Starting phenix.real_space_refine on Wed Aug 27 02:01:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hp9_34928/08_2025/8hp9_34928.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hp9_34928/08_2025/8hp9_34928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hp9_34928/08_2025/8hp9_34928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hp9_34928/08_2025/8hp9_34928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hp9_34928/08_2025/8hp9_34928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hp9_34928/08_2025/8hp9_34928.map" } resolution = 2.75 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= -0.001 sd= 0.115 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: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 28843 2.51 5 N 7570 2.21 5 O 8911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 45516 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8318 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 56, 'TRANS': 1004} Chain breaks: 6 Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "H" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "M" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "N" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "B" Number of atoms: 8311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8311 Classifications: {'peptide': 1059} Link IDs: {'CIS': 1, 'PTRANS': 56, 'TRANS': 1001} Chain breaks: 6 Chain: "P" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "Q" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1642 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "C" Number of atoms: 8304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1059, 8304 Classifications: {'peptide': 1059} Link IDs: {'PTRANS': 56, 'TRANS': 1002} Chain breaks: 7 Chain: "I" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1756 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 214} Chain: "J" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "K" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1656 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 210} Chain: "O" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1641 Classifications: {'peptide': 216} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 8.70, per 1000 atoms: 0.19 Number of scatterers: 45516 At special positions: 0 Unit cell: (218.4, 232.68, 247.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 8911 8.00 N 7570 7.00 C 28843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 182 " distance=2.04 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 317 " distance=2.02 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 448 " distance=2.05 Simple disulfide: pdb=" SG CYS A 407 " - pdb=" SG CYS A 541 " distance=2.04 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 554 " - pdb=" SG CYS A 606 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 665 " distance=2.03 Simple disulfide: pdb=" SG CYS A 678 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 754 " - pdb=" SG CYS A 776 " distance=2.03 Simple disulfide: pdb=" SG CYS A 759 " - pdb=" SG CYS A 765 " distance=2.04 Simple disulfide: pdb=" SG CYS A1048 " - pdb=" SG CYS A1059 " distance=1.99 Simple disulfide: pdb=" SG CYS A1098 " - pdb=" SG CYS A1142 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 215 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 149 " - pdb=" SG CYS M 205 " distance=2.03 Simple disulfide: pdb=" SG CYS M 225 " - pdb=" SG CYS N 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 136 " - pdb=" SG CYS N 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 182 " distance=2.05 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 377 " distance=2.02 Simple disulfide: pdb=" SG CYS B 395 " - pdb=" SG CYS B 448 " distance=2.05 Simple disulfide: pdb=" SG CYS B 407 " - pdb=" SG CYS B 541 " distance=2.02 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 504 " distance=2.03 Simple disulfide: pdb=" SG CYS B 554 " - pdb=" SG CYS B 606 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 665 " distance=2.02 Simple disulfide: pdb=" SG CYS B 678 " - pdb=" SG CYS B 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 754 " - pdb=" SG CYS B 776 " distance=2.03 Simple disulfide: pdb=" SG CYS B 759 " - pdb=" SG CYS B 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B1048 " - pdb=" SG CYS B1059 " distance=2.04 Simple disulfide: pdb=" SG CYS B1098 " - pdb=" SG CYS B1142 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 155 " - pdb=" SG CYS P 211 " distance=2.03 Simple disulfide: pdb=" SG CYS P 231 " - pdb=" SG CYS Q 215 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 135 " - pdb=" SG CYS Q 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 149 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 152 " distance=2.04 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 182 " distance=2.05 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 317 " distance=2.02 Simple disulfide: pdb=" SG CYS C 352 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS C 395 " - pdb=" SG CYS C 448 " distance=2.04 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 541 " distance=2.03 Simple disulfide: pdb=" SG CYS C 496 " - pdb=" SG CYS C 504 " distance=2.03 Simple disulfide: pdb=" SG CYS C 554 " - pdb=" SG CYS C 606 " distance=2.04 Simple disulfide: pdb=" SG CYS C 633 " - pdb=" SG CYS C 665 " distance=2.03 