Starting phenix.real_space_refine on Tue Aug 26 18:25:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k35_36844/08_2025/8k35_36844.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k35_36844/08_2025/8k35_36844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k35_36844/08_2025/8k35_36844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k35_36844/08_2025/8k35_36844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k35_36844/08_2025/8k35_36844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k35_36844/08_2025/8k35_36844.map" } resolution = 3.44 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= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 174 5.16 5 C 25305 2.51 5 N 6996 2.21 5 O 7866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.04s 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: 40353 Number of models: 1 Model: "" Number of chains: 27 Chain: "I" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6633 Classifications: {'peptide': 851} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 40, 'TRANS': 810} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6633 Classifications: {'peptide': 851} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 40, 'TRANS': 810} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6633 Classifications: {'peptide': 851} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 40, 'TRANS': 810} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "G" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "N" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "H" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "D" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 884 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "x" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 652 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "K" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 652 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "Q" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 652 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "L" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "R" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "T" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "U" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "V" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "W" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1174 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "P" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 241 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "M" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 241 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "S" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 241 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21326 SG CYS J 182 21.673 62.015 141.149 1.00 15.31 S ATOM 21497 SG CYS J 205 21.822 68.505 141.072 1.00 16.55 S ATOM 21248 SG CYS J 173 27.299 64.828 142.114 1.00 10.73 S ATOM 21542 SG CYS J 212 22.575 65.735 146.364 1.00 13.69 S ATOM 23127 SG CYS G 182 75.808 105.289 141.190 1.00 14.24 S ATOM 23298 SG CYS G 205 81.357 101.813 141.082 1.00 16.22 S ATOM 23049 SG CYS G 173 75.368 99.067 142.141 1.00 10.74 S ATOM 23343 SG CYS G 212 78.543 102.582 146.411 1.00 13.37 S ATOM 24928 SG CYS N 182 86.187 36.682 141.052 1.00 15.07 S ATOM 25099 SG CYS N 205 80.290 33.809 141.043 1.00 17.51 S ATOM 24850 SG CYS N 173 81.010 40.211 142.137 1.00 11.01 S ATOM 25144 SG CYS N 212 82.515 35.637 146.375 1.00 14.24 S Time building chain proxies: 10.47, per 1000 atoms: 0.26 Number of scatterers: 40353 At special positions: 0 Unit cell: (127.84, 129.2, 299.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 174 16.00 O 7866 8.00 N 6996 7.00 C 25305 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: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 G 301 " pdb="FE2 SF4 G 301 " - pdb=" SG CYS G 205 " pdb="FE1 SF4 G 301 " - pdb=" SG CYS G 182 " pdb="FE4 SF4 G 301 " - pdb=" SG CYS G 212 " pdb="FE3 SF4 G 301 " - pdb=" SG CYS G 173 " pdb=" SF4 J 301 " pdb="FE2 SF4 J 301 " - pdb=" SG CYS J 205 " pdb="FE1 SF4 J 301 " - pdb=" SG CYS J 182 " pdb="FE4 SF4 J 301 " - pdb=" SG CYS J 212 " pdb="FE3 SF4 J 301 " - pdb=" SG CYS J 173 " pdb=" SF4 N 301 " pdb="FE2 SF4 N 301 " - pdb=" SG CYS N 205 " pdb="FE1 SF4 N 301 " - pdb=" SG CYS N 182 " pdb="FE4 SF4 N 301 " - pdb=" SG CYS N 212 " pdb="FE3 SF4 N 301 " - pdb=" SG CYS N 173 " Number of angles added : 36 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9480 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 65 sheets defined 16.3% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'I' and resid 40 through 43 Processing helix chain 'I' and resid 271 through 281 Processing helix chain 'I' and resid 297 through 309 removed outlier: 3.798A pdb=" N LEU I 301 " --> pdb=" O ASP I 297 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL I 303 " --> pdb=" O TRP I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 346 removed outlier: 3.532A pdb=" N SER I 344 " --> pdb=" O SER I 340 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA I 345 " --> pdb=" O ASP I 341 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET I 346 " --> pdb=" O PHE I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 427 removed outlier: 3.580A pdb=" N ALA I 424 " --> pdb=" O THR I 420 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG I 425 " --> pdb=" O GLN I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 458 removed outlier: 3.692A pdb=" N LEU I 451 " --> pdb=" O ALA I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 473 removed outlier: 3.996A pdb=" N ARG I 472 " --> pdb=" O GLU I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 483 through 488 Processing helix chain 'I' and resid 594 through 601 removed outlier: 4.022A pdb=" N ILE I 598 " --> pdb=" O GLU I 594 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN I 601 " --> pdb=" O ALA I 597 " (cutoff:3.500A) Processing helix chain 'I' and resid 755 through 757 No H-bonds generated for 'chain 'I' and resid 755 through 757' Processing helix chain 'I' and resid 758 through 763 Processing helix chain 'I' and resid 810 through 816 removed outlier: 3.593A pdb=" N TYR I 814 " --> pdb=" O ASP I 810 " (cutoff:3.500A) Processing helix chain 'I' and resid 817 through 819 No H-bonds generated for 'chain 'I' and resid 817 through 819' Processing helix chain 'I' and resid 823 through 827 Processing helix chain 'I' and resid 828 through 851 removed outlier: 4.424A pdb=" N LYS I 834 " --> pdb=" O GLU I 830 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU I 851 " --> pdb=" O GLU I 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 297 through 309 removed outlier: 3.829A pdb=" N LEU A 301 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL A 303 " --> pdb=" O TRP A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 removed outlier: 3.531A pdb=" N SER A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.583A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 458 removed outlier: 3.735A pdb=" N LEU A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 removed outlier: 4.064A pdb=" N ARG A 472 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 594 through 601 removed outlier: 4.045A pdb=" N ILE A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 810 through 816 removed outlier: 3.502A pdb=" N TYR A 814 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 828 through 851 removed outlier: 4.313A pdb=" N LYS A 834 " --> pdb=" O GLU A 830 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 removed outlier: 3.687A pdb=" N LYS B 43 " --> pdb=" O ASP B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 43' Processing helix chain 'B' and resid 271 through 281 Processing helix chain 'B' and resid 297 through 309 removed outlier: 3.801A pdb=" N LEU B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B 303 " --> pdb=" O TRP B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.588A pdb=" N SER B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.514A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 458 removed outlier: 3.730A pdb=" N LEU B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 removed outlier: 4.035A pdb=" N ARG B 472 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 594 through 601 removed outlier: 4.072A pdb=" N ILE B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 763 Processing helix chain 'B' and resid 810 through 816 Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 823 through 827 removed outlier: 3.530A pdb=" N LEU B 827 " --> pdb=" O GLU B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 851 removed outlier: 4.431A pdb=" N LYS B 834 " --> pdb=" O GLU B 830 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 14 Processing helix chain 'J' and resid 86 through 95 removed outlier: 3.542A pdb=" N ASP J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 99 removed outlier: 3.603A pdb=" N VAL J 99 " --> pdb=" O GLN J 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 96 through 99' Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 208 through 214 Processing helix chain 'J' and resid 215 through 216 No H-bonds generated for 'chain 'J' and resid 215 through 216' Processing helix chain 'J' and resid 217 through 221 Processing helix chain 'J' and resid 226 through 232 removed outlier: 4.297A pdb=" N LEU J 230 " --> pdb=" O SER J 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 14 Processing helix chain 'G' and resid 86 through 95 Processing helix chain 'G' and resid 96 through 99 removed outlier: 3.641A pdb=" N VAL G 99 " --> pdb=" O GLN G 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 96 through 99' Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 208 through 214 Processing helix chain 'G' and resid 215 through 216 No H-bonds generated for 'chain 'G' and