - 7.41: 57 7.41 - 9.89: 2 9.89 - 12.36: 3 Bond angle restraints: 54726 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 127.51 12.36 1.00e+00 1.00e+00 1.53e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 128.42 11.45 1.00e+00 1.00e+00 1.31e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 129.28 10.59 1.00e+00 1.00e+00 1.12e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 131.10 8.77 1.00e+00 1.00e+00 7.68e+01 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 129.24 7.59 1.00e+00 1.00e+00 5.75e+01 ... (remaining 54721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.08: 23376 21.08 - 42.16: 995 42.16 - 63.23: 228 63.23 - 84.31: 24 84.31 - 105.39: 5 Dihedral angle restraints: 24628 sinusoidal: 9857 harmonic: 14771 Sorted by residual: dihedral pdb=" CA MET N 136 " pdb=" C MET N 136 " pdb=" N PRO N 137 " pdb=" CA PRO N 137 " ideal model delta harmonic sigma weight residual 180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA SER F 45 " pdb=" C SER F 45 " pdb=" N PRO F 46 " pdb=" CA PRO F 46 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA VAL F 221 " pdb=" C VAL F 221 " pdb=" N TYR F 222 " pdb=" CA TYR F 222 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 24625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3869 0.031 - 0.062: 1558 0.062 - 0.094: 516 0.094 - 0.125: 298 0.125 - 0.156: 33 Chirality restraints: 6274 Sorted by residual: chirality pdb=" C3' ATP A 601 " pdb=" C2' ATP A 601 " pdb=" C4' ATP A 601 " pdb=" O3' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" C3' ATP D 601 " pdb=" C2' ATP D 601 " pdb=" C4' ATP D 601 " pdb=" O3' ATP D 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA PRO N 87 " pdb=" N PRO N 87 " pdb=" C PRO N 87 " pdb=" CB PRO N 87 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 6271 not shown) Planarity restraints: 7019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 69 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO R 70 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 70 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 70 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 464 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO E 465 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 465 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 465 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 45 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO F 46 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 46 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 46 " -0.032 5.00e-02 4.00e+02 ... (remaining 7016 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 132 2.42 - 3.04: 22311 3.04 - 3.66: 61641 3.66 - 4.28: 94532 4.28 - 4.90: 154938 Nonbonded interactions: 333554 Sorted by model distance: nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 1.797 2.170 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.827 2.170 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 1.872 2.170 nonbonded pdb=" O2G ATP D 601 " pdb="MG MG D 602 " model vdw 1.923 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.960 2.170 ... (remaining 333549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } ncs_group { reference = (chain 'A' and (resid 8 through 508 or resid 601 through 602)) selection = (chain 'B' and (resid 8 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 602)) selection = (chain 'C' and (resid 8 through 21 or (resid 22 through 23 and (name N or name C \ A or name C or name O or name CB )) or resid 24 through 602)) } ncs_group { reference = (chain 'D' and resid 12 through 476) selection = (chain 'E' and resid 12 through 476) selection = (chain 'F' and resid 12 through 476) } 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: 8.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 32.040 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.120 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:6.660 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40498 Z= 0.154 Angle : 0.553 12.358 54726 Z= 0.308 Chirality : 0.042 0.156 6274 Planarity : 0.005 0.068 7019 Dihedral : 12.419 105.388 15168 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 3.06 % Allowed : 6.33 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.11), residues: 5089 helix: -0.66 (0.08), residues: 2711 sheet: 0.02 (0.24), residues: 515 loop : -0.77 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 38 TYR 0.017 0.001 TYR G 44 PHE 0.015 0.001 PHE H 45 TRP 0.013 0.001 TRP N 107 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00349 (40498) covalent geometry : angle 0.55253 (54726) hydrogen bonds : bond 0.20188 ( 2307) hydrogen bonds : angle 7.32755 ( 6726) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 985 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 58 GLU cc_start: 0.7338 (tt0) cc_final: 0.7061 (tp30) REVERT: 1 64 CYS cc_start: 0.6280 (OUTLIER) cc_final: 0.5866 (m) REVERT: 1 69 PHE cc_start: 0.4271 (m-10) cc_final: 0.3968 (m-80) REVERT: 3 67 MET cc_start: 0.6625 (tpp) cc_final: 0.6219 (tpp) REVERT: 4 38 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7463 (ptt180) REVERT: 6 51 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6514 (mp) REVERT: 7 38 ARG cc_start: 0.6496 (ptm-80) cc_final: 0.6176 (ptp90) REVERT: 8 18 VAL cc_start: 0.3417 (OUTLIER) cc_final: 0.3169 (p) REVERT: A 26 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6938 (tt0) REVERT: A 40 ARG cc_start: 0.8418 (mtt-85) cc_final: 0.8121 (mtp85) REVERT: A 195 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7837 (tp30) REVERT: A 253 MET cc_start: 0.8951 (mtt) cc_final: 0.8733 (mtt) REVERT: A 355 GLU cc_start: 0.8274 (tt0) cc_final: 0.7920 (tp30) REVERT: A 392 LEU cc_start: 0.8032 (mt) cc_final: 0.7691 (mp) REVERT: A 420 ARG cc_start: 0.7703 (tpp80) cc_final: 0.7453 (tpt-90) REVERT: A 426 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 460 LYS cc_start: 0.8631 (mttt) cc_final: 0.8299 (mmtt) REVERT: A 488 GLN cc_start: 0.7919 (pt0) cc_final: 0.7616 (pt0) REVERT: A 496 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8122 (mttt) REVERT: B 15 LYS cc_start: 0.7952 (mmtp) cc_final: 0.7743 (mppt) REVERT: B 54 GLU cc_start: 0.8196 (tt0) cc_final: 0.7948 (tp30) REVERT: B 59 LEU cc_start: 0.8460 (mt) cc_final: 0.8218 (mp) REVERT: B 67 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 143 ARG cc_start: 0.7445 (ptp-110) cc_final: 0.7144 (pmm-80) REVERT: B 181 ASP cc_start: 0.8376 (m-30) cc_final: 0.8160 (m-30) REVERT: B 196 LYS cc_start: 0.8200 (mttt) cc_final: 0.7538 (mptp) REVERT: B 266 ILE cc_start: 0.8685 (mm) cc_final: 0.8417 (tp) REVERT: B 367 VAL cc_start: 0.8068 (t) cc_final: 0.7796 (m) REVERT: B 385 GLN cc_start: 0.7830 (tt0) cc_final: 0.7372 (mt0) REVERT: B 440 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: B 468 PHE cc_start: 0.7566 (t80) cc_final: 0.7298 (t80) REVERT: C 26 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8083 (mp0) REVERT: C 127 GLN cc_start: 0.8359 (tp40) cc_final: 0.8059 (tt0) REVERT: C 170 ASP cc_start: 0.8187 (m-30) cc_final: 0.7829 (m-30) REVERT: C 227 ARG cc_start: 0.8315 (mtt90) cc_final: 0.8111 (mtm-85) REVERT: C 301 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8472 (tp) REVERT: C 355 GLU cc_start: 0.8374 (tt0) cc_final: 0.8111 (tt0) REVERT: C 376 SER cc_start: 0.8938 (p) cc_final: 0.8555 (p) REVERT: C 385 GLN cc_start: 0.8357 (tt0) cc_final: 0.7936 (pt0) REVERT: C 457 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7480 (pt0) REVERT: C 463 LYS cc_start: 0.8225 (mtpt) cc_final: 0.8023 (ttpm) REVERT: C 488 GLN cc_start: 0.7542 (pt0) cc_final: 0.7036 (pt0) REVERT: D 15 GLN cc_start: 0.8498 (mt0) cc_final: 0.8217 (mt0) REVERT: D 20 ILE cc_start: 0.8557 (mt) cc_final: 0.8183 (tp) REVERT: D 128 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7190 (pt0) REVERT: D 129 MET cc_start: 0.8565 (mmt) cc_final: 0.8353 (mmt) REVERT: D 178 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7773 (mptt) REVERT: D 212 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7864 (mtmm) REVERT: D 214 LYS cc_start: 0.8717 (mttt) cc_final: 0.8358 (mtpp) REVERT: D 409 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7807 (mtt180) REVERT: D 438 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7933 (ttpp) REVERT: D 446 MET cc_start: 0.8349 (mtt) cc_final: 0.8046 (mtp) REVERT: E 15 GLN cc_start: 0.8357 (mt0) cc_final: 0.7808 (mm-40) REVERT: E 92 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8520 (tp30) REVERT: E 227 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8339 (mm-30) REVERT: E 291 ASP cc_start: 0.8601 (m-30) cc_final: 0.8359 (m-30) REVERT: E 342 ILE cc_start: 0.8807 (mm) cc_final: 0.8580 (mp) REVERT: E 362 ASP cc_start: 0.8452 (t0) cc_final: 0.8129 (t0) REVERT: E 387 LEU cc_start: 0.7888 (mt) cc_final: 0.7686 (mt) REVERT: E 422 GLN cc_start: 0.8374 (tp40) cc_final: 0.8058 (tp40) REVERT: E 446 MET cc_start: 0.8174 (mtt) cc_final: 0.7837 (mtp) REVERT: F 15 GLN cc_start: 0.8674 (mt0) cc_final: 0.8465 (mt0) REVERT: F 31 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7764 (mm110) REVERT: F 47 ARG cc_start: 0.7946 (mmm-85) cc_final: 0.7502 (mmm160) REVERT: F 115 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8126 (mttt) REVERT: F 344 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7739 (mm-30) REVERT: F 385 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8094 (ttpp) REVERT: F 422 GLN cc_start: 0.8071 (tt0) cc_final: 0.7682 (tm130) REVERT: G 11 LYS cc_start: 0.8508 (tttt) cc_final: 0.8296 (tptp) REVERT: G 56 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7696 (tm-30) REVERT: G 233 LYS cc_start: 0.8351 (mttt) cc_final: 0.7952 (mtmt) REVERT: G 237 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7731 (mm-30) REVERT: G 244 MET cc_start: 0.8183 (mtm) cc_final: 0.7960 (mmm) REVERT: H 19 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7764 (p) REVERT: I 25 ASP cc_start: 0.7363 (m-30) cc_final: 0.7084 (p0) REVERT: I 28 VAL cc_start: 0.8111 (p) cc_final: 0.7649 (p) REVERT: K 113 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8277 (mtm-85) REVERT: K 125 PHE cc_start: 0.8087 (m-80) cc_final: 0.7757 (m-80) REVERT: L 10 LEU cc_start: 0.6832 (tp) cc_final: 0.6253 (tm) REVERT: M 44 TYR cc_start: 0.7861 (m-80) cc_final: 0.7611 (m-80) REVERT: M 89 ILE cc_start: 0.9201 (mt) cc_final: 0.8861 (pt) REVERT: M 141 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6642 (pt0) REVERT: N 1 MET cc_start: 0.3494 (mtt) cc_final: 0.1679 (pmm) REVERT: N 80 ASN cc_start: 0.8701 (m-40) cc_final: 0.8434 (m110) REVERT: N 90 PHE cc_start: 0.5317 (OUTLIER) cc_final: 0.4699 (p90) REVERT: N 142 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.5633 (tmm) REVERT: N 189 PHE cc_start: 0.8522 (t80) cc_final: 0.8241 (t80) REVERT: O 6 LYS cc_start: 0.8257 (tttt) cc_final: 0.7916 (tppt) REVERT: O 12 PHE cc_start: 0.7294 (m-80) cc_final: 0.7040 (m-80) REVERT: O 17 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.8292 (ttm-80) REVERT: O 41 GLN cc_start: 0.7893 (tt0) cc_final: 0.7591 (tp40) REVERT: O 49 PHE cc_start: 0.7867 (m-80) cc_final: 0.7544 (m-80) REVERT: O 97 LYS cc_start: 0.8267 (mmtp) cc_final: 0.8012 (tmtm) REVERT: O 125 LYS cc_start: 0.7804 (mtmm) cc_final: 0.7375 (ptmm) REVERT: O 140 LYS cc_start: 0.8197 (tttt) cc_final: 0.7878 (mmtp) REVERT: O 174 MET cc_start: 0.5342 (ttm) cc_final: 0.4615 (ptm) REVERT: O 176 ILE cc_start: 0.7225 (mm) cc_final: 0.6907 (mt) REVERT: Q 26 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6460 (tmt) REVERT: Q 52 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7666 (mmtt) REVERT: R 21 ARG cc_start: 0.5928 (ttt180) cc_final: 0.5698 (ttp-170) REVERT: S 63 LYS cc_start: 0.6601 (mmtp) cc_final: 0.5526 (pptt) REVERT: T 46 GLU cc_start: 0.8889 (tp30) cc_final: 0.8572 (tp30) outliers start: 127 outliers final: 40 residues processed: 1085 average time/residue: 0.6527 time to fit residues: 859.8849 Evaluate side-chains 687 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 635 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 64 CYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 4 residue 32 LEU Chi-restraints excluded: chain 4 residue 38 ARG Chi-restraints excluded: chain 4 residue 45 GLN Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 63 PHE Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 18 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 145 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 90 PHE Chi-restraints excluded: chain N residue 142 MET Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain N residue 163 ILE Chi-restraints excluded: chain