Simple disulfide: pdb=" SG CYS C 678 " - pdb=" SG CYS C 687 " distance=2.04 Simple disulfide: pdb=" SG CYS C 754 " - pdb=" SG CYS C 776 " distance=2.03 Simple disulfide: pdb=" SG CYS C 759 " - pdb=" SG CYS C 765 " distance=2.04 Simple disulfide: pdb=" SG CYS C1048 " - pdb=" SG CYS C1059 " distance=2.02 Simple disulfide: pdb=" SG CYS C1098 " - pdb=" SG CYS C1142 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.04 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.03 Simple disulfide: pdb=" SG CYS I 231 " - pdb=" SG CYS J 215 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.04 Simple disulfide: pdb=" SG CYS K 149 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 225 " - pdb=" SG CYS O 216 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 136 " - pdb=" SG CYS O 196 " distance=2.03 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 Links applied NAG-ASN " NAG A1201 " - " ASN A 359 " " NAG A1202 " - " ASN A 77 " " NAG A1203 " - " ASN A 347 " " NAG A1204 " - " ASN A 632 " " NAG A1205 " - " ASN A 725 " " NAG A1206 " - " ASN A 733 " " NAG A1207 " - " ASN A 817 " " NAG A1208 " - " ASN A1090 " " NAG A1209 " - " ASN A1114 " " NAG A1210 " - " ASN A1150 " " NAG B2201 " - " ASN B 725 " " NAG B2202 " - " ASN B 359 " " NAG B2203 " - " ASN B 138 " " NAG B2204 " - " ASN B 298 " " NAG B2205 " - " ASN B 347 " " NAG B2206 " - " ASN B 632 " " NAG B2207 " - " ASN B 733 " " NAG B2208 " - " ASN B 817 " " NAG B2209 " - " ASN B1090 " " NAG B2210 " - " ASN B1114 " " NAG B2211 " - " ASN B1150 " " NAG C1201 " - " ASN C 359 " " NAG C1202 " - " ASN C 138 " " NAG C1203 " - " ASN C 77 " " NAG C1204 " - " ASN C 347 " " NAG C1205 " - " ASN C 632 " " NAG C1206 " - " ASN C 725 " " NAG C1207 " - " ASN C 733 " " NAG C1208 " - " ASN C 817 " " NAG C1209 " - " ASN C1090 " " NAG C1210 " - " ASN C1114 " " NAG C1211 " - " ASN C1150 " Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10864 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 104 sheets defined 17.0% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.780A pdb=" N TYR A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.551A pdb=" N TRP A 369 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.905A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 421 through 426 removed outlier: 4.371A pdb=" N SER A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.755A pdb=" N SER A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 759 Processing helix chain 'A' and resid 762 through 773 Processing helix chain 'A' and resid 774 through 799 removed outlier: 3.853A pdb=" N GLN A 778 " --> pdb=" O SER A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 842 Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 882 through 901 Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.941A pdb=" N ALA A 906 " --> pdb=" O TRP A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 924 Processing helix chain 'A' and resid 928 through 935 removed outlier: 4.028A pdb=" N LEU A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 957 Processing helix chain 'A' and resid 958 through 960 No H-bonds generated for 'chain 'A' and resid 958 through 960' Processing helix chain 'A' and resid 961 through 981 Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 992 through 1000 removed outlier: 3.506A pdb=" N LEU A1000 " --> pdb=" O ILE A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1049 removed outlier: 4.995A pdb=" N VAL A1007 " --> pdb=" O PRO A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1163 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 122 through 128 Processing helix chain 'L' and resid 184 through 188 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 146 through 150 removed outlier: 3.687A pdb=" N THR H 150 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.822A pdb=" N ASN M 32 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.554A pdb=" N LYS M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing helix chain 'M' and resid 86 through 90 removed outlier: 4.151A pdb=" N THR M 90 " --> pdb=" O ALA M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 199 removed outlier: 3.993A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.212A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 185 through 189 Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.820A pdb=" N TYR B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.893A pdb=" N TRP B 369 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 454 through 459 removed outlier: 3.640A pdb=" N SER B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 759 Processing helix chain 'B' and resid 762 through 770 Processing helix chain 'B' and resid 771 through 773 No H-bonds generated for 'chain 'B' and resid 771 through 773' Processing helix chain 'B' and resid 774 through 799 removed outlier: 3.877A pdb=" N LYS B 780 " --> pdb=" O CYS B 776 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 842 Processing helix chain 'B' and resid 882 through 901 Processing helix chain 'B' and resid 902 through 906 Processing helix chain 'B' and resid 913 through 925 Processing helix chain 'B' and resid 928 through 934 removed outlier: 3.942A pdb=" N LEU B 932 " --> pdb=" O THR B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 956 Processing helix chain 'B' and resid 961 through 981 removed outlier: 