resid 215 through 216' Processing helix chain 'G' and resid 217 through 221 Processing helix chain 'G' and resid 226 through 232 removed outlier: 4.257A pdb=" N LEU G 230 " --> pdb=" O SER G 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 Processing helix chain 'N' and resid 86 through 95 removed outlier: 3.552A pdb=" N ASP N 94 " --> pdb=" O GLY N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 99 removed outlier: 3.558A pdb=" N VAL N 99 " --> pdb=" O GLN N 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 96 through 99' Processing helix chain 'N' and resid 111 through 113 No H-bonds generated for 'chain 'N' and resid 111 through 113' Processing helix chain 'N' and resid 208 through 214 Processing helix chain 'N' and resid 215 through 216 No H-bonds generated for 'chain 'N' and resid 215 through 216' Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'N' and resid 226 through 232 removed outlier: 4.240A pdb=" N LEU N 230 " --> pdb=" O SER N 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 65 removed outlier: 4.356A pdb=" N THR H 56 " --> pdb=" O ARG H 52 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 66 removed outlier: 3.650A pdb=" N LEU O 58 " --> pdb=" O GLU O 54 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS O 65 " --> pdb=" O PHE O 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 65 removed outlier: 4.334A pdb=" N THR C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 66 removed outlier: 3.529A pdb=" N LEU E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 65 removed outlier: 4.216A pdb=" N THR D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.617A pdb=" N LEU F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) Processing helix chain 'x' and resid 142 through 147 Processing helix chain 'x' and resid 150 through 156 removed outlier: 3.696A pdb=" N MET x 154 " --> pdb=" O GLY x 150 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU x 155 " --> pdb=" O VAL x 151 " (cutoff:3.500A) Processing helix chain 'x' and resid 165 through 169 Processing helix chain 'K' and resid 142 through 147 Processing helix chain 'K' and resid 150 through 156 removed outlier: 3.548A pdb=" N MET K 154 " --> pdb=" O GLY K 150 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU K 155 " --> pdb=" O VAL K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'Q' and resid 142 through 147 Processing helix chain 'Q' and resid 150 through 156 removed outlier: 3.955A pdb=" N MET Q 154 " --> pdb=" O GLY Q 150 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU Q 155 " --> pdb=" O VAL Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 169 removed outlier: 3.558A pdb=" N ASP Q 168 " --> pdb=" O GLN Q 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 102 Processing helix chain 'L' and resid 151 through 155 removed outlier: 3.507A pdb=" N ARG L 155 " --> pdb=" O ALA L 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 102 removed outlier: 3.505A pdb=" N GLN R 94 " --> pdb=" O GLU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.675A pdb=" N ASP R 154 " --> pdb=" O MET R 151 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG R 155 " --> pdb=" O ALA R 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 151 through 155' Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'U' and resid 90 through 102 Processing helix chain 'V' and resid 90 through 102 removed outlier: 3.582A pdb=" N GLN V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 90 through 102 Processing helix chain 'P' and resid 819 through 843 removed outlier: 3.954A pdb=" N LEU P 823 " --> pdb=" O GLY P 819 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG P 843 " --> pdb=" O GLN P 839 " (cutoff:3.500A) Processing helix chain 'M' and resid 819 through 843 removed outlier: 3.902A pdb=" N LEU M 823 " --> pdb=" O GLY M 819 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG M 843 " --> pdb=" O GLN M 839 " (cutoff:3.500A) Processing helix chain 'S' and resid 819 through 843 removed outlier: 3.929A pdb=" N LEU S 823 " --> pdb=" O GLY S 819 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG S 843 " --> pdb=" O GLN S 839 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 5 through 9 removed outlier: 6.873A pdb=" N ALA I 216 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU I 23 " --> pdb=" O ILE x 207 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE x 207 " --> pdb=" O LEU I 23 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER I 25 " --> pdb=" O GLN x 205 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN x 205 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE I 27 " --> pdb=" O VAL x 203 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG x 201 " --> pdb=" O ALA I 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 50 through 51 Processing sheet with id=AA3, first strand: chain 'I' and resid 82 through 94 removed outlier: 3.590A pdb=" N SER I 84 " --> pdb=" O ILE I 206 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR I 202 " --> pdb=" O THR I 88 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER I 200 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR I 92 " --> pdb=" O LEU I 198 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU I 198 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TRP I 199 " --> pdb=" O GLY I 117 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY I 117 " --> pdb=" O TRP I 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 100 through 103 removed outlier: 5.206A pdb=" N ASN I 178 " --> pdb=" O GLN I 142 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N SER I 133 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS I 156 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL I 135 " --> pdb=" O THR I 154 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR I 154 " --> pdb=" O VAL I 135 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU I 137 " --> pdb=" O ASP I 152 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP I 152 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL I 139 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG I 143 " --> pdb=" O GLY I 146 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL x 219 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASP I 152 " --> pdb=" O VAL x 219 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE x 221 " --> pdb=" O ASP I 152 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR I 154 " --> pdb=" O ILE x 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 123 through 124 Processing sheet with id=AA6, first strand: chain 'I' and resid 243 through 246 Processing sheet with id=AA7, first strand: chain 'I' and resid 311 through 313 Processing sheet with id=AA8, first strand: chain 'I' and resid 328 through 329 Processing sheet with id=AA9, first strand: chain 'I' and resid 348 through 352 Processing sheet with id=AB1, first strand: chain 'I' and resid 370 through 371 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 370 through 371 current: chain 'I' and resid 460 through 467 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 460 through 467 current: chain 'I' and resid 570 through 578 removed outlier: 6.737A pdb=" N THR I 587 " --> pdb=" O VAL I 574 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE I 576 " --> pdb=" O ALA I 585 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA I 585 " --> pdb=" O ILE I 576 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLU I 578 " --> pdb=" O THR I 583 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR I 583 " --> pdb=" O GLU I 578 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 412 through 418 removed outlier: 6.356A pdb=" N ALA I 398 " --> pdb=" O THR I 431 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N MET I 433 " --> pdb=" O ALA I 398 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLU I 400 " --> pdb=" O MET I 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 492 through 494 removed outlier: 6.857A pdb=" N VAL I 558 " --> pdb=" O VAL I 524 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL I 524 " --> pdb=" O VAL I 558 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER I 537 " --> pdb=" O LYS I 545 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA I 497 " --> pdb=" O THR I 506 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 625 through 629 Processing sheet with id=AB5, first strand: chain 'I' and resid 646 through 647 removed outlier: 3.910A pdb=" N ARG K 201 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 27 " --> pdb=" O VAL K 203 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN K 205 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER A 25 " --> pdb=" O GLN K 205 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE K 207 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 23 " --> pdb=" O ILE K 207 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 216 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 665 through 673 removed outlier: 7.183A pdb=" N LEU I 656 " --> pdb=" O VAL I 668 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR I 670 " --> pdb=" O LEU I 654 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU I 654 " --> pdb=" O THR I 670 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG I 672 " --> pdb=" O PHE I 652 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE I 652 " --> pdb=" O ARG I 672 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR I 659 " --> pdb=" O ASN I 687 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN I 687 " --> pdb=" O THR I 659 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE I 709 " --> pdb=" O TYR I 688 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 719 through 724 removed outlier: 3.813A pdb=" N ARG I 719 " --> pdb=" O HIS I 734 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR I 730 " --> pdb=" O THR I 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 