N residue 204 ILE Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 87 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 494 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN A 172 GLN A 385 GLN B 316 ASN B 470 GLN C 127 GLN C 215 GLN C 416 GLN D 15 GLN D 37 ASN D 76 GLN D 133 GLN D 180 HIS ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 HIS D 372 ASN D 388 GLN E 27 GLN E 54 GLN E 77 ASN E 174 ASN E 180 HIS E 224 GLN E 331 HIS E 382 GLN E 419 GLN E 449 ASN F 13 ASN F 15 GLN F 27 GLN F 31 GLN F 37 ASN F 55 HIS F 59 ASN F 77 ASN F 174 ASN F 249 GLN F 311 GLN F 364 ASN F 388 GLN F 414 GLN F 419 GLN F 430 HIS F 480 GLN H 32 ASN H 85 ASN H 102 ASN J 4 GLN L 75 ASN O 41 GLN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 57 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.178033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.147578 restraints weight = 75293.566| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.45 r_work: 0.3722 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 40498 Z= 0.146 Angle : 0.594 9.807 54726 Z= 0.307 Chirality : 0.043 0.169 6274 Planarity : 0.005 0.067 7019 Dihedral : 8.932 102.389 5960 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.14 % Allowed : 14.52 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.12), residues: 5089 helix: 1.00 (0.10), residues: 2744 sheet: -0.07 (0.23), residues: 521 loop : -0.52 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 157 TYR 0.022 0.001 TYR G 44 PHE 0.028 0.001 PHE 3 63 TRP 0.015 0.001 TRP S 73 HIS 0.011 0.001 HIS N 95 Details of bonding type rmsd covalent geometry : bond 0.00316 (40498) covalent geometry : angle 0.59381 (54726) hydrogen bonds : bond 0.04864 ( 2307) hydrogen bonds : angle 4.93852 ( 6726) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 714 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 18 VAL cc_start: 0.5850 (m) cc_final: 0.5555 (p) REVERT: 4 58 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7072 (tm-30) REVERT: 5 3 ASP cc_start: 0.6906 (m-30) cc_final: 0.6384 (p0) REVERT: 5 71 LEU cc_start: 0.8007 (mt) cc_final: 0.7622 (mt) REVERT: 6 51 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6515 (mp) REVERT: 7 18 VAL cc_start: 0.6789 (OUTLIER) cc_final: 0.6501 (p) REVERT: A 26 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7176 (tt0) REVERT: A 40 ARG cc_start: 0.8435 (mtt-85) cc_final: 0.8183 (mtp85) REVERT: A 195 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7538 (tp30) REVERT: A 335 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8428 (p) REVERT: A 355 GLU cc_start: 0.8075 (tt0) cc_final: 0.7502 (tp30) REVERT: A 359 LYS cc_start: 0.8252 (mttm) cc_final: 0.8040 (mtpt) REVERT: A 371 VAL cc_start: 0.7783 (OUTLIER) cc_final: 0.7440 (p) REVERT: A 415 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7771 (mt0) REVERT: A 423 ARG cc_start: 0.7014 (mpt90) cc_final: 0.6775 (mtt90) REVERT: A 426 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 460 LYS cc_start: 0.8386 (mttt) cc_final: 0.8149 (mmtt) REVERT: A 496 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8130 (mttt) REVERT: B 15 LYS cc_start: 0.7914 (mmtp) cc_final: 0.7692 (mppt) REVERT: B 54 GLU cc_start: 0.8313 (tt0) cc_final: 0.7998 (tp30) REVERT: B 59 LEU cc_start: 0.8498 (mt) cc_final: 0.8241 (mp) REVERT: B 143 ARG cc_start: 0.7431 (ptp-110) cc_final: 0.7169 (pmm-80) REVERT: B 181 ASP cc_start: 0.8295 (m-30) cc_final: 0.8036 (m-30) REVERT: B 196 LYS cc_start: 0.8175 (mttt) cc_final: 0.7529 (mptp) REVERT: B 353 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7545 (mp0) REVERT: B 367 VAL cc_start: 0.8149 (t) cc_final: 0.7935 (m) REVERT: B 369 LEU cc_start: 0.8519 (mt) cc_final: 0.8254 (mt) REVERT: B 381 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7569 (ttp80) REVERT: B 385 GLN cc_start: 0.7922 (tt0) cc_final: 0.7565 (tt0) REVERT: B 418 LEU cc_start: 0.7073 (tm) cc_final: 0.6669 (mt) REVERT: B 446 TYR cc_start: 0.7534 (t80) cc_final: 0.7260 (t80) REVERT: B 468 PHE cc_start: 0.7547 (t80) cc_final: 0.7318 (t80) REVERT: C 26 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8148 (mp0) REVERT: C 52 MET cc_start: 0.8951 (mmm) cc_final: 0.8697 (mmm) REVERT: C 89 LYS cc_start: 0.8600 (mtmp) cc_final: 0.7927 (mttp) REVERT: C 101 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: C 127 GLN cc_start: 0.8321 (tp-100) cc_final: 0.8026 (tt0) REVERT: C 143 ARG cc_start: 0.8031 (ptp90) cc_final: 0.7751 (mtm110) REVERT: C 170 ASP cc_start: 0.8251 (m-30) cc_final: 0.8001 (m-30) REVERT: C 355 GLU cc_start: 0.8061 (tt0) cc_final: 0.7794 (tt0) REVERT: C 385 GLN cc_start: 0.8346 (tt0) cc_final: 0.7951 (pt0) REVERT: C 457 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7503 (pt0) REVERT: C 463 LYS cc_start: 0.8246 (mtpt) cc_final: 0.8008 (ttpm) REVERT: C 470 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8056 (mp10) REVERT: C 488 GLN cc_start: 0.7684 (pt0) cc_final: 0.7196 (pt0) REVERT: C 500 VAL cc_start: 0.8532 (t) cc_final: 0.7680 (t) REVERT: D 15 GLN cc_start: 0.8486 (mt0) cc_final: 0.8197 (mt0) REVERT: D 170 MET cc_start: 0.8186 (mmm) cc_final: 0.7814 (mmp) REVERT: D 178 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7774 (mptt) REVERT: D 212 LYS cc_start: 0.8229 (mmtm) cc_final: 0.7874 (mtmm) REVERT: D 214 LYS cc_start: 0.8737 (mttt) cc_final: 0.8372 (mtpp) REVERT: D 359 ARG cc_start: 0.6992 (ttm-80) cc_final: 0.6754 (ttm-80) REVERT: D 389 ASP cc_start: 0.7037 (t0) cc_final: 0.6809 (p0) REVERT: D 398 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: D 409 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7747 (mtt180) REVERT: E 15 GLN cc_start: 0.8308 (mt0) cc_final: 0.7720 (mm-40) REVERT: E 227 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8309 (mm-30) REVERT: E 362 ASP cc_start: 0.8549 (t0) cc_final: 0.8157 (t0) REVERT: E 364 ASN cc_start: 0.8774 (m-40) cc_final: 0.8325 (m110) REVERT: E 415 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.5927 (mpt90) REVERT: E 422 GLN cc_start: 0.8391 (tp40) cc_final: 0.8097 (tp40) REVERT: E 446 MET cc_start: 0.7987 (mtt) cc_final: 0.7681 (mtp) REVERT: F 15 GLN cc_start: 0.8523 (mt0) cc_final: 0.8216 (mt0) REVERT: F 31 GLN cc_start: 0.8017 (mp10) cc_final: 0.7709 (mm-40) REVERT: F 37 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8660 (m-40) REVERT: F 47 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7575 (mmm160) REVERT: F 344 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7555 (mm-30) REVERT: F 364 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8074 (m110) REVERT: F 385 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8055 (ttpp) REVERT: F 422 GLN cc_start: 0.8074 (tt0) cc_final: 0.7266 (tm-30) REVERT: G 7 SER cc_start: 0.8381 (t) cc_final: 0.8021 (p) REVERT: G 11 LYS cc_start: 0.8364 (tttt) cc_final: 0.8131 (tptp) REVERT: G 237 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7750 (mm-30) REVERT: H 95 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7370 (tm-30) REVERT: H 109 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8314 (tpt90) REVERT: K 121 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7695 (tp40) REVERT: K 123 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.6927 (ptt) REVERT: K 191 ARG cc_start: 0.7370 (mmp80) cc_final: 0.7147 (mmp80) REVERT: L 10 LEU cc_start: 0.6796 (tp) cc_final: 0.6549 (tm) REVERT: M 141 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7128 (pm20) REVERT: N 80 ASN cc_start: 0.8431 (m-40) cc_final: 0.8211 (m110) REVERT: N 102 LEU cc_start: 0.8911 (mt) cc_final: 0.8656 (mt) REVERT: N 142 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.5750 (tmm) REVERT: N 213 MET cc_start: 0.8254 (mmp) cc_final: 0.7549 (tmt) REVERT: O 6 LYS cc_start: 0.8252 (tttt) cc_final: 0.7849 (tppt) REVERT: O 12 PHE cc_start: 0.7173 (m-80) cc_final: 0.6873 (m-80) REVERT: O 17 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8161 (ttm-80) REVERT: O 41 GLN cc_start: 0.7822 (tt0) cc_final: 0.7598 (tp40) REVERT: O 49 PHE cc_start: 0.7804 (m-80) cc_final: 0.7547 (m-80) REVERT: O 73 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8118 (ttt) REVERT: O 95 ARG cc_start: 0.8531 (mmt-90) cc_final: 0.8317 (mmt-90) REVERT: O 140 LYS cc_start: 0.8372 (tttt) cc_final: 0.7988 (mppt) REVERT: O 174 MET cc_start: 0.5875 (ttm) cc_final: 0.5148 (ptm) REVERT: O 176 ILE cc_start: 0.7398 (mm) cc_final: 0.7048 (mt) REVERT: Q 17 MET cc_start: 0.8077 (mmp) cc_final: 0.7813 (tpt) REVERT: S 63 LYS cc_start: 0.6670 (mmtp) cc_final: 0.5852 (tmtt) REVERT: T 48 ARG cc_start: 0.7838 (ptm-80) cc_final: 0.6936 (ptm-80) outliers start: 172 outliers final: 71 residues processed: 829 average time/residue: 0.6481 time to fit residues: 657.8542 Evaluate side-chains 678 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 593 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 2 residue 15 THR Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 69 PHE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 63 PHE Chi-restraints excluded: chain 6 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 LEU Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 364 ASN Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 241 LYS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 121 GLN Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 82 PHE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 142 MET Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 73 MET Chi-restraints excluded: chain O residue 118 ILE Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 26 VAL Chi-restraints excluded: chain T residue 32 PHE Chi-restraints excluded: chain T residue 35 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 472 optimal weight: 3.9990 chunk 437 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 440 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 0.1980 chunk 490 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 484 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 45 GLN A 65 ASN B 396 GLN C 396 GLN C 476 HIS D 37 ASN D 388 GLN F 37 ASN F 364 ASN F 430 HIS H 32 ASN M 92 GLN R 48 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.178116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.147190 restraints weight = 75210.084| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.49 r_work: 0.3715 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 40498 Z= 0.144 Angle : 0.585 14.786 54726 Z= 0.298 Chirality : 0.043 0.235 6274 Planarity : 0.004 0.064 7019 Dihedral : 8.452 102.454 5914 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.95 % Allowed : 15.77 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.12), residues: 5089 helix: 1.34 (0.10), residues: 2721 sheet: -0.04 (0.23), residues: 510 loop : -0.39 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 43 TYR 0.023 0.001 TYR 1 36 PHE 0.035 0.001 PHE T 32 TRP 0.015 0.001 TRP T 42 HIS 0.009 0.001 HIS N 95 Details of bonding type rmsd covalent geometry : bond 0.00319 (40498) covalent geometry : angle 0.58517 (54726) hydrogen bonds : bond 0.04498 ( 2307) hydrogen bonds : angle 4.70758 ( 6726) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 629 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 15 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7315 (t) REVERT: 2 67 MET cc_start: 0.4253 (tpp) cc_final: 0.3799 (tpp) REVERT: 4 45 GLN cc_start: 0.4935 (OUTLIER) cc_final: 0.4699 (tt0) REVERT: 4 46 LEU cc_start: 0.5151 (pp) cc_final: 0.4772 (mt) REVERT: 4 58 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7386 (tm-30) REVERT: 5 3 ASP cc_start: 0.6998 (m-30) cc_final: 0.6482 (p0) REVERT: 5 71 LEU cc_start: 0.7908 (mt) cc_final: 0.7678 (mt) REVERT: 6 51 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6410 (mp) REVERT: 7 7 LYS cc_start: 0.7299 (mtmt) cc_final: 0.7062 (pttm) REVERT: A 26 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7241 (tt0) REVERT: A 40 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.8152 (mtp85) REVERT: A 128 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8707 (mtm-85) REVERT: A 150 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7832 (mmp) REVERT: A 195 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7498 (tp30) REVERT: A 335 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 355 GLU cc_start: 0.8040 (tt0) cc_final: 0.7764 (mm-30) REVERT: A 359 LYS cc_start: 0.8218 (mttm) cc_final: 0.7988 (mtpt) REVERT: A 371 VAL cc_start: 0.7869 (t) cc_final: 0.7546 (p) REVERT: A 415 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7697 (mt0) REVERT: A 423 ARG cc_start: 0.7125 (mpt90) cc_final: 0.6802 (mtt90) REVERT: A 426 