3.581A pdb=" N ASN B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1000 Processing helix chain 'B' and resid 1001 through 1049 removed outlier: 3.712A pdb=" N VAL B1007 " --> pdb=" O PRO B1003 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B1008 " --> pdb=" O GLU B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1156 through 1162 removed outlier: 4.037A pdb=" N GLU B1160 " --> pdb=" O PRO B1156 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 66 Processing helix chain 'P' and resid 88 through 92 removed outlier: 3.756A pdb=" N THR P 92 " --> pdb=" O PRO P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 173 No H-bonds generated for 'chain 'P' and resid 171 through 173' Processing helix chain 'P' and resid 200 through 204 removed outlier: 3.606A pdb=" N LEU P 204 " --> pdb=" O SER P 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 32 No H-bonds generated for 'chain 'Q' and resid 30 through 32' Processing helix chain 'Q' and resid 80 through 84 Processing helix chain 'Q' and resid 122 through 129 Processing helix chain 'Q' and resid 184 through 188 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'F' and resid 123 through 129 Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.969A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 removed outlier: 4.176A pdb=" N SER C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 420 through 424' Processing helix chain 'C' and resid 432 through 438 Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 632 through 636 removed outlier: 3.545A pdb=" N GLU C 635 " --> pdb=" O ASN C 632 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 636 " --> pdb=" O CYS C 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 632 through 636' Processing helix chain 'C' and resid 753 through 759 Processing helix chain 'C' and resid 762 through 770 Processing helix chain 'C' and resid 771 through 773 No H-bonds generated for 'chain 'C' and resid 771 through 773' Processing helix chain 'C' and resid 774 through 799 removed outlier: 3.626A pdb=" N GLN C 778 " --> pdb=" O SER C 774 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 791 " --> pdb=" O ALA C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 842 Processing helix chain 'C' and resid 882 through 901 Processing helix chain 'C' and resid 902 through 906 removed outlier: 3.600A pdb=" N GLY C 905 " --> pdb=" O TRP C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 925 Processing helix chain 'C' and resid 928 through 935 removed outlier: 3.969A pdb=" N LEU C 932 " --> pdb=" O THR C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 956 Processing helix chain 'C' and resid 961 through 981 Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.611A pdb=" N LEU C1000 " --> pdb=" O ILE C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1048 Processing helix chain 'C' and resid 1156 through 1163 removed outlier: 3.600A pdb=" N GLU C1160 " --> pdb=" O PRO C1156 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 200 through 204 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'J' and resid 122 through 127 Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.520A pdb=" N ASN K 32 " --> pdb=" O VAL K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 90 Processing helix chain 'K' and resid 140 through 144 Processing helix chain 'K' and resid 165 through 167 No H-bonds generated for 'chain 'K' and resid 165 through 167' Processing helix chain 'K' and resid 196 through 201 removed outlier: 3.944A pdb=" N THR K 200 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN K 201 " --> pdb=" O SER K 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 196 through 201' Processing helix chain 'O' and resid 123 through 128 Processing helix chain 'O' and resid 185 through 191 removed outlier: 4.207A pdb=" N HIS O 191 " --> pdb=" O ASP O 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 7.870A pdb=" N ASN A 77 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 285 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER A 221 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N HIS A 223 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N LEU A 239 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 52 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 71 removed outlier: 7.512A pdb=" N THR A 290 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASP A 306 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 292 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 304 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS A 294 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 335 removed outlier: 4.043A pdb=" N VAL A 611 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN A 333 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY A 609 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY A 610 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 344 removed outlier: 5.516A pdb=" N ASP A 590 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 591 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE A 581 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 374 removed outlier: 4.060A pdb=" N GLY A 447 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 670 through 671 removed outlier: 6.021A pdb=" N GLU A 670 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR A 712 " --> pdb=" O GLU A 670 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA A 688 " --> pdb=" O PRO A 681 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 720 Processing sheet with id=AB2, first strand: chain 'A' and resid 727 through 731 removed outlier: 3.512A pdb=" N THR A1092 " --> pdb=" O SER A1113 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE A1111 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 744 removed outlier: 5.985A pdb=" N TYR A1083 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS A1064 " --> pdb=" O TYR A1083 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 749 through 752 removed outlier: 4.391A pdb=" N LYS A 749 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 804 through 806 removed outlier: 5.816A pdb=" N ILE A 804 " --> pdb=" O ASN B 719 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1136 through 1141 removed outlier: 4.463A pdb=" N ALA A1103 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.704A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.922A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER L 175 " --> pdb=" O THR L 165 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 146 through 151 Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.536A pdb=" N VAL H 12 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.536A pdb=" N VAL H 12 " --> pdb=" O THR H 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 135 through 139 Processing sheet with id=AC7, first strand: chain 'H' and resid 135 through 139 Processing sheet with id=AC8, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.707A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.441A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.033A pdb=" N ILE M 111 " --> pdb=" O ARG M 97 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 130 through 133 removed outlier: 5.902A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 130 through 133 removed outlier: 5.902A pdb=" N TYR M 185 " --> pdb=" O ASP M 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 159 through 163 Processing sheet with id=AD6, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.594A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.582A pdb=" N LEU N 11 " --> pdb=" O LYS N 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU N 107 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 116 through 120 removed outlier: 4.275A pdb=" N SER N 176 " --> pdb=" O THR N 166 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 156 through 157 removed outlier: 4.597A pdb=" N TRP N 150 " --> pdb=" O GLN N 157 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 44 through 46 removed outlier: 7.446A pdb=" N ASN B 77 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR B 285 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER B 221 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 58 through 59 removed outlier: 6.346A pdb=" N GLY C 582 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP C 590 " --> pdb=" O ILE C 603 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 63 through 71 removed outlier: 7.606A pdb=" N THR B 290 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASP B 306 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 292 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA B 304 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS B 294 " --> pdb=" O THR B 302 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 100 through 101 removed outlier: 3.503A pdb=" N LEU B 100 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY B 119 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG B 118 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 137 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.899A pdb=" N GLU B 148 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN B 180 " --> pdb=" O GLU B 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'B' and resid 327 through 335 removed outlier: 6.598A pdb=" N VAL B 611 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN B 333 " --> pdb=" O GLY B 609 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY B 609 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY B 610 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 341 through 344 Processing sheet with id=AE8, first strand: chain 'B' and resid 370 through 374 removed outlier: 3.871A pdb=" N GLY B 447 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AF1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AF2, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AF3, first strand: chain 'B' and resid 670 through 671 removed outlier: 6.518A pdb=" N ALA B 688 " --> pdb=" O PRO B 681 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 727 through 731 removed outlier: 3.719A pdb=" N ALA B1094 " --> pdb=" O PHE B1111 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE B1111 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 734 through 744 removed outlier: 6.964A pdb=" N GLY B1075 " --> pdb=" O SER B1071 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER B1071 " --> pdb=" O GLY B1075 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B1077 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B1079 " --> pdb=" O SER B1067 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B1067 " --> pdb=" O LEU B1079 