764 through 769 removed outlier: 7.076A pdb=" N PHE I 746 " --> pdb=" O LEU I 766 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR I 768 " --> pdb=" O PHE I 744 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE I 744 " --> pdb=" O THR I 768 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AC1, first strand: chain 'A' and resid 82 through 93 removed outlier: 3.605A pdb=" N SER A 84 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 202 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER A 200 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR A 92 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU A 198 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N THR A 115 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR A 202 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG A 113 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU A 204 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG A 111 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 112 " --> pdb=" O MET A 169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 100 through 103 removed outlier: 5.259A pdb=" N ASN A 178 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER A 133 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS A 156 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 135 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR A 154 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 137 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP A 152 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 139 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 143 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL K 219 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP A 152 " --> pdb=" O VAL K 219 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE K 221 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR A 154 " --> pdb=" O ILE K 221 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AC4, first strand: chain 'A' and resid 243 through 246 Processing sheet with id=AC5, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AC6, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AC7, first strand: chain 'A' and resid 348 through 352 Processing sheet with id=AC8, first strand: chain 'A' and resid 370 through 371 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 370 through 371 current: chain 'A' and resid 460 through 467 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 460 through 467 current: chain 'A' and resid 570 through 578 removed outlier: 6.726A pdb=" N THR A 587 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 576 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA A 585 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU A 578 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR A 583 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 412 through 418 removed outlier: 6.372A pdb=" N ALA A 398 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET A 433 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLU A 400 " --> pdb=" O MET A 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 492 through 494 removed outlier: 7.086A pdb=" N VAL A 558 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 524 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS A 545 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 538 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS A 543 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 497 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 625 through 629 Processing sheet with id=AD3, first strand: chain 'A' and resid 646 through 647 removed outlier: 3.809A pdb=" N ARG Q 201 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 27 " --> pdb=" O VAL Q 203 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN Q 205 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER B 25 " --> pdb=" O GLN Q 205 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE Q 207 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 23 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 216 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 665 through 673 removed outlier: 5.519A pdb=" N LEU A 667 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 658 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 669 " --> pdb=" O LEU A 656 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 719 through 724 removed outlier: 3.746A pdb=" N ARG A 719 " --> pdb=" O HIS A 734 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 721 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 730 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 764 through 769 removed outlier: 7.121A pdb=" N PHE A 746 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR A 768 " --> pdb=" O PHE A 744 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 744 " --> pdb=" O THR A 768 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AD8, first strand: chain 'B' and resid 82 through 93 removed outlier: 3.581A pdb=" N SER B 84 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 202 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B 200 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR B 92 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU B 198 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR B 115 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR B 202 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG B 113 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU B 204 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG B 111 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 100 through 103 removed outlier: 5.277A pdb=" N ASN B 178 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N SER B 133 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS B 156 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 135 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 154 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 137 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASP B 152 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 139 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 143 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL Q 219 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASP B 152 " --> pdb=" O VAL Q 219 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE Q 221 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N THR B 154 " --> pdb=" O ILE Q 221 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AE2, first strand: chain 'B' and resid 243 through 246 Processing sheet with id=AE3, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AE4, first strand: chain 'B' and resid 328 through 329 Processing sheet with id=AE5, first strand: chain 'B' and resid 348 through 352 Processing sheet with id=AE6, first strand: chain 'B' and resid 370 through 371 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 370 through 371 current: chain 'B' and resid 460 through 467 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 460 through 467 current: chain 'B' and resid 570 through 578 removed outlier: 6.704A pdb=" N THR B 587 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE B 576 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA B 585 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLU B 578 " --> pdb=" O THR B 583 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR B 583 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 412 through 418 removed outlier: 6.371A pdb=" N ALA B 398 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET B 433 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU B 400 " --> pdb=" O MET B 433 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 492 through 494 removed outlier: 7.055A pdb=" N VAL B 558 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 524 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 537 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 497 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 625 through 629 Processing sheet with id=AF1, first strand: chain 'B' and resid 665 through 673 removed outlier: 5.422A pdb=" N LEU B 667 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 658 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B 669 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 659 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN B 687 " --> pdb=" O THR B 659 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 709 " --> pdb=" O TYR B 688 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 719 through 724 removed outlier: 3.752A pdb=" N ARG B 719 " --> pdb=" O HIS B 734 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 730 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 729 " --> pdb=" O ALA B 774 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 764 through 769 removed outlier: 5.733A pdb=" N TYR B 765 " --> pdb=" O PHE B 748 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE B 748 " --> pdb=" O TYR B 765 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 767 " --> pdb=" O PHE B 746 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 744 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 57 through 58 removed outlier: 3.743A pdb=" N GLN J 57 " --> pdb=" O PHE J 37 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL J 151 " --> pdb=" O GLU J 138 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N CYS J 140 " --> pdb=" O SER J 149 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER J 149 " --> pdb=" O CYS J 140 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU J 142 " --> pdb=" O SER J 147 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N SER J 147 " --> pdb=" O GLU J 142 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 57 through 58 removed outlier: 3.792A pdb=" N GLN G 57 " --> pdb=" O PHE G 37 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL G 151 " --> pdb=" O GLU G 138 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS G 140 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER G 149 " --> pdb=" O CYS G 140 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU G 142 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER G 147 " --> pdb=" O GLU G 142 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 57 through 58 removed outlier: 3.707A pdb=" N GLN N 57 " --> pdb=" O PHE N 37 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL N 151 " --> pdb=" O GLU N 138 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N CYS N 140 " --> pdb=" O SER N 149 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER N 149 " --> pdb=" O CYS N 140 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU N 142 " --> pdb=" O SER N 147 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER N 147 " --> pdb=" O GLU N 142 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 13 through 16 removed outlier: 3.651A pdb=" N ALA H 15 " --> pdb=" O THR H 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 43 through 51 current: chain 'H' and resid 82 through 93 removed outlier: 5.492A pdb=" N CYS H 86 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU H 105 " --> pdb=" O CYS H 86 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS H 88 " --> pdb=" O GLU H 103 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU H 103 " --> pdb=" O LYS H 88 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 97 through 106 current: chain 'O' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 43 through 51 current: chain 'O' and resid 82 through 93 removed outlier: 4.676A pdb=" N LYS O 83 " --> pdb=" O VAL O 107 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA O 87 " --> pdb=" O GLU O 103 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU O 103 " --> pdb=" O ALA O 87 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TRP O 89 " --> pdb=" O SER O 101 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER O 101 " --> pdb=" O TRP O 89 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER O 91 " --> pdb=" O GLU O 99 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU O 99 " --> pdb=" O SER O 91 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL O 93 " --> pdb=" O ARG O 97 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ARG O 97 " --> pdb=" O VAL O 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 97 through 107 current: chain 'C' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 43 through 51 current: chain 'C' and resid 82 through 93 removed outlier: 5.562A pdb=" N CYS C 86 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLU C 105 " --> pdb=" O CYS C 86 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS C 88 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU C 103 " --> pdb=" O LYS C 88 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 97 through 106 current: chain 'E' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 43 through 51 current: chain 'E' and resid 82 through 93 removed outlier: 5.952A pdb=" N CYS E 86 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLU E 105 " --> pdb=" O CYS E 86 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS E 88 " --> pdb=" O GLU E 103 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU E 103 " --> pdb=" O LYS E 88 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 97 through 106 current: chain 'D' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 43 through 51 current: chain 'D' and resid 82 through 93 removed outlier: 5.567A pdb=" N CYS D 86 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLU D 105 " --> pdb=" O CYS D 86 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LYS D 88 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU D 103 " --> pdb=" O LYS D 88 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 97 through 106 current: chain 'F' and resid 43 through 51 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 43 through 51 current: chain 'F' and resid 82 through 93 removed outlier: 5.798A pdb=" N CYS F 86 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLU F 105 " --> pdb=" O CYS F 86 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS F 88 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU F 103 " --> pdb=" O LYS F 88 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 20 through 24 Processing sheet with id=AF9, first strand: chain 'O' and resid 20 through 23 Processing sheet with id=AG1, first strand: chain 'C' and resid 20 through 24 Processing sheet with id=AG2, first strand: chain 'E' and resid 20 through 23 Processing sheet with id=AG3, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AG4, first strand: chain 'F' and resid 20 through 23 Processing sheet with id=AG5, first strand: chain 'L' and resid 16 through 20 removed outlier: 4.570A pdb=" N LEU L 17 " --> pdb=" O LEU L 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 36 through 39 current: chain 'L' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 79 through 85 current: chain 'L' and resid 117 through 130 removed outlier: 5.683A pdb=" N VAL L 124 " --> pdb=" O THR L 144 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR L 144 " --> pdb=" O VAL L 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 138 through 145 current: chain 'W' and resid 70 through 76 Processing sheet with id=AG6, first strand: chain 'L' and resid 70 through 77 removed outlier: 5.638A pdb=" N GLN L 72 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TYR L 55 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN L 74 " --> pdb=" O GLU L 53 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU L 53 " --> pdb=" O GLN L 74 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER R 125 " --> pdb=" O ALA L 52 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N SER L 54 " --> pdb=" O TRP R 123 " (cutoff:3.500A) removed outlier: 12.126A pdb=" N TRP R 123 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL R 124 " --> pdb=" O THR R 144 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N THR R 144 " --> pdb=" O VAL R 124 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA R 85 " --> pdb=" O VAL R 42 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL R 42 " --> pdb=" O ALA R 85 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 36 through 39 removed outlier: 4.592A pdb=" N LEU R 17 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 50 through 56 removed outlier: 3.789A pdb=" N GLU R 53 " --> pdb=" O GLN R 74 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN R 74 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR R 55 " --> pdb=" O GLN R 72 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLN R 72 " --> pdb=" O TYR R 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 70 through 76 current: chain 'T' and resid 36 through 39 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 36 through 39 current: chain 'T' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 79 through 85 current: chain 'T' and resid 117 through 130 removed outlier: 5.627A pdb=" N VAL T 124 " --> pdb=" O THR T 144 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR T 144 " --> pdb=" O VAL T 124 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'T' and resid 50 through 56 removed outlier: 3.766A pdb=" N GLU T 53 " --> pdb=" O GLN T 74 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN T 74 " --> pdb=" O GLU T 53 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR T 55 " --> pdb=" O GLN T 72 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN T 72 " --> pdb=" O TYR T 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 70 through 77 current: chain 'U' and resid 36 through 39 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 36 through 39 current: chain 'U' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 79 through 85 current: chain 'U' and resid 117 through 132 removed outlier: 5.431A pdb=" N VAL U 124 " --> pdb=" O THR U 144 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR U 144 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR U 132 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL U 136 " --> pdb=" O THR U 132 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 50 through 56 removed outlier: 4.445A pdb=" N GLN U 74 " --> pdb=" O GLU U 53 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR U 55 " --> pdb=" O GLN U 72 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLN U 72 " --> pdb=" O TYR U 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 70 through 76 current: chain 'V' and resid 36 through 39 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 36 through 39 current: chain 'V' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 79 through 85 current: chain 'V' and resid 117 through 130 removed outlier: 5.690A pdb=" N VAL V 124 " --> pdb=" O THR V 144 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR V 144 " --> pdb=" O VAL V 124 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 50 through 56 removed outlier: 3.760A pdb=" N GLU V 53 " --> pdb=" O GLN V 74 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN V 74 " --> pdb=" O GLU V 53 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR V 55 " --> pdb=" O GLN V 72 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN V 72 " --> pdb=" O TYR V 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 70 through 77 current: chain 'W' and resid 36 through 39 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 36 through 39 current: chain 'W' and resid 79 through 85 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 79 through 85 current: chain 'W' and resid 117 through 132 removed outlier: 5.397A pdb=" N VAL W 124 " --> pdb=" O THR W 144 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR W 144 " --> pdb=" O VAL W 124 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N THR W 132 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL W 136 " --> pdb=" O THR W 132 " (cutoff:3.500A) 1070 hydrogen bonds defined for protein. 