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 460 LYS cc_start: 0.8367 (mttt) cc_final: 0.8156 (mmtt) REVERT: A 496 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8112 (mttt) REVERT: B 15 LYS cc_start: 0.7927 (mmtp) cc_final: 0.7660 (mppt) REVERT: B 54 GLU cc_start: 0.8293 (tt0) cc_final: 0.7965 (tp30) REVERT: B 59 LEU cc_start: 0.8486 (mt) cc_final: 0.8172 (mp) REVERT: B 143 ARG cc_start: 0.7439 (ptp-110) cc_final: 0.7199 (pmm-80) REVERT: B 181 ASP cc_start: 0.8314 (m-30) cc_final: 0.8069 (m-30) REVERT: B 196 LYS cc_start: 0.8198 (mttt) cc_final: 0.7551 (mptp) REVERT: B 227 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7933 (mtp85) REVERT: B 353 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7523 (mp0) REVERT: B 367 VAL cc_start: 0.8106 (t) cc_final: 0.7883 (m) REVERT: B 418 LEU cc_start: 0.7000 (tm) cc_final: 0.6614 (mt) REVERT: B 468 PHE cc_start: 0.7592 (t80) cc_final: 0.7387 (t80) REVERT: C 26 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8158 (mp0) REVERT: C 89 LYS cc_start: 0.8586 (mtmp) cc_final: 0.7901 (mttp) REVERT: C 127 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7947 (mt0) REVERT: C 170 ASP cc_start: 0.8247 (m-30) cc_final: 0.8004 (m-30) REVERT: C 209 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8027 (ttmt) REVERT: C 355 GLU cc_start: 0.8074 (tt0) cc_final: 0.7811 (tt0) REVERT: C 381 ARG cc_start: 0.7755 (ttp-110) cc_final: 0.7062 (ttp-110) REVERT: C 385 GLN cc_start: 0.8302 (tt0) cc_final: 0.7940 (pt0) REVERT: C 427 LEU cc_start: 0.7928 (tp) cc_final: 0.7645 (tt) REVERT: C 457 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7511 (pt0) REVERT: C 463 LYS cc_start: 0.8227 (mtpt) cc_final: 0.8004 (ttpm) REVERT: C 488 GLN cc_start: 0.7501 (pt0) cc_final: 0.7044 (pt0) REVERT: D 15 GLN cc_start: 0.8486 (mt0) cc_final: 0.8211 (mt0) REVERT: D 178 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7767 (mptt) REVERT: D 212 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7915 (mtmm) REVERT: D 214 LYS cc_start: 0.8736 (mttt) cc_final: 0.8379 (mtpp) REVERT: D 389 ASP cc_start: 0.7027 (t0) cc_final: 0.6775 (p0) REVERT: D 409 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7701 (mtt180) REVERT: E 15 GLN cc_start: 0.8305 (mt0) cc_final: 0.7706 (mm-40) REVERT: E 227 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8316 (mm-30) REVERT: E 291 ASP cc_start: 0.8570 (m-30) cc_final: 0.8219 (m-30) REVERT: E 362 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8118 (t0) REVERT: E 364 ASN cc_start: 0.8770 (m-40) cc_final: 0.8299 (m110) REVERT: E 415 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.5945 (mpt90) REVERT: E 422 GLN cc_start: 0.8384 (tp40) cc_final: 0.8084 (tp40) REVERT: E 446 MET cc_start: 0.7925 (mtt) cc_final: 0.7631 (mtp) REVERT: F 15 GLN cc_start: 0.8533 (mt0) cc_final: 0.8248 (mt0) REVERT: F 31 GLN cc_start: 0.8056 (mp10) cc_final: 0.7759 (mm110) REVERT: F 47 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7580 (mmm160) REVERT: F 291 ASP cc_start: 0.8292 (m-30) cc_final: 0.8033 (m-30) REVERT: F 344 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7518 (mm-30) REVERT: F 385 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8054 (ttpp) REVERT: F 422 GLN cc_start: 0.8059 (tt0) cc_final: 0.7226 (tm-30) REVERT: G 7 SER cc_start: 0.8371 (t) cc_final: 0.7994 (p) REVERT: G 11 LYS cc_start: 0.8351 (tttt) cc_final: 0.8109 (tptp) REVERT: G 237 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7699 (mm-30) REVERT: G 257 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: H 19 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7683 (p) REVERT: H 95 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7031 (tm-30) REVERT: H 126 MET cc_start: 0.7280 (pmm) cc_final: 0.6767 (pmm) REVERT: K 113 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.8283 (mtm-85) REVERT: K 123 MET cc_start: 0.7910 (mtm) cc_final: 0.6937 (ptt) REVERT: K 173 MET cc_start: 0.5833 (ptt) cc_final: 0.5624 (ptm) REVERT: K 182 MET cc_start: 0.7545 (mmp) cc_final: 0.7245 (mpp) REVERT: K 193 MET cc_start: 0.7501 (mmt) cc_final: 0.7110 (mmm) REVERT: L 10 LEU cc_start: 0.6725 (tp) cc_final: 0.6521 (tm) REVERT: L 76 MET cc_start: 0.7892 (mtp) cc_final: 0.7483 (mtt) REVERT: N 102 LEU cc_start: 0.8965 (mt) cc_final: 0.8713 (mt) REVERT: N 142 MET cc_start: 0.6855 (mpt) cc_final: 0.5861 (tmm) REVERT: N 206 SER cc_start: 0.8671 (m) cc_final: 0.8356 (p) REVERT: O 6 LYS cc_start: 0.8277 (tttt) cc_final: 0.7845 (tppt) REVERT: O 12 PHE cc_start: 0.7048 (m-80) cc_final: 0.6725 (m-80) REVERT: O 17 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8216 (ttm-80) REVERT: O 49 PHE cc_start: 0.7676 (m-80) cc_final: 0.7422 (m-80) REVERT: O 64 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: O 75 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7890 (mttp) REVERT: O 84 SER cc_start: 0.7495 (m) cc_final: 0.6899 (p) REVERT: O 95 ARG cc_start: 0.8498 (mmt-90) cc_final: 0.8185 (mmt-90) REVERT: O 140 LYS cc_start: 0.8302 (tttt) cc_final: 0.7842 (mppt) REVERT: O 174 MET cc_start: 0.5945 (ttm) cc_final: 0.5204 (ptm) REVERT: O 176 ILE cc_start: 0.7481 (mm) cc_final: 0.6889 (mt) REVERT: Q 11 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6544 (mpt) REVERT: Q 17 MET cc_start: 0.8102 (mmp) cc_final: 0.7823 (tpt) REVERT: S 63 LYS cc_start: 0.6635 (mmtp) cc_final: 0.5914 (tmtt) REVERT: T 44 VAL cc_start: 0.8264 (m) cc_final: 0.8017 (p) outliers start: 164 outliers final: 73 residues processed: 745 average time/residue: 0.6537 time to fit residues: 595.9809 Evaluate side-chains 664 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 577 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 2 residue 15 THR Chi-restraints excluded: chain 2 residue 52 LEU Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 69 PHE Chi-restraints excluded: chain 4 residue 45 GLN Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 34 ILE Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 69 PHE Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain 8 residue 70 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 364 ASN Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 241 LYS Chi-restraints excluded: chain G residue 257 GLU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 82 PHE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain Q residue 11 MET Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 225 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 490 optimal weight: 2.9990 chunk 376 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 426 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 213 optimal weight: 4.9990 chunk 441 optimal weight: 0.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN A 385 GLN B 396 GLN D 37 ASN D 59 ASN D 388 GLN F 364 ASN F 430 HIS K 121 GLN K 180 ASN T 57 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.178900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.149295 restraints weight = 75133.889| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.53 r_work: 0.3721 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40498 Z= 0.126 Angle : 0.567 11.843 54726 Z= 0.287 Chirality : 0.043 0.213 6274 Planarity : 0.004 0.063 7019 Dihedral : 8.155 102.612 5902 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.07 % Favored : 96.91 % Rotamer: Outliers : 3.83 % Allowed : 16.69 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.12), residues: 5089 helix: 1.52 (0.10), residues: 2746 sheet: -0.10 (0.23), residues: 504 loop : -0.32 (0.15), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 109 TYR 0.023 0.001 TYR 1 36 PHE 0.027 0.001 PHE 5 47 TRP 0.023 0.002 TRP T 42 HIS 0.005 0.001 HIS N 95 Details of bonding type rmsd covalent geometry : bond 0.00277 (40498) covalent geometry : angle 0.56745 (54726) hydrogen bonds : bond 0.04179 ( 2307) hydrogen bonds : angle 4.56008 ( 6726) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 650 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 67 MET cc_start: 0.4128 (tpp) cc_final: 0.3739 (tpp) REVERT: 3 25 ILE cc_start: 0.7964 (mt) cc_final: 0.7696 (mt) REVERT: 3 69 PHE cc_start: 0.5443 (OUTLIER) cc_final: 0.5064 (m-10) REVERT: 4 46 LEU cc_start: 0.5367 (pp) cc_final: 0.5052 (mt) REVERT: 4 58 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7334 (tm-30) REVERT: 5 3 ASP cc_start: 0.7042 (m-30) cc_final: 0.6540 (p0) REVERT: 6 51 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6345 (mp) REVERT: 7 7 LYS cc_start: 0.7271 (mtmt) cc_final: 0.7066 (pttm) REVERT: 7 18 VAL cc_start: 0.6701 (OUTLIER) cc_final: 0.6337 (p) REVERT: A 26 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7252 (tt0) REVERT: A 40 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8078 (mtp85) REVERT: A 128 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8672 (mtm-85) REVERT: A 195 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7471 (tp30) REVERT: A 335 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8421 (p) REVERT: A 355 GLU cc_start: 0.8046 (tt0) cc_final: 0.7751 (mm-30) REVERT: A 359 LYS cc_start: 0.8191 (mttm) cc_final: 0.7892 (mtpt) REVERT: A 371 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7473 (p) REVERT: A 415 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7719 (mt0) REVERT: A 423 ARG cc_start: 0.7059 (mpt90) cc_final: 0.6726 (mtt90) REVERT: A 426 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 496 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8055 (mttp) REVERT: B 15 LYS cc_start: 0.7906 (mmtp) cc_final: 0.7641 (mppt) REVERT: B 54 GLU cc_start: 0.8313 (tt0) cc_final: 0.7948 (tp30) REVERT: B 59 LEU cc_start: 0.8445 (mt) cc_final: 0.8094 (mp) REVERT: B 143 ARG cc_start: 0.7403 (ptp-110) cc_final: 0.7172 (pmm-80) REVERT: B 181 ASP cc_start: 0.8448 (m-30) cc_final: 0.8242 (m-30) REVERT: B 196 LYS cc_start: 0.8178 (mttt) cc_final: 0.7517 (mptp) REVERT: B 353 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7517 (mp0) REVERT: B 367 VAL cc_start: 0.8021 (t) cc_final: 0.7800 (m) REVERT: B 369 LEU cc_start: 0.8547 (mt) cc_final: 0.8288 (mt) REVERT: B 385 GLN cc_start: 0.7804 (tt0) cc_final: 0.7475 (pt0) REVERT: B 418 LEU cc_start: 0.6947 (tm) cc_final: 0.6576 (mt) REVERT: B 468 PHE cc_start: 0.7571 (t80) cc_final: 0.7356 (t80) REVERT: C 26 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8112 (mp0) REVERT: C 67 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: C 89 LYS cc_start: 0.8481 (mtmp) cc_final: 0.7844 (mttp) REVERT: C 101 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8216 (mm-30) REVERT: C 127 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7866 (mt0) REVERT: C 170 ASP cc_start: 0.8361 (m-30) cc_final: 0.8161 (m-30) REVERT: C 355 GLU cc_start: 0.8106 (tt0) cc_final: 0.7846 (tt0) REVERT: C 381 ARG cc_start: 0.7716 (ttp-110) cc_final: 0.6995 (ttp-110) REVERT: C 385 GLN cc_start: 0.8265 (tt0) cc_final: 0.7904 (pt0) REVERT: C 416 GLN cc_start: 0.7390 (tp40) cc_final: 0.6929 (tp40) REVERT: C 427 LEU cc_start: 0.7818 (tp) cc_final: 0.7590 (tt) REVERT: C 457 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7489 (pt0) REVERT: C 463 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7508 (ttpm) REVERT: C 467 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7849 (mp0) REVERT: C 488 GLN cc_start: 0.7471 (pt0) cc_final: 0.6989 (pt0) REVERT: D 15 GLN cc_start: 0.8497 (mt0) cc_final: 0.8211 (mt0) REVERT: D 170 MET cc_start: 0.8081 (mmm) cc_final: 0.7766 (mmp) REVERT: D 178 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7755 (mptt) REVERT: D 212 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7871 (mtmm) REVERT: D 214 LYS cc_start: 0.8718 (mttt) cc_final: 0.8347 (mtpp) REVERT: D 261 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8776 (tp) REVERT: D 389 ASP cc_start: 0.7018 (t0) cc_final: 0.6752 (p0) REVERT: D 396 MET cc_start: 0.7468 (mmm) cc_final: 0.7030 (tpt) REVERT: D 409 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7638 (mtt180) REVERT: E 15 GLN cc_start: 0.8276 (mt0) cc_final: 0.7708 (mm-40) REVERT: E 227 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8493 (mp0) REVERT: E 291 ASP cc_start: 0.8560 (m-30) cc_final: 0.8222 (m-30) REVERT: E 362 ASP cc_start: 0.8412 (t0) cc_final: 0.8051 (t0) REVERT: E 364 ASN cc_start: 0.8770 (m-40) cc_final: 0.8255 (m110) REVERT: E 415 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.5541 (mpt90) REVERT: E 422 GLN cc_start: 0.8365 (tp40) cc_final: 0.8059 (tp40) REVERT: E 446 MET cc_start: 0.7874 (mtt) cc_final: 0.7630 (mtp) REVERT: F 15 GLN cc_start: 0.8487 (mt0) cc_final: 0.8195 (mt0) REVERT: F 31 GLN cc_start: 0.8048 (mp10) cc_final: 0.7684 (mm110) REVERT: F 47 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7534 (mmm160) REVERT: F 203 MET cc_start: 0.8965 (mtt) cc_final: 0.8692 (mtt) REVERT: F 340 ARG cc_start: 0.8291 (ttm-80) cc_final: 0.7902 (ttm-80) REVERT: F 344 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7496 (mm-30) REVERT: F 368 GLU cc_start: 0.7537 (tp30) cc_final: 0.7287 (tp30) REVERT: F 385 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8055 (ttpp) REVERT: F 422 GLN cc_start: 0.8027 (tt0) cc_final: 0.7164 (tm-30) REVERT: G 7 SER cc_start: 0.8259 (t) cc_final: 0.7913 (p) REVERT: G 11 LYS cc_start: 0.8313 (tttt) cc_final: 0.8062 (tptp) REVERT: G 237 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7699 (mm-30) REVERT: G 257 GLU cc_start: 0.7609 (tt0) cc_final: 0.7365 (tm-30) REVERT: H 19 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7713 (p) REVERT: H 95 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7275 (tm-30) REVERT: H 126 MET cc_start: 0.7113 (pmm) cc_final: 0.6749 (pmm) REVERT: K 113 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8356 (mtm-85) REVERT: K 123 MET cc_start: 0.7916 (mtm) cc_final: 0.6964 (ptt) REVERT: K 124 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8314 (tm) REVERT: K 182 MET cc_start: 0.7675 (mmp) cc_final: 0.7292 (mpp) REVERT: L 4 VAL cc_start: 0.5148 (OUTLIER) cc_final: 0.4725 (m) REVERT: L 76 MET cc_start: 0.7939 (mtp) cc_final: 0.7581 (mtt) REVERT: M 141 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6956 (pm20) REVERT: M 144 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5586 (pt) REVERT: N 9 PHE cc_start: 0.3735 (OUTLIER) cc_final: 0.2739 (m-80) REVERT: N 142 MET cc_start: 0.6910 (mpt) cc_final: 0.5954 (tmm) REVERT: N 198 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: N 206 SER cc_start: 0.8817 (m) cc_final: 0.8505 (p) REVERT: N 213 MET cc_start: 0.8205 (mmp) cc_final: 0.7791 (tpt) REVERT: O 6 LYS cc_start: 0.8262 (tttt) cc_final: 0.7832 (tppt) REVERT: O 12 PHE cc_start: 0.6999 (m-80) cc_final: 0.6681 (m-80) REVERT: O 17 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8191 (ttm-80) REVERT: O 30 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8284 (mmtm) REVERT: O 64 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: O 84 SER cc_start: 0.7367 (m) cc_final: 0.6766 (p) REVERT: O 95 ARG cc_start: 0.8453 (mmt-90) cc_final: 0.8044 (mmm-85) REVERT: O 140 LYS cc_start: 0.8336 (tttt) cc_final: 0.7849 (mppt) REVERT: O 174 MET cc_start: 0.5949 (ttm) cc_final: 0.5269 (ptm) REVERT: O 176 ILE cc_start: 0.7364 (mm) cc_final: 0.6953 (mt) REVERT: S 63 LYS cc_start: 0.6666 (mmtp) cc_final: 0.5982 (tmtt) REVERT: S 76 THR cc_start: 0.9083 (p) cc_final: 0.8881 (p) REVERT: T 44 VAL cc_start: 0.8114 (m) cc_final: 0.7688 (p) REVERT: T 69 MET cc_start: 0.6647 (tpt) cc_final: 0.6273 (mmm) outliers start: 159 outliers final: 76 residues processed: 763 average time/residue: 0.6498 time to fit residues: 609.3992 Evaluate side-chains 681 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 587 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 2 residue 52 LEU Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 69 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 34 ILE Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 69 PHE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 364 ASN Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 13 ASP Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 144 LEU Chi-restraints excluded: chain N residue 9 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain N residue 198 GLU Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain T residue 17 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 224 optimal weight: 1.9990 chunk 335 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 478 optimal weight: 0.9980 chunk 426 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 423 optimal weight: 20.0000 chunk 502 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 45 GLN B 396 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN D 388 GLN F 430 HIS J 4 GLN O 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.177486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146839 restraints weight = 74676.786| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.43 r_work: 0.3707 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40498 Z= 0.153 Angle : 0.589 11.602 54726 Z= 0.299 Chirality : 0.044 0.205 6274 Planarity : 0.004 0.066 7019 Dihedral : 8.114 102.858 5897 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 4.05 % Allowed : 17.36 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.12), residues: 5089 helix: 1.57 (0.10), residues: 2752 sheet: -0.11 (0.23), residues: 518 loop : -0.33 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG I 16 TYR 0.025 0.001 TYR B 446 PHE 0.034 0.001 PHE 8 63 TRP 0.034 0.002 TRP S 73 HIS 0.005 0.001 HIS N 95 Details of bonding type rmsd covalent geometry : bond 0.00347 (40498) covalent geometry : angle 0.58905 (54726) hydrogen bonds : bond 0.04242 ( 2307) hydrogen bonds : angle 4.54905 ( 6726) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 611 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 45 GLN cc_start: 0.5239 (OUTLIER) cc_final: 0.4874 (tp-100) REVERT: 2 67 MET cc_start: 0.4164 (tpp) cc_final: 0.3762 (tpp) REVERT: 3 69 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.5238 (m-10) REVERT: 4 46 LEU cc_start: 0.5708 (pp) cc_final: 0.5368 (mt) REVERT: 4 58 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7521 (tm-30) REVERT: 5 3 ASP cc_start: 0.7159 (m-30) cc_final: 0.6591 (p0) REVERT: 6 51 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6547 (mp) REVERT: 7 7 LYS cc_start: 0.7451 (mtmt) cc_final: 0.7162 (pttm) REVERT: 7 18 VAL cc_start: 0.6811 (OUTLIER) cc_final: 0.6470 (p) REVERT: A 26 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7315 (tt0) REVERT: A 40 ARG cc_start: 0.8586 (mtt-85) cc_final: 0.8266 (mtp85) REVERT: A 128 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8773 (mtm-85) REVERT: A 195 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7454 (tp30) REVERT: A 335 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8428 (p) REVERT: A 355 GLU cc_start: 0.8162 (tt0) cc_final: 0.7732 (mm-30) REVERT: A 359 LYS cc_start: 0.8136 (mttm) cc_final: 0.7816 (mtpt) REVERT: A 362 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7851 (mtt180) REVERT: A 371 VAL cc_start: 0.7872 (t) cc_final: 0.7532 (p) REVERT: A 415 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7715 (mt0) REVERT: A 423 ARG cc_start: 0.7225 (mpt90) cc_final: 0.6906 (mtt90) REVERT: A 426 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 496 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7989 (mttt) REVERT: B 15 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7740 (mppt) REVERT: B 54 GLU cc_start: 0.8570 (tt0) cc_final: 0.8140 (tp30) REVERT: B 59 LEU cc_start: 0.8555 (mt) cc_final: 0.8172 (mp) REVERT: B 143 ARG cc_start: 0.7471 (ptp-110) cc_final: 0.7191 (pmm-80) REVERT: B 196 LYS cc_start: 0.8210 (mttt) cc_final: 0.7510 (mptp) REVERT: B 227 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8090 (mtp85) REVERT: B 367 VAL cc_start: 0.8042 (t) cc_final: 0.7802 (m) REVERT: B 385 GLN cc_start: 0.7854 (tt0) cc_final: 0.7575 (pt0) REVERT: B 418 LEU cc_start: 0.6908 (tm) cc_final: 0.6520 (mt) REVERT: C 26 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8247 (mp0) REVERT: C 67 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: C 89 LYS cc_start: 0.8655 (mtmp) cc_final: 0.7968 (mttp) REVERT: C 101 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8386 (mm-30) REVERT: C 127 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7932 (mt0) REVERT: C 143 ARG cc_start: 0.8159 (ptp90) cc_final: 0.7836 (mtm110) REVERT: C 355 GLU cc_start: 0.8236 (tt0) cc_final: 0.7969 (tt0) REVERT: C 381 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7271 (ttp-110) REVERT: C 385 GLN cc_start: 0.8317 (tt0) cc_final: 0.7964 (pt0) REVERT: C 416 GLN cc_start: 0.7425 (tp40) cc_final: 0.6971 (tp40) REVERT: C 457 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7502 (pt0) REVERT: C 463 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7667 (ttpm) REVERT: C 467 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8024 (mp0) REVERT: C 488 GLN cc_start: 0.7471 (pt0) cc_final: 0.6956 (pt0) REVERT: D 15 GLN cc_start: 0.8680 (mt0) cc_final: 0.8357 (mt0) REVERT: D 170 MET cc_start: 0.8244 (mmm) cc_final: 0.7944 (mmp) REVERT: D 178 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7755 (mptt) REVERT: D 212 LYS cc_start: 0.8299 (mmtm) cc_final: 0.7896 (mtmm) REVERT: D 214 LYS cc_start: 0.8736 (mttt) cc_final: 0.8352 (mtpp) REVERT: D 261 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8824 (tp) REVERT: D 389 ASP cc_start: 0.7091 (t0) cc_final: 0.6773 (p0) REVERT: D 396 MET cc_start: 0.7510 (mmm) cc_final: 0.7025 (tpt) REVERT: D 409 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7809 (mtt180) REVERT: E 15 GLN cc_start: 0.8450 (mt0) cc_final: 0.7843 (mm-40) REVERT: E 227 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8582 (mp0) REVERT: E 291 ASP cc_start: 0.8743 (m-30) cc_final: 0.8472 (m-30) REVERT: E 362 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8199 (t0) REVERT: E 415 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6044 (mpt90) REVERT: E 422 GLN cc_start: 0.8407 (tp40) cc_final: 0.8092 (tp40) REVERT: F 47 ARG cc_start: 0.8136 (mmm-85) cc_final: 0.7642 (mmm160) REVERT: F 340 ARG cc_start: 0.8408 (ttm-80) cc_final: 0.8055 (ttm-80) REVERT: F 344 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7462 (mm-30) REVERT: F 385 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8135 (ttpp) REVERT: F 422 GLN cc_start: 0.8131 (tt0) cc_final: 0.7221 (tm-30) REVERT: G 7 SER cc_start: 0.8281 (t) cc_final: 0.7933 (p) REVERT: G 11 LYS cc_start: 0.8441 (tttt) cc_final: 0.8180 (tptp) REVERT: G 237 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7857 (mm-30) REVERT: G 257 GLU cc_start: 0.7847 (tt0) cc_final: 0.7637 (tm-30) REVERT: H 19 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7971 (p) REVERT: H 95 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7463 (tm-30) REVERT: H 96 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6432 (pm20) REVERT: I 30 MET cc_start: 0.8397 (mmp) cc_final: 0.8130 (mmt) REVERT: K 113 ARG cc_start: 0.8728 (mmm-85) cc_final: 0.8314 (mtm-85) REVERT: K 123 MET cc_start: 0.7961 (mtm) cc_final: 0.7064 (ptt) REVERT: K 124 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8215 (tm) REVERT: K 173 MET cc_start: 0.5858 (ptt) cc_final: 0.5592 (ptm) REVERT: K 182 MET cc_start: 0.7625 (mmp) cc_final: 0.7291 (mpp) REVERT: K 193 MET cc_start: 0.6834 (mmt) cc_final: 0.6353 (mmm) REVERT: L 4 VAL cc_start: 0.5208 (OUTLIER) cc_final: 0.4881 (m) REVERT: L 76 MET cc_start: 0.7991 (mtp) cc_final: 0.7628 (mtt) REVERT: M 141 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: N 9 PHE cc_start: 0.3706 (OUTLIER) cc_final: 0.2873 (m-80) REVERT: N 54 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: N 142 MET cc_start: 0.7054 (mpt) cc_final: 0.6006 (tmm) REVERT: N 157 ARG cc_start: 0.8586 (ptm-80) cc_final: 0.8353 (ptm160) REVERT: N 206 SER cc_start: 0.8817 (m) cc_final: 0.8545 (p) REVERT: N 213 MET cc_start: 0.8580 (mmp) cc_final: 0.7927 (tpt) REVERT: O 6 LYS cc_start: 0.8225 (tttt) cc_final: 0.7803 (tppt) REVERT: O 12 PHE cc_start: 0.7056 (m-80) cc_final: 0.6645 (m-80) REVERT: O 17 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8390 (ttm-80) REVERT: O 30 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8315 (mmtm) REVERT: O 41 GLN cc_start: 0.7592 (tp40) cc_final: 0.7261 (tp40) REVERT: O 64 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: O 84 SER cc_start: 0.7545 (m) cc_final: 0.6969 (p) REVERT: O 95 ARG cc_start: 0.8504 (mmt-90) cc_final: 0.8080 (mmm-85) REVERT: O 140 LYS cc_start: 0.8248 (tttt) cc_final: 0.7773 (mppt) REVERT: O 174 MET cc_start: 0.5751 (ttm) cc_final: 0.4956 (ptm) REVERT: O 176 ILE cc_start: 0.7220 (mm) cc_final: 0.6800 (mt) REVERT: Q 17 MET cc_start: 0.8119 (mmp) cc_final: 0.7771 (tpt) REVERT: S 63 LYS cc_start: 0.6698 (mmtp) cc_final: 0.6025 (tmtt) REVERT: S 101 ARG cc_start: 0.6123 (pmm-80) cc_final: 0.5694 (mpp80) REVERT: T 69 MET cc_start: 0.6695 (tpt) cc_final: 0.6327 (mmm) outliers start: 168 outliers final: 94 residues processed: 732 average time/residue: 0.6834 time to fit residues: 611.4136 Evaluate side-chains 700 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 585 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 2 residue 33 