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B1081 " --> pdb=" O LEU B1065 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 749 through 752 removed outlier: 4.470A pdb=" N LYS B 749 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 803 through 806 removed outlier: 5.711A pdb=" N ILE B 804 " --> pdb=" O ASN C 719 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'B' and resid 1136 through 1141 removed outlier: 4.436A pdb=" N ALA B1103 " --> pdb=" O SER B1139 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'P' and resid 11 through 12 removed outlier: 6.696A pdb=" N VAL P 36 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU P 52 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP P 38 " --> pdb=" O LEU P 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.674A pdb=" N HIS P 99 " --> pdb=" O ASP P 116 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE P 101 " --> pdb=" O TRP P 114 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP P 114 " --> pdb=" O PHE P 101 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 135 through 139 removed outlier: 6.370A pdb=" N TYR P 191 " --> pdb=" O ASP P 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 135 through 139 removed outlier: 6.370A pdb=" N TYR P 191 " --> pdb=" O ASP P 159 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 166 through 169 removed outlier: 3.914A pdb=" N TYR P 209 " --> pdb=" O VAL P 226 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 7.154A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'Q' and resid 54 through 55 removed outlier: 6.855A pdb=" N TRP Q 36 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 115 through 119 removed outlier: 5.820A pdb=" N TYR Q 174 " --> pdb=" O ASN Q 139 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 146 through 151 Processing sheet with id=AH2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AH3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.279A pdb=" N GLY E 10 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR E 33 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 129 through 133 removed outlier: 5.996A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 160 through 163 removed outlier: 4.949A pdb=" N TYR E 203 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 220 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.732A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 10 through 12 removed outlier: 5.794A pdb=" N LEU F 11 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 116 through 120 removed outlier: 5.992A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER F 176 " --> pdb=" O THR F 166 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 155 through 157 removed outlier: 4.168A pdb=" N TRP F 150 " --> pdb=" O GLN F 157 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 43 through 46 removed outlier: 7.658A pdb=" N ASN C 77 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR C 285 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER C 221 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 63 through 71 removed outlier: 7.716A pdb=" N THR C 290 " --> pdb=" O ASP C 306 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP C 306 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU C 292 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA C 304 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS C 294 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.546A pdb=" N LEU C 100 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY C 119 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ARG C 118 " --> pdb=" O ASN C 137 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.797A pdb=" N GLU C 148 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN C 180 " --> pdb=" O GLU C 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'C' and resid 327 through 334 removed outlier: 6.761A pdb=" N VAL C 611 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN C 333 " --> pdb=" O GLY C 609 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY C 609 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY C 610 " --> pdb=" O GLN C 629 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 370 through 374 Processing sheet with id=AI7, first strand: chain 'C' and resid 377 through 378 removed outlier: 6.713A pdb=" N CYS C 377 " --> pdb=" O CYS C 541 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 468 through 470 Processing sheet with id=AI9, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AJ1, first strand: chain 'C' and resid 670 through 671 Processing sheet with id=AJ2, first strand: chain 'C' and resid 727 through 731 removed outlier: 3.745A pdb=" N ALA C1094 " --> pdb=" O PHE C1111 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C1111 " --> pdb=" O ALA C1094 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN C1122 " --> pdb=" O GLU C1127 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU C1127 " --> pdb=" O GLN C1122 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'C' and resid 734 through 744 removed outlier: 5.888A pdb=" N TYR C1083 " --> pdb=" O HIS C1064 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS C1064 " --> pdb=" O TYR C1083 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'C' and resid 749 through 752 removed outlier: 4.485A pdb=" N LYS C 749 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'C' and