2889 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: 10.80 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 17045 1.41 - 1.63: 23896 1.63 - 1.84: 267 1.84 - 2.06: 0 2.06 - 2.28: 36 Bond restraints: 41244 Sorted by residual: bond pdb=" CA TYR A 486 " pdb=" C TYR A 486 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.26e-02 6.30e+03 1.77e+01 bond pdb=" C LEU A 172 " pdb=" N PRO A 173 " ideal model delta sigma weight residual 1.329 1.374 -0.044 1.18e-02 7.18e+03 1.42e+01 bond pdb=" C LEU B 172 " pdb=" N PRO B 173 " ideal model delta sigma weight residual 1.329 1.373 -0.044 1.18e-02 7.18e+03 1.39e+01 bond pdb=" C MET G 91 " pdb=" O MET G 91 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.26e-02 6.30e+03 1.19e+01 bond pdb=" CA GLY T 73 " pdb=" C GLY T 73 " ideal model delta sigma weight residual 1.513 1.477 0.036 1.06e-02 8.90e+03 1.17e+01 ... (remaining 41239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 54788 1.71 - 3.43: 1122 3.43 - 5.14: 117 5.14 - 6.85: 23 6.85 - 8.57: 5 Bond angle restraints: 56055 Sorted by residual: angle pdb=" N ALA G 92 " pdb=" CA ALA G 92 " pdb=" C ALA G 92 " ideal model delta sigma weight residual 111.36 117.87 -6.51 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N LEU B 172 " pdb=" CA LEU B 172 " pdb=" C LEU B 172 " ideal model delta sigma weight residual 109.57 116.65 -7.08 1.23e+00 6.61e-01 3.31e+01 angle pdb=" N TYR T 55 " pdb=" CA TYR T 55 " pdb=" C TYR T 55 " ideal model delta sigma weight residual 110.14 102.87 7.27 1.55e+00 4.16e-01 2.20e+01 angle pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" C LEU A 172 " ideal model delta sigma weight residual 109.57 115.28 -5.71 1.23e+00 6.61e-01 2.16e+01 angle pdb=" N ASP J 94 " pdb=" CA ASP J 94 " pdb=" C ASP J 94 " ideal model delta sigma weight residual 111.40 116.54 -5.14 1.22e+00 6.72e-01 1.78e+01 ... (remaining 56050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 22605 18.04 - 36.08: 1585 36.08 - 54.12: 248 54.12 - 72.16: 29 72.16 - 90.20: 31 Dihedral angle restraints: 24498 sinusoidal: 9687 harmonic: 14811 Sorted by residual: dihedral pdb=" CA PRO G 164 " pdb=" C PRO G 164 " pdb=" N GLY G 165 " pdb=" CA GLY G 165 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA LEU A 47 " pdb=" C LEU A 47 " pdb=" N ASN A 48 " pdb=" CA ASN A 48 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LEU U 39 " pdb=" C LEU U 39 " pdb=" N ALA U 40 " pdb=" CA ALA U 40 " ideal model delta harmonic sigma weight residual 180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 24495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 5620 0.081 - 0.161: 556 0.161 - 0.242: 10 0.242 - 0.323: 0 0.323 - 0.404: 3 Chirality restraints: 6189 Sorted by residual: chirality pdb=" CA ALA G 92 " pdb=" N ALA G 92 " pdb=" C ALA G 92 " pdb=" CB ALA G 92 " both_signs ideal model delta sigma weight residual False 2.48 2.08 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ALA J 92 " pdb=" N ALA J 92 " pdb=" C ALA J 92 " pdb=" CB ALA J 92 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA ALA N 92 " pdb=" N ALA N 92 " pdb=" C ALA N 92 " pdb=" CB ALA N 92 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 6186 not shown) Planarity restraints: 7290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 172 " -0.032 5.00e-02 4.00e+02 5.05e-02 4.09e+00 pdb=" N PRO B 173 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 173 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 173 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 282 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO I 283 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO I 283 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO I 283 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA T 52 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C ALA T 52 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA T 52 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU T 53 " 0.010 2.00e-02 2.50e+03 ... (remaining 7287 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 306 2.64 - 3.21: 34365 3.21 - 3.77: 55282 3.77 - 4.34: 80421 4.34 - 4.90: 138959 Nonbonded interactions: 309333 Sorted by model distance: nonbonded pdb=" OD1 ASP I 54 " pdb=" N THR I 55 " model vdw 2.079 3.120 nonbonded pdb=" OH TYR V 108 " pdb=" OD1 ASN V 145 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR W 108 " pdb=" OD1 ASN W 145 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR L 108 " pdb=" OD1 ASN L 145 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR U 108 " pdb=" OD1 ASN U 145 " model vdw 2.236 3.040 ... (remaining 309328 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'x' } ncs_group { reference = chain 'L' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.610 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 46.700 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.170 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41256 Z= 0.199 Angle : 0.619 9.431 56091 Z= 0.350 Chirality : 0.044 0.404 6189 Planarity : 0.004 0.051 7290 Dihedral : 12.729 90.200 15018 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.02 (0.11), residues: 5136 helix: 0.36 (0.21), residues: 636 sheet: -0.07 (0.12), residues: 1836 loop : -1.38 (0.10), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 148 TYR 0.023 0.001 TYR I 249 PHE 0.019 0.001 PHE B 116 TRP 0.014 0.001 TRP J 175 HIS 0.005 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00405 (41244) covalent geometry : angle 0.60432 (56055) hydrogen bonds : bond 0.21468 ( 1070) hydrogen bonds : angle 8.36354 ( 2889) metal coordination : bond 0.00624 ( 12) metal coordination : angle 5.23514 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.710 Fit side-chains REVERT: I 685 LEU cc_start: 0.8572 (tp) cc_final: 0.8278 (tt) REVERT: A 202 TYR cc_start: 0.9070 (p90) cc_final: 0.8809 (p90) REVERT: B 259 ILE cc_start: 0.8826 (mm) cc_final: 0.8602 (mm) REVERT: G 180 ASP cc_start: 0.8055 (t70) cc_final: 0.7728 (t0) REVERT: O 22 LYS cc_start: 0.8771 (ptmt) cc_final: 0.8447 (pttt) REVERT: D 95 MET cc_start: 0.8467 (mmm) cc_final: 0.8152 (mmt) REVERT: F 22 LYS cc_start: 0.8776 (ptmt) cc_final: 0.8465 (pttt) REVERT: x 153 GLN cc_start: 0.7455 (mt0) cc_final: 0.7132 (pt0) REVERT: x 178 SER cc_start: 0.8884 (t) cc_final: 0.8683 (t) REVERT: T 87 MET cc_start: 0.8851 (mtm) cc_final: 0.8647 (mtp) REVERT: W 38 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8662 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.2874 time to fit residues: 234.1726 Evaluate side-chains 444 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 0.0170 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 734 HIS B 734 HIS C 109 ASN Q 181 ASN R 29 ASN T 29 ASN V 101 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102126 restraints weight = 52261.795| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.62 r_work: 0.2772 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41256 Z= 0.134 Angle : 0.527 8.733 56091 Z= 0.274 Chirality : 0.043 0.160 6189 Planarity : 0.004 0.050 7290 Dihedral : 4.516 20.198 5640 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.62 % Allowed : 5.24 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.85 (0.11), residues: 5136 helix: 0.59 (0.21), residues: 654 sheet: -0.03 (0.12), residues: 1875 loop : -1.26 (0.11), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 38 TYR 0.018 0.001 TYR I 249 PHE 0.015 0.001 PHE A 748 TRP 0.014 0.001 TRP B 274 HIS 0.004 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00317 (41244) covalent geometry : angle 0.51475 (56055) hydrogen bonds : bond 0.04462 ( 1070) hydrogen bonds : angle 5.87444 ( 2889) metal coordination : bond 0.00567 ( 12) metal coordination : angle 4.53243 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 486 time to evaluate : 1.697 Fit side-chains REVERT: I 54 ASP cc_start: 0.8265 (t0) cc_final: 0.8024 (t0) REVERT: I 685 LEU cc_start: 0.8719 (tp) cc_final: 0.8466 (tt) REVERT: I 748 PHE cc_start: 0.7483 (t80) cc_final: 0.7233 (t80) REVERT: A 116 PHE cc_start: 0.8507 (p90) cc_final: 0.8229 (p90) REVERT: A 202 TYR cc_start: 0.9008 (p90) cc_final: 0.8763 (p90) REVERT: A 341 ASP cc_start: 0.8650 (m-30) cc_final: 0.8430 (m-30) REVERT: B 1 MET cc_start: 0.6697 (mpp) cc_final: 0.6309 (mpp) REVERT: B 97 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: B 259 ILE cc_start: 0.9037 (mm) cc_final: 0.8757 (mm) REVERT: G 180 ASP cc_start: 0.8699 (t70) cc_final: 0.8208 (t0) REVERT: H 95 MET cc_start: 0.9046 (mmm) cc_final: 0.8837 (mmm) REVERT: O 22 LYS cc_start: 0.9049 (ptmt) cc_final: 0.8745 (pttt) REVERT: F 22 LYS cc_start: 0.8999 (ptmt) cc_final: 0.8609 (pttt) REVERT: x 153 GLN cc_start: 0.8152 (mt0) cc_final: 0.7493 (pt0) REVERT: T 87 MET cc_start: 0.8911 (mtm) cc_final: 0.8683 (mtp) REVERT: V 137 ILE cc_start: 0.8537 (mt) cc_final: 0.8310 (mt) REVERT: W 38 ARG cc_start: 0.8946 (ttp80) cc_final: 0.8724 (ttt-90) outliers start: 27 outliers final: 18 residues processed: 498 average time/residue: 0.2870 time to fit residues: 226.8886 Evaluate side-chains 465 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 446 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 208 SER Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain T residue 84 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 51 optimal weight: 0.9980 chunk 431 optimal weight: 20.0000 chunk 414 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 319 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 326 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 396 HIS I 734 HIS A 270 ASN L 101 ASN R 29 ASN T 29 ASN U 29 ASN V 101 ASN W 94 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098315 restraints weight = 