ILE Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 52 LEU Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 69 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 34 ILE Chi-restraints excluded: chain 5 residue 64 CYS Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 6 residue 69 PHE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 364 ASN Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 9 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 17 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 482 optimal weight: 3.9990 chunk 382 optimal weight: 0.9980 chunk 416 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 254 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 215 optimal weight: 0.0770 chunk 2 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 431 optimal weight: 7.9990 chunk 494 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 45 GLN B 396 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN F 430 HIS J 4 GLN N 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.178233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147702 restraints weight = 75230.225| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.43 r_work: 0.3721 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40498 Z= 0.138 Angle : 0.588 17.903 54726 Z= 0.296 Chirality : 0.043 0.208 6274 Planarity : 0.004 0.063 7019 Dihedral : 7.986 102.079 5897 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 3.71 % Allowed : 18.56 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.12), residues: 5089 helix: 1.63 (0.10), residues: 2746 sheet: -0.10 (0.23), residues: 506 loop : -0.27 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG M 39 TYR 0.022 0.001 TYR A 397 PHE 0.032 0.001 PHE 8 63 TRP 0.027 0.002 TRP Q 21 HIS 0.005 0.001 HIS N 95 Details of bonding type rmsd covalent geometry : bond 0.00310 (40498) covalent geometry : angle 0.58819 (54726) hydrogen bonds : bond 0.04130 ( 2307) hydrogen bonds : angle 4.50074 ( 6726) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 611 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 67 MET cc_start: 0.4144 (tpp) cc_final: 0.3789 (tpp) REVERT: 3 69 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5283 (m-80) REVERT: 4 45 GLN cc_start: 0.5179 (OUTLIER) cc_final: 0.4860 (tt0) REVERT: 5 3 ASP cc_start: 0.7263 (m-30) cc_final: 0.6627 (p0) REVERT: 6 51 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6463 (mp) REVERT: 7 7 LYS cc_start: 0.7463 (mtmt) cc_final: 0.7137 (pttm) REVERT: 7 18 VAL cc_start: 0.6793 (OUTLIER) cc_final: 0.6461 (p) REVERT: A 26 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7329 (tt0) REVERT: A 40 ARG cc_start: 0.8547 (mtt-85) cc_final: 0.8227 (mtp85) REVERT: A 128 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8763 (mtm-85) REVERT: A 195 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7464 (tp30) REVERT: A 335 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8441 (p) REVERT: A 355 GLU cc_start: 0.8153 (tt0) cc_final: 0.7702 (mm-30) REVERT: A 359 LYS cc_start: 0.8097 (mttm) cc_final: 0.7775 (mtpt) REVERT: A 362 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7852 (mtt180) REVERT: A 371 VAL cc_start: 0.7955 (t) cc_final: 0.7613 (p) REVERT: A 415 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7673 (mt0) REVERT: A 423 ARG cc_start: 0.7254 (mpt90) cc_final: 0.6933 (mtt90) REVERT: A 426 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 453 LEU cc_start: 0.8336 (mt) cc_final: 0.8123 (mp) REVERT: A 496 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7971 (mttt) REVERT: B 14 GLU cc_start: 0.7886 (pt0) cc_final: 0.7659 (pt0) REVERT: B 15 LYS cc_start: 0.8012 (mmtp) cc_final: 0.7743 (mppt) REVERT: B 54 GLU cc_start: 0.8560 (tt0) cc_final: 0.8150 (tp30) REVERT: B 59 LEU cc_start: 0.8514 (mt) cc_final: 0.8166 (mp) REVERT: B 143 ARG cc_start: 0.7498 (ptp-110) cc_final: 0.7233 (pmm-80) REVERT: B 196 LYS cc_start: 0.8162 (mttt) cc_final: 0.7457 (mptp) REVERT: B 227 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8067 (mtp85) REVERT: B 367 VAL cc_start: 0.8036 (t) cc_final: 0.7821 (m) REVERT: B 385 GLN cc_start: 0.7893 (tt0) cc_final: 0.7638 (pt0) REVERT: B 418 LEU cc_start: 0.6896 (tm) cc_final: 0.6514 (mt) REVERT: C 26 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8255 (mp0) REVERT: C 67 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: C 89 LYS cc_start: 0.8574 (mtmp) cc_final: 0.7945 (mttp) REVERT: C 101 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8381 (mm-30) REVERT: C 127 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7928 (mt0) REVERT: C 143 ARG cc_start: 0.8154 (ptp90) cc_final: 0.7831 (mtm110) REVERT: C 355 GLU cc_start: 0.8259 (tt0) cc_final: 0.8033 (tt0) REVERT: C 381 ARG cc_start: 0.7995 (ttp-110) cc_final: 0.7276 (ttp-110) REVERT: C 385 GLN cc_start: 0.8321 (tt0) cc_final: 0.7987 (pt0) REVERT: C 390 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8537 (tpp) REVERT: C 416 GLN cc_start: 0.7388 (tp40) cc_final: 0.6933 (tp40) REVERT: C 457 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7443 (pt0) REVERT: C 463 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7633 (ttpm) REVERT: C 467 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8025 (mp0) REVERT: C 488 GLN cc_start: 0.7454 (pt0) cc_final: 0.6933 (pt0) REVERT: D 15 GLN cc_start: 0.8669 (mt0) cc_final: 0.8340 (mt0) REVERT: D 170 MET cc_start: 0.8221 (mmm) cc_final: 0.7942 (mmp) REVERT: D 178 LYS cc_start: 0.8353 (mtpt) cc_final: 0.7755 (mptt) REVERT: D 212 LYS cc_start: 0.8315 (mmtm) cc_final: 0.7923 (mtmm) REVERT: D 214 LYS cc_start: 0.8716 (mttt) cc_final: 0.8338 (mtpp) REVERT: D 261 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8793 (tp) REVERT: D 389 ASP cc_start: 0.7065 (t0) cc_final: 0.6744 (p0) REVERT: D 396 MET cc_start: 0.7570 (mmm) cc_final: 0.7077 (tpt) REVERT: D 409 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7751 (mtt180) REVERT: E 15 GLN cc_start: 0.8451 (mt0) cc_final: 0.7841 (mm-40) REVERT: E 227 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8563 (mp0) REVERT: E 291 ASP cc_start: 0.8734 (m-30) cc_final: 0.8393 (m-30) REVERT: E 362 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8226 (t0) REVERT: E 415 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.5804 (mpt90) REVERT: F 47 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7613 (mmm160) REVERT: F 340 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7974 (ttm-80) REVERT: F 344 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7441 (mm-30) REVERT: F 385 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8166 (ttpp) REVERT: F 409 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7821 (mmt90) REVERT: F 422 GLN cc_start: 0.8112 (tt0) cc_final: 0.7205 (tm-30) REVERT: G 7 SER cc_start: 0.8259 (t) cc_final: 0.7913 (p) REVERT: G 11 LYS cc_start: 0.8433 (tttt) cc_final: 0.8162 (tptp) REVERT: G 237 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7868 (mm-30) REVERT: G 257 GLU cc_start: 0.7821 (tt0) cc_final: 0.7614 (tm-30) REVERT: H 19 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.8016 (p) REVERT: I 30 MET cc_start: 0.8438 (mmp) cc_final: 0.8205 (mmt) REVERT: K 113 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8304 (mtm-85) REVERT: K 123 MET cc_start: 0.7928 (mtm) cc_final: 0.7081 (ptt) REVERT: K 124 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8189 (tm) REVERT: K 173 MET cc_start: 0.5879 (ptt) cc_final: 0.5676 (ptm) REVERT: K 182 MET cc_start: 0.7440 (mmp) cc_final: 0.7123 (mpp) REVERT: K 193 MET cc_start: 0.6886 (mmt) cc_final: 0.6350 (mmm) REVERT: L 4 VAL cc_start: 0.5185 (OUTLIER) cc_final: 0.4862 (m) REVERT: L 76 MET cc_start: 0.7908 (mtp) cc_final: 0.7521 (mtt) REVERT: N 9 PHE cc_start: 0.3660 (OUTLIER) cc_final: 0.2992 (m-80) REVERT: N 80 ASN cc_start: 0.8718 (m-40) cc_final: 0.8415 (m110) REVERT: N 136 MET cc_start: 0.6500 (ttm) cc_final: 0.6218 (ttm) REVERT: N 142 MET cc_start: 0.7001 (mpt) cc_final: 0.6042 (tmm) REVERT: N 206 SER cc_start: 0.8832 (m) cc_final: 0.8512 (p) REVERT: N 213 MET cc_start: 0.8559 (mmp) cc_final: 0.7835 (tpt) REVERT: O 6 LYS cc_start: 0.8247 (tttt) cc_final: 0.7798 (tppt) REVERT: O 12 PHE cc_start: 0.7066 (m-80) cc_final: 0.6467 (m-80) REVERT: O 17 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8406 (ttm-80) REVERT: O 30 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8260 (mmtm) REVERT: O 41 GLN cc_start: 0.7615 (tp40) cc_final: 0.7269 (tp40) REVERT: O 64 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: O 84 SER cc_start: 0.7555 (m) cc_final: 0.6985 (p) REVERT: O 95 ARG cc_start: 0.8497 (mmt-90) cc_final: 0.8084 (mmm-85) REVERT: O 140 LYS cc_start: 0.8231 (tttt) cc_final: 0.7765 (mppt) REVERT: O 174 MET cc_start: 0.5987 (ttm) cc_final: 0.5059 (ptm) REVERT: O 176 ILE cc_start: 0.7212 (mm) cc_final: 0.6840 (mt) REVERT: Q 17 MET cc_start: 0.8113 (mmp) cc_final: 0.7753 (tpt) REVERT: R 37 GLU cc_start: 0.8086 (mp0) cc_final: 0.6273 (tm-30) REVERT: R 98 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7816 (p) REVERT: S 57 HIS cc_start: 0.8474 (t70) cc_final: 0.7999 (m-70) REVERT: S 63 LYS cc_start: 0.6650 (mmtp) cc_final: 0.5995 (tmtt) REVERT: S 92 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8547 (tp) REVERT: S 101 ARG cc_start: 0.6142 (pmm-80) cc_final: 0.5728 (mpp80) REVERT: T 69 MET cc_start: 0.6537 (tpt) cc_final: 0.6172 (mmm) outliers start: 154 outliers final: 84 residues processed: 717 average time/residue: 0.7867 time to fit residues: 686.7091 Evaluate side-chains 676 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 571 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 2 residue 52 LEU Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 69 PHE Chi-restraints excluded: chain 4 residue 45 GLN Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 34 ILE Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 69 PHE Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 364 ASN Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 209 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 9 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain S residue 98 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 294 optimal weight: 0.0570 chunk 453 optimal weight: 0.5980 chunk 145 optimal weight: 9.9990 chunk 467 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 326 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 379 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 44 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 45 GLN B 396 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN D 37 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 430 HIS J 4 GLN ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.178566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.147835 restraints weight = 74986.284| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.46 r_work: 0.3721 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40498 Z= 0.130 Angle : 0.600 16.081 54726 Z= 0.299 Chirality : 0.043 0.234 6274 Planarity : 0.004 0.064 7019 Dihedral : 7.831 101.445 5895 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 3.47 % Allowed : 19.26 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.12), residues: 5089 helix: 1.67 (0.10), residues: 2746 sheet: -0.14 (0.23), residues: 502 loop : -0.23 (0.15), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 43 TYR 0.025 0.001 TYR B 446 PHE 0.032 0.001 PHE 8 63 TRP 0.031 0.002 TRP S 73 HIS 0.005 0.001 HIS I 17 Details of bonding type rmsd covalent geometry : bond 0.00289 (40498) covalent geometry : angle 0.60028 (54726) hydrogen bonds : bond 0.04070 ( 2307) hydrogen bonds : angle 4.45081 ( 6726) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 610 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 67 MET cc_start: 0.3907 (tpp) cc_final: 0.3692 (tpp) REVERT: 3 69 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.5350 (m-80) REVERT: 5 3 ASP cc_start: 0.7115 (m-30) cc_final: 0.6552 (p0) REVERT: 6 47 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.6068 (m-80) REVERT: 6 51 ILE cc_start: 0.6442 (OUTLIER) cc_final: 0.6087 (mp) REVERT: 7 7 LYS cc_start: 0.7377 (mtmt) cc_final: 0.7083 (pttm) REVERT: 7 18 VAL cc_start: 0.6621 (OUTLIER) cc_final: 0.6287 (p) REVERT: A 26 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7264 (tt0) REVERT: A 40 ARG cc_start: 0.8359 (mtt-85) cc_final: 0.8065 (mtp85) REVERT: A 128 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8703 (mtm-85) REVERT: A 195 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7534 (tp30) REVERT: A 355 GLU cc_start: 0.8106 (tt0) cc_final: 0.7802 (mm-30) REVERT: A 359 LYS cc_start: 0.8201 (mttm) cc_final: 0.7924 (mtpt) REVERT: A 362 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7844 (mtt180) REVERT: A 371 VAL cc_start: 0.7913 (t) cc_final: 0.7622 (p) REVERT: A 415 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7710 (mt0) REVERT: A 426 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 496 LYS cc_start: 0.8424 (mtpt) cc_final: 0.8049 (mttp) REVERT: B 15 LYS cc_start: 0.8009 (mmtp) cc_final: 0.7749 (mppt) REVERT: B 54 GLU cc_start: 0.8304 (tt0) cc_final: 0.8004 (tp30) REVERT: B 59 LEU cc_start: 0.8471 (mt) cc_final: 0.8171 (mp) REVERT: B 196 LYS cc_start: 0.8155 (mttt) cc_final: 0.7510 (mptp) REVERT: B 227 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7951 (mtp85) REVERT: B 381 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7285 (ttm110) REVERT: B 385 GLN cc_start: 0.7842 (tt0) cc_final: 0.7602 (pt0) REVERT: B 418 LEU cc_start: 0.7139 (tm) cc_final: 0.6709 (mt) REVERT: C 26 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8116 (mp0) REVERT: C 67 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: C 89 LYS cc_start: 0.8548 (mtmp) cc_final: 0.7915 (mttp) REVERT: C 127 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7859 (mt0) REVERT: C 143 ARG cc_start: 0.8060 (ptp90) cc_final: 0.7768 (mtm110) REVERT: C 355 GLU cc_start: 0.8133 (tt0) cc_final: 0.7907 (tt0) REVERT: C 381 ARG cc_start: 0.7862 (ttp-110) cc_final: 0.7451 (ttp-110) REVERT: C 385 GLN cc_start: 0.8235 (tt0) cc_final: 0.7941 (pt0) REVERT: C 416 GLN cc_start: 0.7431 (tp40) cc_final: 0.6954 (tp40) REVERT: C 457 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7457 (pt0) REVERT: C 463 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7804 (tttp) REVERT: C 467 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7824 (mp0) REVERT: C 488 GLN cc_start: 0.7436 (pt0) cc_final: 0.6898 (pt0) REVERT: C 499 LYS cc_start: 0.8667 (mmtp) cc_final: 0.8436 (mmmm) REVERT: C 503 ASP cc_start: 0.8271 (p0) cc_final: 0.7916 (p0) REVERT: D 15 GLN cc_start: 0.8512 (mt0) cc_final: 0.8201 (mt0) REVERT: D 170 MET cc_start: 0.8104 (mmm) cc_final: 0.7837 (mmp) REVERT: D 178 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7784 (mptt) REVERT: D 212 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7982 (mtmm) REVERT: D 214 LYS cc_start: 0.8727 (mttt) cc_final: 0.8392 (mtpp) REVERT: D 261 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8759 (tp) REVERT: D 389 ASP cc_start: 0.7065 (t0) cc_final: 0.6776 (p0) REVERT: D 396 MET cc_start: 0.7636 (mmm) cc_final: 0.7219 (tpt) REVERT: D 409 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7691 (mtt180) REVERT: E 15 GLN cc_start: 0.8325 (mt0) cc_final: 0.7750 (mm-40) REVERT: E 291 ASP cc_start: 0.8598 (m-30) cc_final: 0.8235 (m-30) REVERT: E 362 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8141 (t0) REVERT: E 415 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.5614 (mpt90) REVERT: F 47 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7499 (mmm160) REVERT: F 340 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.7929 (ttm-80) REVERT: F 344 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7430 (mm-30) REVERT: F 385 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8181 (ttpp) REVERT: F 409 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7699 (mmt90) REVERT: F 422 GLN cc_start: 0.8011 (tt0) cc_final: 0.7167 (tm-30) REVERT: G 7 SER cc_start: 0.8333 (t) cc_final: 0.8010 (p) REVERT: G 11 LYS cc_start: 0.8272 (tttt) cc_final: 0.8026 (tptp) REVERT: G 161 PHE cc_start: 0.7827 (t80) cc_final: 0.7306 (t80) REVERT: G 237 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7786 (mm-30) REVERT: K 113 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8338 (mtm-85) REVERT: K 123 MET cc_start: 0.7804 (mtm) cc_final: 0.6965 (ptt) REVERT: K 124 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8190 (tm) REVERT: K 173 MET cc_start: 0.5733 (ptt) cc_final: 0.5531 (ptm) REVERT: K 182 MET cc_start: 0.7273 (mmp) cc_final: 0.7053 (mpp) REVERT: K 193 MET cc_start: 0.6961 (mmt) cc_final: 0.6419 (mmm) REVERT: L 4 VAL cc_start: 0.5299 (OUTLIER) cc_final: 0.4892 (m) REVERT: L 76 MET cc_start: 0.7842 (mtp) cc_final: 0.7489 (mtt) REVERT: M 141 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6770 (pm20) REVERT: N 9 PHE cc_start: 0.3502 (OUTLIER) cc_final: 0.2975 (m-80) REVERT: N 80 ASN cc_start: 0.8622 (m-40) cc_final: 0.8321 (m110) REVERT: N 136 MET cc_start: 0.6342 (ttm) cc_final: 0.5958 (ptm) REVERT: N 142 MET cc_start: 0.6932 (mpt) cc_final: 0.5924 (tmm) REVERT: N 189 PHE cc_start: 0.8400 (t80) cc_final: 0.8144 (t80) REVERT: N 206 SER cc_start: 0.8771 (m) cc_final: 0.8444 (p) REVERT: N 213 MET cc_start: 0.8316 (mmp) cc_final: 0.7707 (tpt) REVERT: O 6 LYS cc_start: 0.8278 (tttt) cc_final: 0.7847 (tppt) REVERT: O 12 PHE cc_start: 0.7033 (m-80) cc_final: 0.6536 (m-80) REVERT: O 17 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.8327 (ttm-80) REVERT: O 30 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8221 (mmtm) REVERT: O 41 GLN cc_start: 0.7684 (tp40) cc_final: 0.7318 (tp40) REVERT: O 64 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: O 68 ASP cc_start: 0.7806 (m-30) cc_final: 0.6886 (m-30) REVERT: O 76 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6949 (pm20) REVERT: O 84 SER cc_start: 0.7536 (m) cc_final: 0.6938 (p) REVERT: O 95 ARG cc_start: 0.8472 (mmt-90) cc_final: 0.8100 (mmm-85) REVERT: O 140 LYS cc_start: 0.8281 (tttt) cc_final: 0.7834 (mppt) REVERT: O 174 MET cc_start: 0.6230 (ttm) cc_final: 0.5335 (ptm) REVERT: O 176 ILE cc_start: 0.7306 (mm) cc_final: 0.6923 (mt) REVERT: Q 17 MET cc_start: 0.8037 (mmp) cc_final: 0.7679 (tpt) REVERT: R 98 VAL cc_start: 0.7990 (OUTLIER) cc_final: 0.7702 (p) REVERT: S 57 HIS cc_start: 0.8377 (t70) cc_final: 0.7945 (m-70) REVERT: S 63 LYS cc_start: 0.6499 (mmtp) cc_final: 0.6027 (tmtt) REVERT: S 92 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8391 (tp) REVERT: T 69 MET cc_start: 0.6538 (tpt) cc_final: 0.6168 (mmm) outliers start: 144 outliers final: 86 residues processed: 708 average time/residue: 0.7448 time to fit residues: 646.7413 Evaluate side-chains 683 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 577 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 49 TYR Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 2 residue 52 LEU Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 69 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 34 ILE Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 47 PHE Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 69 PHE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 70 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 9 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 76 GLU Chi-restraints excluded: chain O residue 118 ILE Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 92 ILE Chi-restraints excluded: chain S residue 98 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 424 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 435 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 341 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 363 optimal weight: 0.6980 chunk 379 optimal weight: 1.9990 chunk 467 optimal weight: 5.9990 chunk 330 optimal weight: 3.9990 chunk 362 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 ASN B 396 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 430 HIS H 32 ASN ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 57 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.178468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.147888 restraints weight = 75088.604| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.47 r_work: 0.3725 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 40498 Z= 0.137 Angle : 0.610 14.906 54726 Z= 0.305 Chirality : 0.043 0.282 6274 Planarity : 0.004 0.061 7019 Dihedral : 7.758 101.158 5895 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 3.44 % Allowed : 19.96 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.12), residues: 5089 helix: 1.68 (0.10), residues: 2744 sheet: -0.14 (0.23), residues: 507 loop : -0.22 (0.15), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 16 TYR 0.025 0.001 TYR A 397 PHE 0.046 0.001 PHE B 468 TRP 0.028 0.002 TRP T 42 HIS 0.005 0.001 HIS F 430 Details of bonding type rmsd covalent geometry : bond 0.00309 (40498) covalent geometry : angle 0.61032 (54726) hydrogen bonds : bond 0.04089 ( 2307) hydrogen bonds : angle 4.45253 ( 6726) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 598 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 69 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.5201 (m-80) REVERT: 5 3 ASP cc_start: 0.7078 (m-30) cc_final: 0.6495 (p0) REVERT: 6 47 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5978 (m-80) REVERT: 6 51 ILE cc_start: 0.6505 (OUTLIER) cc_final: 0.6168 (mp) REVERT: 7 7 LYS cc_start: 0.7416 (mtmt) cc_final: 0.7132 (pttm) REVERT: 7 18 VAL cc_start: 0.6628 (OUTLIER) cc_final: 0.6297 (p) REVERT: A 26 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7216 (tt0) REVERT: A 40 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.8060 (mtp85) REVERT: A 128 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8678 (mtm-85) REVERT: A 150 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7706 (mmp) REVERT: A 195 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7543 (tp30) REVERT: A 355 GLU cc_start: 0.8104 (tt0) cc_final: 0.7796 (mm-30) REVERT: A 359 LYS cc_start: 0.8202 (mttm) cc_final: 0.7917 (mtpt) REVERT: A 362 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7853 (mtt180) REVERT: A 371 VAL cc_start: 0.7891 (t) cc_final: 0.7640 (p) REVERT: A 415 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7731 (mt0) REVERT: A 426 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 428 LEU cc_start: 0.7203 (mt) cc_final: 0.6834 (mt) REVERT: A 496 LYS cc_start: 0.8368 (mtpt) cc_final: 0.8002 (mttt) REVERT: B 15 LYS cc_start: 0.8003 (mmtp) cc_final: 0.7729 (mppt) REVERT: B 54 GLU cc_start: 0.8272 (tt0) cc_final: 0.7973 (tp30) REVERT: B 59 LEU cc_start: 0.8464 (mt) cc_final: 0.8161 (mp) REVERT: B 196 LYS cc_start: 0.8171 (mttt) cc_final: 0.7534 (mptp) REVERT: B 227 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7975 (mtp85) REVERT: B 385 GLN cc_start: 0.7879 (tt0) cc_final: 0.7659 (pt0) REVERT: B 418 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6658 (mt) REVERT: C 26 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8111 (mp0) REVERT: C 67 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: C 89 LYS cc_start: 0.8538 (mtmp) cc_final: 0.7972 (mttp) REVERT: C 127 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7838 (mt0) REVERT: C 143 ARG cc_start: 0.8094 (ptp90) cc_final: 0.7799 (mtm110) REVERT: C 355 GLU cc_start: 0.8124 (tt0) cc_final: 0.7894 (tt0) REVERT: C 381 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7512 (ttp-110) REVERT: C 385 GLN cc_start: 0.8236 (tt0) cc_final: 0.7941 (pt0) REVERT: C 392 LEU cc_start: 0.8474 (mt) cc_final: 0.8273 (mm) REVERT: C 416 GLN cc_start: 0.7458 (tp40) cc_final: 0.6986 (tp40) REVERT: C 457 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7439 (pt0) REVERT: C 463 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7902 (tttp) REVERT: C 467 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7849 (mp0) REVERT: C 488 GLN cc_start: 0.7625 (pt0) cc_final: 0.7181 (pt0) REVERT: C 503 ASP cc_start: 0.8220 (p0) cc_final: 0.7869 (p0) REVERT: D 15 GLN cc_start: 0.8519 (mt0) cc_final: 0.8204 (mt0) REVERT: D 170 MET cc_start: 0.8086 (mmm) cc_final: 0.7819 (mmp) REVERT: D 178 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7773 (mptt) REVERT: D 212 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7970 (mtmm) REVERT: D 214 LYS cc_start: 0.8724 (mttt) cc_final: 0.8375 (mtpp) REVERT: D 261 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8783 (tp) REVERT: D 389 ASP cc_start: 0.7125 (t0) cc_final: 0.6826 (p0) REVERT: D 396 MET cc_start: 0.7664 (mmm) cc_final: 0.7219 (tpt) REVERT: D 409 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7655 (mtt180) REVERT: E 15 GLN cc_start: 0.8328 (mt0) cc_final: 0.7753 (mm-40) REVERT: E 227 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: E 291 ASP cc_start: 0.8596 (m-30) cc_final: 0.8227 (m-30) REVERT: E 362 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8119 (t0) REVERT: E 415 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.5490 (mpt90) REVERT: F 47 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7507 (mmm160) REVERT: F 340 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7919 (ttm-80) REVERT: F 344 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7412 (mm-30) REVERT: F 385 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8179 (ttpp) REVERT: F 409 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7660 (mmt90) REVERT: F 422 GLN cc_start: 0.8045 (tt0) cc_final: 0.7213 (tm-30) REVERT: G 7 SER cc_start: 0.8335 (t) cc_final: 0.8013 (p) REVERT: G 11 LYS cc_start: 0.8278 (tttt) cc_final: 0.8019 (tptp) REVERT: G 161 PHE cc_start: 0.7819 (t80) cc_final: 0.7331 (t80) REVERT: G 229 ASP cc_start: 0.8463 (t70) cc_final: 0.8243 (m-30) REVERT: G 237 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7781 (mm-30) REVERT: H 96 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.5987 (pm20) REVERT: I 30 MET cc_start: 0.7517 (mmt) cc_final: 0.7284 (mpt) REVERT: K 113 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8378 (mtm-85) REVERT: K 123 MET cc_start: 0.7722 (mtm) cc_final: 0.6942 (ptt) REVERT: K 182 MET cc_start: 0.7350 (mmp) cc_final: 0.7076 (mpp) REVERT: K 193 MET cc_start: 0.6934 (mmt) cc_final: 0.6506 (mmm) REVERT: L 4 VAL cc_start: 0.5313 (OUTLIER) cc_final: 0.4874 (m) REVERT: L 76 MET cc_start: 0.7837 (mtp) cc_final: 0.7489 (mtt) REVERT: M 39 ARG cc_start: 0.8366 (mmm160) cc_final: 0.8113 (tpm-80) REVERT: M 141 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: N 9 PHE cc_start: 0.3322 (OUTLIER) cc_final: 0.2930 (m-80) REVERT: N 80 ASN cc_start: 0.8572 (m-40) cc_final: 0.8265 (m110) REVERT: N 136 MET cc_start: 0.6218 (ttm) cc_final: 0.5897 (ptm) REVERT: N 142 MET cc_start: 0.6890 (mpt) cc_final: 0.5983 (tmm) REVERT: N 189 PHE cc_start: 0.8420 (t80) cc_final: 0.8165 (t80) REVERT: N 206 SER cc_start: 0.8743 (m) cc_final: 0.8423 (p) REVERT: N 213 MET cc_start: 0.8266 (mmp) cc_final: 0.7699 (tpt) REVERT: O 6 LYS cc_start: 0.8283 (tttt) cc_final: 0.7861 (tppt) REVERT: O 12 PHE cc_start: 0.7027 (m-80) cc_final: 0.6389 (m-80) REVERT: O 17 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8307 (ttm-80) REVERT: O 30 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8137 (mmtm) REVERT: O 41 GLN cc_start: 0.7707 (tp40) cc_final: 0.7357 (tp40) REVERT: O 49 PHE cc_start: 0.7139 (m-80) cc_final: 0.6934 (m-80) REVERT: O 64 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: O 84 SER cc_start: 0.7486 (m) cc_final: 0.6902 (p) REVERT: O 95 ARG cc_start: 0.8466 (mmt-90) cc_final: 0.7700 (mmm-85) REVERT: O 140 LYS cc_start: 0.8268 (tttt) cc_final: 0.7813 (mppt) REVERT: O 174 MET cc_start: 0.6204 (ttm) cc_final: 0.5332 (ptm) REVERT: O 176 ILE cc_start: 0.7267 (mm) cc_final: 0.6940 (mt) REVERT: Q 17 MET cc_start: 0.7946 (mmp) cc_final: 0.7579 (tpt) REVERT: R 37 GLU cc_start: 0.7952 (mp0) cc_final: 0.6415 (tm-30) REVERT: S 57 HIS cc_start: 0.8393 (t70) cc_final: 0.7973 (m-70) REVERT: S 63 LYS cc_start: 0.6542 (mmtp) cc_final: 0.6040 (tmtt) REVERT: T 49 ARG cc_start: 0.8087 (ptp-110) cc_final: 0.7755 (ptp-170) REVERT: T 69 MET cc_start: 0.6522 (tpt) cc_final: 0.6148 (mmm) outliers start: 143 outliers final: 90 residues processed: 698 average time/residue: 0.7541 time to fit residues: 643.3191 Evaluate side-chains 686 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 577 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 2 residue 52 LEU Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 69 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 5 residue 34 ILE Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 6 residue 47 PHE Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 69 PHE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 38 ARG Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 70 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 89 ILE Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 9 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 166 SER Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 21 TRP Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 32 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 133 optimal weight: 0.7980 chunk 202 optimal weight: 0.0970 chunk 502 optimal weight: 1.9990 chunk 412 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 358 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 361 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 417 optimal weight: 0.0370 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 45 GLN 3 44 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 45 GLN B 396 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 226 ASN ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS G 230 ASN ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 57 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.179704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149332 restraints weight = 75249.575| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.48 r_work: 0.3740 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 40498 Z= 0.121 Angle : 0.605 14.533 54726 Z= 0.302 Chirality : 0.043 0.351 6274 Planarity : 0.004 0.073 7019 Dihedral : 7.613 100.366 5895 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 2.79 % Allowed : 20.85 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.12), residues: 5089 helix: 1.73 (0.10), residues: 2750 sheet: -0.08 (0.23), residues: 495 loop : -0.19 (0.15), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 109 TYR 0.026 0.001 TYR B 446 PHE 0.043 0.001 PHE T 32 TRP 0.030 0.002 TRP T 42 HIS 0.005 0.001 HIS F 430 Details of bonding type rmsd covalent geometry : bond 0.00266 (40498) covalent geometry : angle 0.60537 (54726) hydrogen bonds : bond 0.03976 ( 2307) hydrogen bonds : angle 4.40009 ( 6726) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 617 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 69 PHE cc_start: 0.5856 (OUTLIER) cc_final: 0.5455 (m-80) REVERT: 5 3 ASP cc_start: 0.7188 (m-30) cc_final: 0.6527 (p0) REVERT: 6 47 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.6148 (m-80) REVERT: 6 51 ILE cc_start: 0.6546 (OUTLIER) cc_final: 0.6199 (mp) REVERT: 6 75 PHE cc_start: 0.5402 (m-10) cc_final: 0.5162 (m-10) REVERT: 7 7 LYS cc_start: 0.7457 (mtmt) cc_final: 0.7147 (pttm) REVERT: 7 18 VAL cc_start: 0.6697 (OUTLIER) cc_final: 0.6369 (p) REVERT: A 26 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7350 (tt0) REVERT: A 40 ARG cc_start: 0.8550 (mtt-85) cc_final: 0.8244 (mtp85) REVERT: A 150 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7927 (mmp) REVERT: A 195 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7467 (tp30) REVERT: A 355 GLU cc_start: 0.8212 (tt0) cc_final: 0.7810 (mm-30) REVERT: A 359 LYS cc_start: 0.8180 (mttm) cc_final: 0.7855 (mtpt) REVERT: A 362 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7754 (mtt180) REVERT: A 371 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7677 (p) REVERT: A 415 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7749 (mt0) REVERT: A 426 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 496 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7992 (mttt) REVERT: B 14 GLU cc_start: 0.7918 (pt0) cc_final: 0.7696 (pt0) REVERT: B 15 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7789 (mppt) REVERT: B 54 GLU cc_start: 0.8560 (tt0) cc_final: 0.8164 (tp30) REVERT: B 59 LEU cc_start: 0.8466 (mt) cc_final: 0.8120 (mp) REVERT: B 196 LYS cc_start: 0.8182 (mttt) cc_final: 0.7620 (tttm) REVERT: B 353 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7501 (mp0) REVERT: B 369 LEU cc_start: 0.8563 (mt) cc_final: 0.8352 (mt) REVERT: B 385 GLN cc_start: 0.7874 (tt0) cc_final: 0.7638 (pt0) REVERT: B 418 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6462 (mt) REVERT: C 26 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8196 (mp0) REVERT: C 67 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: C 89 LYS cc_start: 0.8639 (mtmp) cc_final: 0.8098 (mttp) REVERT: C 91 THR cc_start: 0.8969 (m) cc_final: 0.8665 (p) REVERT: C 127 GLN cc_start: 0.8318 (tp-100) cc_final: 0.7871 (mt0) REVERT: C 143 ARG cc_start: 0.8221 (ptp90) cc_final: 0.7914 (mtm110) REVERT: C 355 GLU cc_start: 0.8257 (tt0) cc_final: 0.8014 (tt0) REVERT: C 381 ARG cc_start: 0.8012 (ttp-110) cc_final: 0.7659 (ttp-110) REVERT: C 385 GLN cc_start: 0.8289 (tt0) cc_final: 0.8002 (pt0) REVERT: C 416 GLN cc_start: 0.7433 (tp40) cc_final: 0.6980 (tp40) REVERT: C 457 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7428 (pt0) REVERT: C 463 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7903 (tttp) REVERT: C 467 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7889 (mp0) REVERT: C 488 GLN cc_start: 0.7584 (pt0) cc_final: 0.7151 (pt0) REVERT: C 503 ASP cc_start: 0.8233 (p0) cc_final: 0.7980 (p0) REVERT: D 15 GLN cc_start: 0.8671 (mt0) cc_final: 0.8393 (mt0) REVERT: D 170 MET cc_start: 0.8292 (mmm) cc_final: 0.8002 (mmp) REVERT: D 178 LYS cc_start: 0.8371 (mtpt) cc_final: 0.7784 (mptt) REVERT: D 212 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7954 (mtmm) REVERT: D 214 LYS cc_start: 0.8718 (mttt) cc_final: 0.8359 (mtpp) REVERT: D 253 ASP cc_start: 0.7907 (m-30) cc_final: 0.7554 (t0) REVERT: D 261 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8752 (tp) REVERT: D 389 ASP cc_start: 0.7072 (t0) cc_final: 0.6776 (p0) REVERT: D 396 MET cc_start: 0.7715 (mmm) cc_final: 0.7225 (tpt) REVERT: D 409 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7752 (mtt180) REVERT: E 15 GLN cc_start: 0.8461 (mt0) cc_final: 0.7874 (mm-40) REVERT: E 291 ASP cc_start: 0.8690 (m-30) cc_final: 0.8372 (m-30) REVERT: E 362 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8220 (t0) REVERT: F 47 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7562 (mmm160) REVERT: F 340 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8075 (ttm-80) REVERT: F 344 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7466 (mm-30) REVERT: F 379 LYS cc_start: 0.8473 (tttm) cc_final: 0.8170 (ttmm) REVERT: F 385 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8219 (ttpp) REVERT: F 387 LEU cc_start: 0.7821 (mt) cc_final: 0.7331 (pp) REVERT: F 409 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7834 (mmt90) REVERT: F 422 GLN cc_start: 0.8166 (tt0) cc_final: 0.7297 (tm-30) REVERT: G 7 SER cc_start: 0.8326 (t) cc_final: 0.8008 (p) REVERT: G 11 LYS cc_start: 0.8376 (tttt) cc_final: 0.8107 (tptp) REVERT: G 161 PHE cc_start: 0.7843 (t80) cc_final: 0.7392 (t80) REVERT: G 229 ASP cc_start: 0.8574 (t70) cc_final: 0.8371 (m-30) REVERT: G 237 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7879 (mm-30) REVERT: H 109 ARG cc_start: 0.8496 (mmm160) cc_final: 0.8244 (tpp-160) REVERT: I 30 MET cc_start: 0.7689 (mmt) cc_final: 0.7445 (mmt) REVERT: K 113 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8446 (mtm-85) REVERT: K 123 MET cc_start: 0.7925 (mtm) cc_final: 0.7054 (ptt) REVERT: K 182 MET cc_start: 0.7337 (mmp) cc_final: 0.7101 (mpp) REVERT: K 193 MET cc_start: 0.6860 (mmt) cc_final: 0.6472 (mmm) REVERT: L 4 VAL cc_start: 0.5415 (OUTLIER) cc_final: 0.4996 (m) REVERT: L 76 MET cc_start: 0.7846 (mtp) cc_final: 0.7494 (mtt) REVERT: M 39 ARG cc_start: 0.8492 (mmm160) cc_final: 0.8254 (tpm-80) REVERT: M 141 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: N 9 PHE cc_start: 0.3151 (OUTLIER) cc_final: 0.2947 (m-80) REVERT: N 80 ASN cc_start: 0.8581 (m-40) cc_final: 0.8364 (m110) REVERT: N 136 MET cc_start: 0.6223 (ttm) cc_final: 0.5866 (ptm) REVERT: N 142 MET cc_start: 0.6999 (mpt) cc_final: 0.6016 (tmm) REVERT: N 189 PHE cc_start: 0.8499 (t80) cc_final: 0.8296 (t80) REVERT: N 206 SER cc_start: 0.8740 (m) cc_final: 0.8456 (p) REVERT: N 210 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7768 (tmm) REVERT: N 213 MET cc_start: 0.8471 (mmp) cc_final: 0.7763 (tpt) REVERT: O 6 LYS cc_start: 0.8288 (tttt) cc_final: 0.7849 (tppt) REVERT: O 12 PHE cc_start: 0.7116 (m-80) cc_final: 0.6599 (m-80) REVERT: O 17 ARG cc_start: 0.8679 (ttm-80) cc_final: 0.8415 (ttm-80) REVERT: O 30 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8064 (mmtm) REVERT: O 41 GLN cc_start: 0.7767 (tp40) cc_final: 0.7398 (tp40) REVERT: O 64 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: O 68 ASP cc_start: 0.7816 (m-30) cc_final: 0.6986 (m-30) REVERT: O 84 SER cc_start: 0.7529 (m) cc_final: 0.6955 (p) REVERT: O 95 ARG cc_start: 0.8471 (mmt-90) cc_final: 0.7675 (mmm-85) REVERT: O 140 LYS cc_start: 0.8259 (tttt) cc_final: 0.7791 (mppt) REVERT: O 174 MET cc_start: 0.6168 (ttm) cc_final: 0.5298 (ptm) REVERT: O 176 ILE cc_start: 0.7296 (mm) cc_final: 0.6974 (mt) REVERT: R 21 ARG cc_start: 0.5993 (ttp-170) cc_final: 0.5640 (tpp80) REVERT: R 37 GLU cc_start: 0.8006 (mp0) cc_final: 0.6431 (tm-30) REVERT: S 57 HIS cc_start: 0.8401 (t70) cc_final: 0.8099 (m-70) REVERT: S 63 LYS cc_start: 0.6656 (mmtp) cc_final: 0.6057 (tmtt) REVERT: T 69 MET cc_start: 0.6551 (tpt) cc_final: 0.6190 (mmm) outliers start: 116 outliers final: 78 residues processed: 694 average time/residue: 0.7343 time to fit residues: 625.4943 Evaluate side-chains 678 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 584 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 2 residue 52 LEU Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 69 PHE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 6 residue 47 PHE Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 69 PHE Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 70 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 9 PHE Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 118 ILE Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain O residue 166 SER Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 21 TRP Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 90 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 357 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 44 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN E 449 ASN F 430 HIS ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.179001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148450 restraints weight = 74816.955| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.46 r_work: 0.3733 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40498 Z= 0.142 Angle : 0.630 14.033 54726 Z= 0.315 Chirality : 0.044 0.389 6274 Planarity : 0.004 0.075 7019 Dihedral : 7.583 100.588 5895 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.89 % Favored : 97.09 % Rotamer: Outliers : 2.67 % Allowed : 21.33 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.12), residues: 5089 helix: 1.70 (0.10), residues: 2740 sheet: -0.06 (0.22), residues: 516 loop : -0.21 (0.15), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG I 16 TYR 0.025 0.001 TYR A 397 PHE 0.044 0.001 PHE B 468 TRP 0.033 0.002 TRP T 42 HIS 0.005 0.001 HIS F 430 Details of bonding type rmsd covalent geometry : bond 0.00324 (40498) covalent geometry : angle 0.63031 (54726) hydrogen bonds : bond 0.04073 ( 2307) hydrogen bonds : angle 4.42905 ( 6726) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10178 Ramachandran restraints generated. 5089 Oldfield, 0 Emsley, 5089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 593 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 67 MET cc_start: 0.3992 (tpp) cc_final: 0.3641 (tpt) REVERT: 3 69 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5477 (m-80) REVERT: 4 46 LEU cc_start: 0.6209 (mp) cc_final: 0.5778 (pt) REVERT: 5 3 ASP cc_start: 0.7273 (m-30) cc_final: 0.6628 (p0) REVERT: 6 51 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6306 (mp) REVERT: 7 7 LYS cc_start: 0.7399 (mtmt) cc_final: 0.7028 (pttm) REVERT: 7 18 VAL cc_start: 0.6755 (OUTLIER) cc_final: 0.6428 (p) REVERT: A 26 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7331 (tt0) REVERT: A 40 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.8225 (mtp85) REVERT: A 128 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8765 (mtm-85) REVERT: A 150 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7930 (mmp) REVERT: A 195 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7477 (tp30) REVERT: A 355 GLU cc_start: 0.8217 (tt0) cc_final: 0.7780 (mm-30) REVERT: A 359 LYS cc_start: 0.8142 (mttm) cc_final: 0.7853 (mtpt) REVERT: A 362 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7848 (mtt180) REVERT: A 371 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7696 (p) REVERT: A 415 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7731 (mt0) REVERT: A 426 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 496 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7942 (mttt) REVERT: B 14 GLU cc_start: 0.7909 (pt0) cc_final: 0.7702 (pt0) REVERT: B 15 LYS cc_start: 0.8061 (mmtp) cc_final: 0.7783 (mppt) REVERT: B 54 GLU cc_start: 0.8547 (tt0) cc_final: 0.8153 (tp30) REVERT: B 59 LEU cc_start: 0.8483 (mt) cc_final: 0.8132 (mp) REVERT: B 143 ARG cc_start: 0.7468 (pmm-80) cc_final: 0.7243 (pmm-80) REVERT: B 196 LYS cc_start: 0.8177 (mttt) cc_final: 0.7481 (mptp) REVERT: B 353 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7542 (mp0) REVERT: B 369 LEU cc_start: 0.8506 (mt) cc_final: 0.8300 (mt) REVERT: B 381 ARG cc_start: 0.7441 (ttp80) cc_final: 0.7127 (ttm110) REVERT: B 385 GLN cc_start: 0.7873 (tt0) cc_final: 0.7632 (pt0) REVERT: B 418 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6339 (mt) REVERT: C 26 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8201 (mp0) REVERT: C 67 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: C 89 LYS cc_start: 0.8645 (mtmp) cc_final: 0.8096 (mttp) REVERT: C 127 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7871 (mt0) REVERT: C 143 ARG cc_start: 0.8211 (ptp90) cc_final: 0.7897 (mtm110) REVERT: C 355 GLU cc_start: 0.8229 (tt0) cc_final: 0.8012 (tt0) REVERT: C 381 ARG cc_start: 0.8020 (ttp-110) cc_final: 0.7659 (ttp-110) REVERT: C 385 GLN cc_start: 0.8292 (tt0) cc_final: 0.8001 (pt0) REVERT: C 416 GLN cc_start: 0.7460 (tp40) cc_final: 0.7030 (tp40) REVERT: C 457 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7404 (pt0) REVERT: C 463 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7890 (tttp) REVERT: C 467 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7867 (mp0) REVERT: C 488 GLN cc_start: 0.7542 (pt0) cc_final: 0.7024 (pt0) REVERT: C 503 ASP cc_start: 0.8150 (p0) cc_final: 0.7882 (p0) REVERT: D 15 GLN cc_start: 0.8699 (mt0) cc_final: 0.8415 (mt0) REVERT: D 170 MET cc_start: 0.8282 (mmm) cc_final: 0.7976 (mmp) REVERT: D 178 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7760 (mptt) REVERT: D 212 LYS cc_start: 0.8290 (mmtm) cc_final: 0.7937 (mtmm) REVERT: D 214 LYS cc_start: 0.8710 (mttt) cc_final: 0.8342 (mtpp) REVERT: D 253 ASP cc_start: 0.7903 (m-30) cc_final: 0.7563 (t0) REVERT: D 261 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8830 (tp) REVERT: D 389 ASP cc_start: 0.7107 (t0) cc_final: 0.6800 (p0) REVERT: D 396 MET cc_start: 0.7691 (mmm) cc_final: 0.7197 (tpt) REVERT: D 409 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7699 (mtt180) REVERT: E 15 GLN cc_start: 0.8490 (mt0) cc_final: 0.7894 (mm-40) REVERT: E 291 ASP cc_start: 0.8756 (m-30) cc_final: 0.8444 (m-30) REVERT: E 362 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8213 (t0) REVERT: F 47 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7580 (mmm160) REVERT: F 340 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8081 (ttm-80) REVERT: F 344 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7431 (mm-30) REVERT: F 379 LYS cc_start: 0.8455 (tttm) cc_final: 0.8146 (ttmm) REVERT: F 385 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8197 (ttpp) REVERT: F 387 LEU cc_start: 0.7697 (mt) cc_final: 0.7241 (pp) REVERT: F 391 ILE cc_start: 0.8156 (mp) cc_final: 0.7887 (mp) REVERT: F 409 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7809 (mmt90) REVERT: F 422 GLN cc_start: 0.8113 (tt0) cc_final: 0.7229 (tm-30) REVERT: G 7 SER cc_start: 0.8290 (t) cc_final: 0.7975 (p) REVERT: G 11 LYS cc_start: 0.8364 (tttt) cc_final: 0.8101 (tptp) REVERT: G 161 PHE cc_start: 0.7878 (t80) cc_final: 0.7458 (t80) REVERT: G 229 ASP cc_start: 0.8533 (t70) cc_final: 0.8322 (m-30) REVERT: G 237 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7875 (mm-30) REVERT: H 109 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8337 (tpp-160) REVERT: I 30 MET cc_start: 0.7652 (mmt) cc_final: 0.7444 (mmt) REVERT: K 113 ARG cc_start: 0.8725 (mmm-85) cc_final: 0.8416 (mtm-85) REVERT: K 123 MET cc_start: 0.7912 (mtm) cc_final: 0.7045 (ptt) REVERT: K 173 MET cc_start: 0.5912 (ptt) cc_final: 0.5697 (ptm) REVERT: K 182 MET cc_start: 0.7445 (mmp) cc_final: 0.7094 (mpp) REVERT: K 193 MET cc_start: 0.6803 (mmt) cc_final: 0.6428 (mmm) REVERT: L 4 VAL cc_start: 0.5386 (OUTLIER) cc_final: 0.4985 (m) REVERT: L 76 MET cc_start: 0.7681 (mtp) cc_final: 0.7380 (mtt) REVERT: M 39 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8243 (tpm-80) REVERT: M 65 MET cc_start: 0.3225 (tmt) cc_final: 0.3011 (ppp) REVERT: N 80 ASN cc_start: 0.8608 (m-40) cc_final: 0.8342 (m110) REVERT: N 136 MET cc_start: 0.6299 (ttm) cc_final: 0.5957 (ptm) REVERT: N 142 MET cc_start: 0.7012 (mpt) cc_final: 0.6004 (tmm) REVERT: N 206 SER cc_start: 0.8819 (m) cc_final: 0.8523 (p) REVERT: N 213 MET cc_start: 0.8489 (mmp) cc_final: 0.7770 (tpt) REVERT: O 6 LYS cc_start: 0.8299 (tttt) cc_final: 0.7820 (tppt) REVERT: O 12 PHE cc_start: 0.7112 (m-80) cc_final: 0.6689 (m-80) REVERT: O 17 ARG cc_start: 0.8689 (ttm-80) cc_final: 0.8422 (ttm-80) REVERT: O 41 GLN cc_start: 0.7720 (tp40) cc_final: 0.7361 (tp40) REVERT: O 64 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: O 84 SER cc_start: 0.7539 (m) cc_final: 0.6968 (p) REVERT: O 95 ARG cc_start: 0.8464 (mmt-90) cc_final: 0.7794 (mmm-85) REVERT: O 140 LYS cc_start: 0.8188 (tttt) cc_final: 0.7709 (mppt) REVERT: O 174 MET cc_start: 0.6028 (ttm) cc_final: 0.5143 (ptm) REVERT: O 176 ILE cc_start: 0.7258 (mm) cc_final: 0.6961 (mt) REVERT: R 37 GLU cc_start: 0.8093 (mp0) cc_final: 0.6572 (tm-30) REVERT: S 57 HIS cc_start: 0.8398 (t70) cc_final: 0.8057 (m-70) REVERT: S 63 LYS cc_start: 0.6706 (mmtp) cc_final: 0.6203 (tmtt) REVERT: T 49 ARG cc_start: 0.8218 (ptp-110) cc_final: 0.7871 (ptp-170) REVERT: T 69 MET cc_start: 0.6475 (tpt) cc_final: 0.6106 (mmm) outliers start: 111 outliers final: 80 residues processed: 666 average time/residue: 0.7409 time to fit residues: 605.2150 Evaluate side-chains 671 residues out of total 4156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 578 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 16 VAL Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 21 SER Chi-restraints excluded: chain 3 residue 69 PHE Chi-restraints excluded: chain 4 residue 54 PHE Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 6 residue 15 THR Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 69 PHE Chi-restraints excluded: chain 7 residue 18 VAL Chi-restraints excluded: chain 7 residue 69 PHE Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 41 SER Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 70 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain I residue 16 ARG Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 55 HIS Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain M residue 4 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 24 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 161 ASN Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 64 GLN Chi-restraints excluded: chain O residue 118 ILE Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain Q residue 21 TRP Chi-restraints excluded: chain Q residue 50 ASN Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain S residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 493 optimal weight: 6.9990 chunk 278 optimal weight: 0.7980 chunk 455 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 346 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 448 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 478 optimal weight: 0.0370 chunk 504 optimal weight: 3.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 44 GLN ** 4 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN E 449 ASN F 430 HIS ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.179173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.150207 restraints weight = 75319.297| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.47 r_work: 0.3738 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 40498 Z= 0.135 Angle : 0.638 14.623 54726 Z= 0.316 Chirality : 0.044 0.347 6274 Planarity : 0.004 0.061 7019 Dihedral : 7.526 100.181 5893 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.07 % Rotamer: Outliers : 2.60 % Allowed : 21.48 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.12), residues: 5089 helix: 1.71 (0.10), residues: 2744 sheet: -0.07 (0.22), residues: 521 loop : -0.22 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 109 TYR 0.027 0.001 TYR B 446 PHE 0.036 0.001 PHE T 32 TRP 0.036 0.002 TRP Q 53 HIS 0.004 0.001 HIS F 430 Details of bonding type rmsd covalent geometry : bond 0.00305 (40498) covalent geometry : angle 0.63782 (54726) hydrogen bonds : bond 0.04029 ( 2307) hydrogen bonds : angle 4.42367 ( 6726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19918.47 seconds wall clock time: 338 minutes 47.37 seconds (20327.37 seconds total)