resid 1136 through 1141 removed outlier: 4.351A pdb=" N ALA C1103 " --> pdb=" O SER C1139 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AJ7, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.347A pdb=" N VAL I 36 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU I 52 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP I 38 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.966A pdb=" N PHE I 101 " --> pdb=" O TRP I 114 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP I 114 " --> pdb=" O PHE I 101 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'I' and resid 135 through 139 removed outlier: 6.489A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.970A pdb=" N TYR I 209 " --> pdb=" O VAL I 226 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AK3, first strand: chain 'J' and resid 10 through 12 removed outlier: 7.152A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLN J 38 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU J 47 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'J' and resid 115 through 119 removed outlier: 5.698A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'J' and resid 146 through 151 Processing sheet with id=AK6, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AK7, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.553A pdb=" N TYR K 33 " --> pdb=" O GLU K 98 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.042A pdb=" N TYR K 185 " --> pdb=" O ASP K 153 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.042A pdb=" N TYR K 185 " --> pdb=" O ASP K 153 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'K' and resid 159 through 163 Processing sheet with id=AL2, first strand: chain 'O' and resid 5 through 7 Processing sheet with id=AL3, first strand: chain 'O' and resid 10 through 12 removed outlier: 7.074A pdb=" N LEU O 33 " --> pdb=" O SER O 49 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'O' and resid 116 through 120 removed outlier: 5.833A pdb=" N TYR O 175 " --> pdb=" O ASN O 140 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER O 176 " --> pdb=" O THR O 166 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'O' and resid 156 through 157 removed outlier: 4.378A pdb=" N TRP O 150 " --> pdb=" O GLN O 157 " (cutoff:3.500A) 1919 hydrogen bonds defined for protein. 5031 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: 11.77 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.20: 3 1.20 - 1.37: 15477 1.37 - 1.54: 30030 1.54 - 1.71: 834 1.71 - 1.87: 240 Bond restraints: 46584 Sorted by residual: bond pdb=" CG PRO C 637 " pdb=" CD PRO C 637 " ideal model delta sigma weight residual 1.503 1.028 0.475 3.40e-02 8.65e+02 1.95e+02 bond pdb=" CG PRO E 128 " pdb=" CD PRO E 128 " ideal model delta sigma weight residual 1.503 1.130 0.373 3.40e-02 8.65e+02 1.20e+02 bond pdb=" N PRO C 637 " pdb=" CD PRO C 637 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.46e+01 bond pdb=" N PRO E 128 " pdb=" CD PRO E 128 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.20e+01 bond pdb=" C GLU A1047 " pdb=" N CYS A1048 " ideal model delta sigma weight residual 1.332 1.289 0.044 1.40e-02 5.10e+03 9.74e+00 ... (remaining 46579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.36: 63300 5.36 - 10.73: 81 10.73 - 16.09: 7 16.09 - 21.46: 2 21.46 - 26.82: 2 Bond angle restraints: 63392 Sorted by residual: angle pdb=" N PRO C 637 " pdb=" CD PRO C 637 " pdb=" CG PRO C 637 " ideal model delta sigma weight residual 103.20 76.38 26.82 1.50e+00 4.44e-01 3.20e+02 angle pdb=" N PRO E 128 " pdb=" CD PRO E 128 " pdb=" CG PRO E 128 " ideal model delta sigma weight residual 103.20 82.66 20.54 1.50e+00 4.44e-01 1.87e+02 angle pdb=" CA PRO C 637 " pdb=" CB PRO C 637 " pdb=" CG PRO C 637 " ideal model delta sigma weight residual 104.50 84.52 19.98 1.90e+00 2.77e-01 1.11e+02 angle pdb=" CA PRO C 637 " pdb=" N PRO C 637 " pdb=" CD PRO C 637 " ideal model delta sigma weight residual 112.00 101.30 10.70 1.40e+00 5.10e-01 5.84e+01 angle pdb=" CB PRO C 637 " pdb=" CG PRO C 637 " pdb=" CD PRO C 637 " ideal model delta sigma weight residual 106.10 130.27 -24.17 3.20e+00 9.77e-02 5.70e+01 ... (remaining 63387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 25752 17.95 - 35.90: 2056 35.90 - 53.85: 344 53.85 - 71.80: 69 71.80 - 89.75: 48 Dihedral angle restraints: 28269 sinusoidal: 11348 harmonic: 16921 Sorted by residual: dihedral pdb=" CB CYS M 149 " pdb=" SG CYS M 149 " pdb=" SG CYS M 205 " pdb=" CB CYS M 205 " ideal model delta sinusoidal sigma weight residual 93.00 -178.33 -88.67 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS K 149 " pdb=" SG CYS K 149 " pdb=" SG CYS K 205 " pdb=" CB CYS K 205 " ideal model delta sinusoidal sigma weight residual 93.00 -178.64 -88.36 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS C 395 " pdb=" SG CYS C 395 " pdb=" SG CYS C 448 " pdb=" CB CYS C 448 " ideal model delta sinusoidal sigma weight residual -86.00 1.76 -87.76 1 1.00e+01 1.00e-02 9.22e+01 ... (remaining 28266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 7068 0.121 - 0.242: 180 0.242 - 0.363: 5 0.363 - 0.484: 0 0.484 - 0.605: 3 Chirality restraints: 7256 Sorted by residual: chirality pdb=" CG LEU C 932 " pdb=" CB LEU C 932 " pdb=" CD1 LEU C 932 " pdb=" CD2 LEU C 932 " both_signs ideal model delta sigma weight