52498.129| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.64 r_work: 0.2719 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 41256 Z= 0.239 Angle : 0.593 10.404 56091 Z= 0.305 Chirality : 0.046 0.169 6189 Planarity : 0.004 0.050 7290 Dihedral : 4.706 20.688 5640 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.19 % Allowed : 7.75 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.97 (0.11), residues: 5136 helix: 0.53 (0.21), residues: 654 sheet: -0.08 (0.12), residues: 1824 loop : -1.36 (0.11), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 38 TYR 0.028 0.002 TYR I 249 PHE 0.020 0.002 PHE x 176 TRP 0.015 0.001 TRP B 274 HIS 0.005 0.001 HIS I 282 Details of bonding type rmsd covalent geometry : bond 0.00589 (41244) covalent geometry : angle 0.57344 (56055) hydrogen bonds : bond 0.04607 ( 1070) hydrogen bonds : angle 5.55349 ( 2889) metal coordination : bond 0.01076 ( 12) metal coordination : angle 5.98523 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 458 time to evaluate : 1.641 Fit side-chains REVERT: I 54 ASP cc_start: 0.8233 (t0) cc_final: 0.7988 (t0) REVERT: I 685 LEU cc_start: 0.8759 (tp) cc_final: 0.8491 (tt) REVERT: I 748 PHE cc_start: 0.7730 (t80) cc_final: 0.7467 (t80) REVERT: A 202 TYR cc_start: 0.9044 (p90) cc_final: 0.8717 (p90) REVERT: B 97 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: B 259 ILE cc_start: 0.9221 (mm) cc_final: 0.8935 (mm) REVERT: G 180 ASP cc_start: 0.8725 (t70) cc_final: 0.8333 (t0) REVERT: G 199 ASP cc_start: 0.8352 (t0) cc_final: 0.8131 (t0) REVERT: O 22 LYS cc_start: 0.9049 (ptmt) cc_final: 0.8742 (pttt) REVERT: F 22 LYS cc_start: 0.9040 (ptmt) cc_final: 0.8634 (pttt) REVERT: F 96 LEU cc_start: 0.9251 (mt) cc_final: 0.8978 (mt) REVERT: R 41 LYS cc_start: 0.8891 (mttt) cc_final: 0.7330 (tptp) REVERT: R 44 ASP cc_start: 0.7145 (m-30) cc_final: 0.6933 (m-30) REVERT: T 87 MET cc_start: 0.9015 (mtm) cc_final: 0.8809 (mtp) REVERT: V 29 ASN cc_start: 0.9160 (t0) cc_final: 0.8917 (t0) REVERT: V 137 ILE cc_start: 0.8567 (mt) cc_final: 0.8352 (mt) REVERT: W 38 ARG cc_start: 0.9036 (ttp80) cc_final: 0.8829 (ttt-90) REVERT: W 41 LYS cc_start: 0.8878 (mttt) cc_final: 0.7031 (tptp) outliers start: 52 outliers final: 42 residues processed: 483 average time/residue: 0.2830 time to fit residues: 217.6242 Evaluate side-chains 479 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 436 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 773 ILE Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 208 SER Chi-restraints excluded: chain x residue 218 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 185 optimal weight: 9.9990 chunk 452 optimal weight: 9.9990 chunk 440 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 438 optimal weight: 6.9990 chunk 485 optimal weight: 10.0000 chunk 327 optimal weight: 7.9990 chunk 355 optimal weight: 6.9990 chunk 470 optimal weight: 9.9990 chunk 196 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 734 HIS A 604 HIS B 396 HIS H 109 ASN x 153 GLN L 101 ASN T 29 ASN U 29 ASN V 101 ASN W 94 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097508 restraints weight = 52866.444| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.66 r_work: 0.2689 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 41256 Z= 0.294 Angle : 0.649 12.076 56091 Z= 0.330 Chirality : 0.048 0.182 6189 Planarity : 0.005 0.051 7290 Dihedral : 4.946 21.788 5640 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.03 % Allowed : 9.83 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.24 (0.11), residues: 5136 helix: 0.39 (0.21), residues: 651 sheet: -0.33 (0.12), residues: 1806 loop : -1.48 (0.11), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 38 TYR 0.033 0.002 TYR I 249 PHE 0.024 0.002 PHE x 176 TRP 0.016 0.002 TRP B 274 HIS 0.007 0.002 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00726 (41244) covalent geometry : angle 0.62216 (56055) hydrogen bonds : bond 0.04716 ( 1070) hydrogen bonds : angle 5.47770 ( 2889) metal coordination : bond 0.01372 ( 12) metal coordination : angle 7.29489 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 448 time to evaluate : 1.690 Fit side-chains REVERT: I 54 ASP cc_start: 0.8431 (t0) cc_final: 0.8076 (t0) REVERT: I 685 LEU cc_start: 0.8844 (tp) cc_final: 0.8563 (tt) REVERT: A 97 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: A 202 TYR cc_start: 0.9025 (p90) cc_final: 0.8748 (p90) REVERT: A 455 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: A 778 ASN cc_start: 0.8216 (m-40) cc_final: 0.7651 (t0) REVERT: B 97 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: B 259 ILE cc_start: 0.9278 (mm) cc_final: 0.8969 (mm) REVERT: G 180 ASP cc_start: 0.8767 (t70) cc_final: 0.8375 (t0) REVERT: G 199 ASP cc_start: 0.8414 (t0) cc_final: 0.8212 (t0) REVERT: O 22 LYS cc_start: 0.9035 (ptmt) cc_final: 0.8703 (pttt) REVERT: F 22 LYS cc_start: 0.9041 (ptmt) cc_final: 0.8630 (pttt) REVERT: F 95 MET cc_start: 0.9340 (mmm) cc_final: 0.8830 (tpp) REVERT: F 96 LEU cc_start: 0.9249 (mt) cc_final: 0.8880 (mt) REVERT: x 171 LYS cc_start: 0.8099 (tttm) cc_final: 0.7887 (tptp) REVERT: L 38 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.7935 (tpt170) REVERT: R 41 LYS cc_start: 0.8926 (mttt) cc_final: 0.7326 (tptp) REVERT: R 44 ASP cc_start: 0.7170 (m-30) cc_final: 0.6961 (m-30) REVERT: V 29 ASN cc_start: 0.9184 (t0) cc_final: 0.8944 (t0) REVERT: V 137 ILE cc_start: 0.8598 (mt) cc_final: 0.8374 (mt) REVERT: W 38 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8842 (ttt-90) REVERT: W 41 LYS cc_start: 0.8909 (mttt) cc_final: 0.7027 (tptp) REVERT: W 155 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8184 (ptp90) outliers start: 89 outliers final: 70 residues processed: 504 average time/residue: 0.2821 time to fit residues: 227.4671 Evaluate side-chains 511 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 437 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 412 THR Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 773 ILE Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 208 SER Chi-restraints excluded: chain x residue 219 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain V residue 31 LEU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 486 optimal weight: 0.4980 chunk 155 optimal weight: 0.9980 chunk 461 optimal weight: 0.8980 chunk 386 optimal weight: 3.9990 chunk 485 optimal weight: 0.4980 chunk 114 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 385 optimal weight: 0.9980 chunk 487 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 375 ASN A 231 GLN x 153 GLN K 205 GLN L 101 ASN T 29 ASN U 29 ASN V 101 ASN W 94 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.101806 restraints weight = 51814.241| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.64 r_work: 0.2792 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 41256 Z= 0.089 Angle : 0.475 8.858 56091 Z= 0.244 Chirality : 0.042 0.137 6189 Planarity : 0.004 0.049 7290 Dihedral : 4.337 21.034 5640 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.26 % Allowed : 11.66 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.85 (0.11), residues: 5136 helix: 0.84 (0.22), residues: 639 sheet: -0.06 (0.12), residues: 1836 loop : -1.28 (0.11), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 38 TYR 0.011 0.001 TYR A 738 PHE 0.012 0.001 PHE x 176 TRP 0.015 0.001 TRP B 274 HIS 0.005 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00201 (41244) covalent geometry : angle 0.46346 (56055) hydrogen bonds : bond 0.03264 ( 1070) hydrogen bonds : angle 4.91026 ( 2889) metal coordination : bond 0.00320 ( 12) metal coordination : angle 4.05993 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 490 time to evaluate : 1.665 Fit side-chains revert: symmetry clash REVERT: I 54 ASP cc_start: 0.8395 (t0) cc_final: 0.8042 (t0) REVERT: I 685 LEU cc_start: 0.8718 (tp) cc_final: 0.8472 (tt) REVERT: I 748 PHE cc_start: 0.7808 (t80) cc_final: 0.7515 (t80) REVERT: A 116 PHE cc_start: 0.8548 (p90) cc_final: 0.8226 (p90) REVERT: A 202 TYR cc_start: 0.9054 (p90) cc_final: 0.8615 (p90) REVERT: A 455 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: A 726 TYR cc_start: 0.8146 (t80) cc_final: 0.7902 (t80) REVERT: A 778 ASN cc_start: 0.8170 (m-40) cc_final: 0.7742 (t0) REVERT: B 259 ILE cc_start: 0.9339 (mm) cc_final: 0.9011 (mm) REVERT: G 180 ASP cc_start: 0.8638 (t70) cc_final: 0.8220 (t0) REVERT: G 199 ASP cc_start: 0.8350 (t0) cc_final: 0.8124 (t0) REVERT: O 22 LYS cc_start: 0.9035 (ptmt) cc_final: 0.8718 (pttt) REVERT: E 77 TYR cc_start: 0.8982 (t80) cc_final: 0.8703 (t80) REVERT: D 17 VAL cc_start: 0.9266 (OUTLIER) cc_final: 0.9002 (m) REVERT: F 22 LYS cc_start: 0.9056 (ptmt) cc_final: 0.8709 (pttt) REVERT: F 63 GLU cc_start: 0.8440 (tp30) cc_final: 0.8215 (tp30) REVERT: F 64 GLU cc_start: 0.8852 (pt0) cc_final: 0.8601 (pt0) REVERT: L 38 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8106 (ttt180) REVERT: L 44 ASP cc_start: 0.8564 (t0) cc_final: 0.8321 (t0) REVERT: R 41 LYS cc_start: 0.8891 (mttt) cc_final: 0.7305 (tptt) REVERT: R 97 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8037 (mm) REVERT: V 29 ASN cc_start: 0.9165 (t0) cc_final: 0.8916 (t0) REVERT: V 137 ILE cc_start: 0.8529 (mt) cc_final: 0.8299 (mt) REVERT: W 38 ARG cc_start: 0.8940 (ttp80) cc_final: 0.8728 (ttt-90) REVERT: W 41 LYS cc_start: 0.8871 (mttt) cc_final: 0.7028 (tptp) REVERT: W 142 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8441 (tttt) outliers start: 55 outliers final: 31 residues processed: 523 average time/residue: 0.2701 time to fit residues: 223.8834 Evaluate side-chains 491 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 456 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 404 ILE Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 253 optimal weight: 20.0000 chunk 281 optimal weight: 8.9990 chunk 82 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 361 optimal weight: 0.0470 chunk 148 optimal weight: 10.0000 chunk 490 optimal weight: 7.9990 overall best weight: 6.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 734 HIS A 248 ASN A 270 ASN A 282 HIS A 841 ASN H 109 ASN x 153 GLN R 29 ASN T 29 ASN U 29 ASN V 101 ASN W 94 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.096053 restraints weight = 53422.862| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.67 r_work: 0.2663 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.088 41256 Z= 0.397 Angle : 0.730 15.633 56091 Z= 0.370 Chirality : 0.051 0.200 6189 Planarity : 0.005 0.052 7290 Dihedral : 5.031 22.787 5640 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.09 % Rotamer: Outliers : 2.63 % Allowed : 11.82 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.34 (0.11), residues: 5136 helix: 0.34 (0.21), residues: 651 sheet: -0.41 (0.12), residues: 1833 loop : -1.55 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 201 TYR 0.037 0.002 TYR I 249 PHE 0.027 0.003 PHE K 176 TRP 0.016 0.002 TRP J 175 HIS 0.008 0.002 HIS I 282 Details of bonding type rmsd covalent geometry : bond 0.00983 (41244) covalent geometry : angle 0.69853 (56055) hydrogen bonds : bond 0.05007 ( 1070) hydrogen bonds : angle 5.40551 ( 2889) metal coordination : bond 0.01903 ( 12) metal coordination : angle 8.43877 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 431 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: I 54 ASP cc_start: 0.8419 (t0) cc_final: 0.8022 (t0) REVERT: I 463 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.7991 (t0) REVERT: I 685 LEU cc_start: 0.8974 (tp) cc_final: 0.8673 (tt) REVERT: I 806 ARG cc_start: 0.7245 (ttp80) cc_final: 0.6592 (mtp180) REVERT: A 202 TYR cc_start: 0.9025 (p90) cc_final: 0.8719 (p90) REVERT: A 455 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: A 778 ASN cc_start: 0.8044 (m-40) cc_final: 0.7434 (t0) REVERT: B 97 ASP cc_start: 0.8211 (p0) cc_final: 0.7838 (m-30) REVERT: B 169 MET cc_start: 0.8586 (mtm) cc_final: 0.8351 (mtp) REVERT: B 259 ILE cc_start: 0.9310 (mm) cc_final: 0.8989 (mm) REVERT: G 180 ASP cc_start: 0.8859 (t70) cc_final: 0.8487 (t0) REVERT: G 199 ASP cc_start: 0.8444 (t0) cc_final: 0.8240 (t0) REVERT: N 28 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7998 (mm) REVERT: O 22 LYS cc_start: 0.9034 (ptmt) cc_final: 0.8702 (pttt) REVERT: F 22 LYS cc_start: 0.9054 (ptmt) cc_final: 0.8656 (pttt) REVERT: F 96 LEU cc_start: 0.9276 (mt) cc_final: 0.9029 (mt) REVERT: L 44 ASP cc_start: 0.8523 (t0) cc_final: 0.8258 (t0) REVERT: R 41 LYS cc_start: 0.9002 (mttt) cc_final: 0.7367 (tptp) REVERT: V 137 ILE cc_start: 0.8630 (mt) cc_final: 0.8402 (mt) REVERT: W 38 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8836 (ttt-90) REVERT: W 41 LYS cc_start: 0.8869 (mttt) cc_final: 0.6900 (tptp) outliers start: 115 outliers final: 97 residues processed: 512 average time/residue: 0.2669 time to fit residues: 218.7432 Evaluate side-chains 519 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 419 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 153 ILE Chi-restraints excluded: chain I residue 412 THR Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 463 ASP Chi-restraints excluded: chain I residue 625 THR Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain I residue 773 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 208 SER Chi-restraints excluded: chain x residue 219 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain V residue 31 LEU Chi-restraints excluded: chain V residue 42 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 97 LEU Chi-restraints excluded: chain P residue 844 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 91 optimal weight: 0.9980 chunk 314 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 405 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 369 optimal weight: 1.9990 chunk 484 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN x 153 GLN T 29 ASN U 29 ASN V 101 ASN W 94 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101412 restraints weight = 52099.439| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.61 r_work: 0.2742 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 41256 Z= 0.092 Angle : 0.490 9.858 56091 Z= 0.251 Chirality : 0.042 0.136 6189 Planarity : 0.004 0.050 7290 Dihedral : 4.416 21.975 5640 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.53 % Allowed : 13.03 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.96 (0.11), residues: 5136 helix: 0.69 (0.21), residues: 657 sheet: -0.14 (0.12), residues: 1818 loop : -1.33 (0.11), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 38 TYR 0.011 0.001 TYR T 59 PHE 0.012 0.001 PHE J 163 TRP 0.015 0.001 TRP B 274 HIS 0.002 0.001 HIS I 445 Details of bonding type rmsd covalent geometry : bond 0.00210 (41244) covalent geometry : angle 0.47410 (56055) hydrogen bonds : bond 0.03322 ( 1070) hydrogen bonds : angle 4.88117 ( 2889) metal coordination : bond 0.00358 ( 12) metal coordination : angle 4.89636 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 462 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: I 54 ASP cc_start: 0.8386 (t0) cc_final: 0.7987 (t0) REVERT: I 685 LEU cc_start: 0.8746 (tp) cc_final: 0.8496 (tt) REVERT: I 748 PHE cc_start: 0.7895 (t80) cc_final: 0.7582 (t80) REVERT: A 202 TYR cc_start: 0.9043 (p90) cc_final: 0.8606 (p90) REVERT: A 455 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: A 778 ASN cc_start: 0.8163 (m-40) cc_final: 0.7549 (t0) REVERT: B 97 ASP cc_start: 0.8158 (p0) cc_final: 0.7808 (m-30) REVERT: B 259 ILE cc_start: 0.9430 (mm) cc_final: 0.9112 (mm) REVERT: G 180 ASP cc_start: 0.8676 (t70) cc_final: 0.8272 (t0) REVERT: G 202 LYS cc_start: 0.9127 (ptpt) cc_final: 0.8687 (ptmm) REVERT: O 22 LYS cc_start: 0.9004 (ptmt) cc_final: 0.8671 (pttt) REVERT: D 17 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9118 (m) REVERT: F 22 LYS cc_start: 0.9082 (ptmt) cc_final: 0.8725 (pttt) REVERT: F 54 GLU cc_start: 0.8683 (mp0) cc_final: 0.8336 (mt-10) REVERT: F 64 GLU cc_start: 0.8835 (pt0) cc_final: 0.8578 (pt0) REVERT: F 95 MET cc_start: 0.9196 (tpp) cc_final: 0.8954 (tpp) REVERT: F 96 LEU cc_start: 0.9211 (mt) cc_final: 0.8964 (mt) REVERT: Q 182 MET cc_start: 0.9175 (mtm) cc_final: 0.8885 (mpp) REVERT: L 38 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8139 (ttt180) REVERT: L 44 ASP cc_start: 0.8556 (t0) cc_final: 0.8292 (t0) REVERT: R 41 LYS cc_start: 0.8926 (mttt) cc_final: 0.7333 (tptp) REVERT: V 137 ILE cc_start: 0.8599 (mt) cc_final: 0.8382 (mt) REVERT: W 38 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8695 (ttt-90) REVERT: W 41 LYS cc_start: 0.8867 (mttt) cc_final: 0.7027 (tptt) REVERT: W 142 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8445 (tttt) outliers start: 67 outliers final: 49 residues processed: 505 average time/residue: 0.2862 time to fit residues: 229.2927 Evaluate side-chains 505 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 453 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 404 ILE Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain x residue 219 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 329 optimal weight: 7.9990 chunk 415 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 290 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 169 optimal weight: 40.0000 chunk 217 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 492 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 734 HIS A 248 ASN A 270 ASN H 40 ASN H 109 ASN x 153 GLN R 29 ASN T 29 ASN U 29 ASN V 101 ASN W 94 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.097295 restraints weight = 52798.384| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.65 r_work: 0.2691 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 41256 Z= 0.278 Angle : 0.622 11.511 56091 Z= 0.314 Chirality : 0.047 0.177 6189 Planarity : 0.004 0.051 7290 Dihedral : 4.732 22.351 5640 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.03 % Allowed : 13.24 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.19 (0.11), residues: 5136 helix: 0.42 (0.21), residues: 672 sheet: -0.31 (0.12), residues: 1830 loop : -1.47 (0.11), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 38 TYR 0.027 0.002 TYR I 249 PHE 0.021 0.002 PHE x 176 TRP 0.013 0.002 TRP B 274 HIS 0.006 0.001 HIS I 282 Details of bonding type rmsd covalent geometry : bond 0.00689 (41244) covalent geometry : angle 0.59635 (56055) hydrogen bonds : bond 0.04279 ( 1070) hydrogen bonds : angle 5.12611 ( 2889) metal coordination : bond 0.01388 ( 12) metal coordination : angle 7.06944 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 451 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: I 54 ASP cc_start: 0.8445 (t0) cc_final: 0.8054 (t0) REVERT: I 463 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8045 (t0) REVERT: I 685 LEU cc_start: 0.8882 (tp) cc_final: 0.8595 (tt) REVERT: A 455 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: A 778 ASN cc_start: 0.7964 (m-40) cc_final: 0.7381 (t0) REVERT: B 97 ASP cc_start: 0.8190 (p0) cc_final: 0.7811 (m-30) REVERT: B 259 ILE cc_start: 0.9336 (mm) cc_final: 0.8997 (mm) REVERT: G 180 ASP cc_start: 0.8762 (t70) cc_final: 0.8406 (t0) REVERT: N 28 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8041 (mm) REVERT: O 22 LYS cc_start: 0.9018 (ptmt) cc_final: 0.8688 (pttt) REVERT: F 22 LYS cc_start: 0.9045 (ptmt) cc_final: 0.8642 (pttt) REVERT: F 54 GLU cc_start: 0.8720 (mp0) cc_final: 0.8395 (mt-10) REVERT: F 64 GLU cc_start: 0.8920 (pt0) cc_final: 0.8652 (pt0) REVERT: F 95 MET cc_start: 0.9326 (tpp) cc_final: 0.8911 (tpp) REVERT: F 96 LEU cc_start: 0.9263 (mt) cc_final: 0.9015 (mt) REVERT: L 38 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8066 (tpt170) REVERT: L 44 ASP cc_start: 0.8571 (t0) cc_final: 0.8300 (t0) REVERT: R 41 LYS cc_start: 0.9005 (mttt) cc_final: 0.7385 (tptp) REVERT: V 137 ILE cc_start: 0.8606 (mt) cc_final: 0.8369 (mt) REVERT: W 38 ARG cc_start: 0.8963 (ttp80) cc_final: 0.8734 (ttt-90) REVERT: W 41 LYS cc_start: 0.8904 (mttt) cc_final: 0.7062 (tptt) REVERT: W 142 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8523 (tttt) outliers start: 89 outliers final: 78 residues processed: 506 average time/residue: 0.2830 time to fit residues: 228.3803 Evaluate side-chains 520 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 438 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 179 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 404 ILE Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 463 ASP Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain I residue 773 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 219 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain V residue 31 LEU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 123 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 410 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 372 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 397 optimal weight: 0.4980 chunk 265 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 529 ASN N 2 GLN H 40 ASN H 109 ASN x 153 GLN T 29 ASN U 29 ASN W 94 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101747 restraints weight = 52125.152| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.62 r_work: 0.2746 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 41256 Z= 0.096 Angle : 0.494 10.115 56091 Z= 0.252 Chirality : 0.042 0.153 6189 Planarity : 0.004 0.049 7290 Dihedral : 4.346 21.764 5640 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.51 % Allowed : 13.81 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.90 (0.11), residues: 5136 helix: 0.74 (0.21), residues: 657 sheet: -0.09 (0.12), residues: 1818 loop : -1.31 (0.11), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 38 TYR 0.022 0.001 TYR A 202 PHE 0.011 0.001 PHE x 176 TRP 0.016 0.001 TRP B 274 HIS 0.002 0.000 HIS I 282 Details of bonding type rmsd covalent geometry : bond 0.00225 (41244) covalent geometry : angle 0.47899 (56055) hydrogen bonds : bond 0.03248 ( 1070) hydrogen bonds : angle 4.79953 ( 2889) metal coordination : bond 0.00370 ( 12) metal coordination : angle 4.81597 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 474 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: I 54 ASP cc_start: 0.8393 (t0) cc_final: 0.8015 (t0) REVERT: I 685 LEU cc_start: 0.8745 (tp) cc_final: 0.8489 (tt) REVERT: I 748 PHE cc_start: 0.7971 (t80) cc_final: 0.7641 (t80) REVERT: A 455 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: A 778 ASN cc_start: 0.8155 (m-40) cc_final: 0.7548 (t0) REVERT: B 97 ASP cc_start: 0.8081 (p0) cc_final: 0.7849 (m-30) REVERT: B 259 ILE cc_start: 0.9440 (mm) cc_final: 0.9129 (mm) REVERT: G 180 ASP cc_start: 0.8687 (t70) cc_final: 0.8212 (t0) REVERT: G 202 LYS cc_start: 0.9197 (ptpt) cc_final: 0.8732 (ptmm) REVERT: N 28 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7795 (mm) REVERT: O 22 LYS cc_start: 0.9001 (ptmt) cc_final: 0.8724 (pttt) REVERT: D 17 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9127 (m) REVERT: F 22 LYS cc_start: 0.9049 (ptmt) cc_final: 0.8705 (pttt) REVERT: F 54 GLU cc_start: 0.8696 (mp0) cc_final: 0.8350 (mt-10) REVERT: F 64 GLU cc_start: 0.8868 (pt0) cc_final: 0.8578 (pt0) REVERT: F 96 LEU cc_start: 0.9232 (mt) cc_final: 0.8974 (mt) REVERT: Q 182 MET cc_start: 0.9179 (mtm) cc_final: 0.8925 (mpp) REVERT: L 38 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8136 (ttt180) REVERT: L 44 ASP cc_start: 0.8484 (t0) cc_final: 0.8233 (t0) REVERT: R 41 LYS cc_start: 0.8898 (mttt) cc_final: 0.7238 (tptp) REVERT: T 44 ASP cc_start: 0.8435 (t0) cc_final: 0.8209 (t0) REVERT: V 41 LYS cc_start: 0.8476 (mttt) cc_final: 0.6805 (tptp) REVERT: V 137 ILE cc_start: 0.8621 (mt) cc_final: 0.8407 (mt) REVERT: W 38 ARG cc_start: 0.8921 (ttp80) cc_final: 0.8696 (ttt-90) REVERT: W 41 LYS cc_start: 0.8857 (mttt) cc_final: 0.6997 (tptt) REVERT: W 142 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8185 (tttp) outliers start: 66 outliers final: 55 residues processed: 510 average time/residue: 0.2870 time to fit residues: 232.3593 Evaluate side-chains 518 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 459 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 404 ILE Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 219 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 31 optimal weight: 3.9990 chunk 491 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 398 optimal weight: 4.9990 chunk 412 optimal weight: 0.2980 chunk 148 optimal weight: 9.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 248 ASN A 270 ASN H 109 ASN x 153 GLN R 29 ASN T 29 ASN U 29 ASN W 94 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.098769 restraints weight = 52316.503| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.64 r_work: 0.2723 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 41256 Z= 0.206 Angle : 0.564 11.167 56091 Z= 0.285 Chirality : 0.045 0.232 6189 Planarity : 0.004 0.050 7290 Dihedral : 4.519 21.759 5640 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 1.69 % Allowed : 13.81 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.11), residues: 5136 helix: 0.62 (0.21), residues: 672 sheet: -0.20 (0.12), residues: 1821 loop : -1.35 (0.11), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 38 TYR 0.021 0.001 TYR A 202 PHE 0.023 0.002 PHE K 176 TRP 0.013 0.001 TRP B 274 HIS 0.004 0.001 HIS I 282 Details of bonding type rmsd covalent geometry : bond 0.00509 (41244) covalent geometry : angle 0.54239 (56055) hydrogen bonds : bond 0.03832 ( 1070) hydrogen bonds : angle 4.93418 ( 2889) metal coordination : bond 0.01027 ( 12) metal coordination : angle 6.12449 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 461 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: I 54 ASP cc_start: 0.8428 (t0) cc_final: 0.8051 (t0) REVERT: I 685 LEU cc_start: 0.8774 (tp) cc_final: 0.8482 (tt) REVERT: I 812 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7315 (mm-30) REVERT: A 455 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: A 778 ASN cc_start: 0.7931 (m-40) cc_final: 0.7364 (t0) REVERT: B 259 ILE cc_start: 0.9329 (mm) cc_final: 0.8994 (mm) REVERT: G 180 ASP cc_start: 0.8707 (t70) cc_final: 0.8348 (t0) REVERT: N 28 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7990 (mm) REVERT: N 113 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8415 (mp) REVERT: O 22 LYS cc_start: 0.9023 (ptmt) cc_final: 0.8695 (pttt) REVERT: F 22 LYS cc_start: 0.9031 (ptmt) cc_final: 0.8638 (pttt) REVERT: F 54 GLU cc_start: 0.8723 (mp0) cc_final: 0.8380 (mt-10) REVERT: F 96 LEU cc_start: 0.9267 (mt) cc_final: 0.8941 (mt) REVERT: L 38 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8112 (ttt180) REVERT: L 44 ASP cc_start: 0.8593 (t0) cc_final: 0.8343 (t0) REVERT: R 41 LYS cc_start: 0.8948 (mttt) cc_final: 0.7257 (tptp) REVERT: V 41 LYS cc_start: 0.8504 (mttt) cc_final: 0.6854 (tptp) REVERT: V 137 ILE cc_start: 0.8605 (mt) cc_final: 0.8368 (mt) REVERT: W 38 ARG cc_start: 0.8942 (ttp80) cc_final: 0.8712 (ttt-90) REVERT: W 41 LYS cc_start: 0.8877 (mttt) cc_final: 0.7014 (tptt) REVERT: W 142 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8505 (tttt) outliers start: 74 outliers final: 68 residues processed: 506 average time/residue: 0.2892 time to fit residues: 231.9536 Evaluate side-chains 522 residues out of total 4374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 450 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 404 ILE Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 87 MET Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 227 ILE Chi-restraints excluded: chain J residue 231 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 87 MET Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 227 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain C residue 12 MET Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain x residue 161 THR Chi-restraints excluded: chain x residue 219 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 218 VAL Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 209 THR Chi-restraints excluded: chain Q residue 218 VAL Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain T residue 31 LEU Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 349 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 474 optimal weight: 9.9990 chunk 506 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 734 HIS A 248 ASN H 109 ASN x 153 GLN T 29 ASN U 29 ASN W 94 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.097198 restraints weight = 53065.671| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.67 r_work: 0.2685 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 41256 Z= 0.281 Angle : 0.638 13.038 56091 Z= 0.322 Chirality : 0.047 0.181 6189 Planarity : 0.005 0.051 7290 Dihedral : 4.810 22.554 5640 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.21 % Favored : 95.74 % Rotamer: Outliers : 2.03 % Allowed : 13.67 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.21 (0.11), residues: 5136 helix: 0.46 (0.21), residues: 666 sheet: -0.36 (0.12), residues: 1830 loop : -1.46 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 38 TYR 0.028 0.002 TYR I 249 PHE 0.021 0.002 PHE x 176 TRP 0.014 0.002 TRP B 274 HIS 0.006 0.001 HIS I 282 Details of bonding type rmsd covalent geometry : bond 0.00695 (41244) covalent geometry : angle 0.60823 (56055) hydrogen bonds : bond 0.04341 ( 1070) hydrogen bonds : angle 5.15857 ( 2889) metal coordination : bond 0.01367 ( 12) metal coordination : angle 7.61585 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10828.76 seconds wall clock time: 186 minutes 18.28 seconds (11178.28 seconds total)