residual False -2.59 -1.98 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" CG LEU A 932 " pdb=" CB LEU A 932 " pdb=" CD1 LEU A 932 " pdb=" CD2 LEU A 932 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" CG LEU B 932 " pdb=" CB LEU B 932 " pdb=" CD1 LEU B 932 " pdb=" CD2 LEU B 932 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.30e+00 ... (remaining 7253 not shown) Planarity restraints: 8162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 522 " 0.075 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO C 523 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO C 523 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 523 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 127 " 0.074 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO E 128 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 725 " -0.006 2.00e-02 2.50e+03 3.41e-02 1.45e+01 pdb=" CG ASN C 725 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 725 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 725 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG C1206 " -0.031 2.00e-02 2.50e+03 ... (remaining 8159 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 688 2.65 - 3.21: 41314 3.21 - 3.78: 70292 3.78 - 4.34: 99331 4.34 - 4.90: 162433 Nonbonded interactions: 374058 Sorted by model distance: nonbonded pdb=" OE1 GLN A 330 " pdb=" NZ LYS C 780 " model vdw 2.089 3.120 nonbonded pdb=" O LEU A 471 " pdb=" OH TYR M 33 " model vdw 2.089 3.040 nonbonded pdb=" O ASN B 455 " pdb=" OH TYR P 110 " model vdw 2.093 3.040 nonbonded pdb=" O PHE C 156 " pdb=" NH1 ARG C 174 " model vdw 2.108 3.120 nonbonded pdb=" OG SER B 612 " pdb=" OE1 GLN B 629 " model vdw 2.114 3.040 ... (remaining 374053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 85 or resid 97 through 263 or resid 273 through \ 637 or resid 656 through 692 or resid 705 through 847 or resid 870 through 1162 \ or resid 1201 through 1210)) selection = (chain 'B' and (resid 33 through 85 or resid 97 through 263 or resid 273 through \ 847 or resid 870 through 1162 or resid 2202 through 2211)) selection = (chain 'C' and (resid 33 through 263 or resid 273 through 637 or resid 656 throu \ gh 692 or resid 705 through 847 or resid 870 through 1162 or resid 1201 through \ 1210)) } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'M' } ncs_group { reference = (chain 'F' and (resid 1 through 215 or (resid 216 and (name N or name CA or name \ C or name O or name CB or name SG )))) selection = (chain 'N' and (resid 1 through 215 or (resid 216 and (name N or name CA or name \ C or name O or name CB or name SG )))) selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'Q' } 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: 9.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.190 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.475 46688 Z= 0.340 Angle : 0.822 26.821 63632 Z= 0.431 Chirality : 0.053 0.605 7256 Planarity : 0.006 0.108 8130 Dihedral : 13.468 89.754 17189 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.31 % Twisted General : 0.05 % 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: -0.47 (0.11), residues: 5769 helix: 1.23 (0.20), residues: 701 sheet: 0.51 (0.11), residues: 2020 loop : -1.29 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 60 TYR 0.060 0.002 TYR B 889 PHE 0.043 0.003 PHE A 334 TRP 0.061 0.002 TRP C 902 HIS 0.008 0.001 HIS B1080 Details of bonding type rmsd covalent geometry : bond 0.00850 (46584) covalent geometry : angle 0.79712 (63392) SS BOND : bond 0.00846 ( 72) SS BOND : angle 2.41321 ( 144) hydrogen bonds : bond 0.11817 ( 1841) hydrogen bonds : angle 6.82937 ( 5031) link_NAG-ASN : bond 0.00532 ( 32) link_NAG-ASN : angle 4.42150 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 17 GLU cc_start: 0.0697 (pm20) cc_final: 0.0139 (tm-30) REVERT: I 115 PHE cc_start: 0.4691 (m-10) cc_final: 0.3459 (m-10) REVERT: J 40 LYS cc_start: 0.3278 (mmmt) cc_final: 0.3043 (mmtp) REVERT: J 127 LYS cc_start: 0.2946 (pttp) cc_final: 0.2540 (mptt) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.5965 time to fit residues: 210.6591 Evaluate side-chains 207 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 0.7980 chunk 523 optimal weight: 7.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 0.5980 chunk 366 optimal weight: 0.0040 chunk 223 optimal weight: 7.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN H 57 ASN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN B 951 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN C 189 GLN C 234 GLN C 455 ASN C 657 ASN C 778 GLN C 872 ASN J 90 GLN ** O 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.223416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.208888 restraints weight = 79623.773| |-----------------------------------------------------------------------------| r_work (start): 0.4627 rms_B_bonded: 1.09 r_work: 0.3910 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.005 0.106 46688 Z= 0.196 Angle : 0.678 13.344 63632 Z= 0.347 Chirality : 0.047 0.320 7256 Planarity : 0.005 0.071 8130 Dihedral : 5.784 56.252 6926 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 0.83 % Allowed : 6.36 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.29 (0.11), residues: 5769 helix: 1.56 (0.19), residues: 713 sheet: 0.60 (0.11), residues: 2001 loop : -1.21 (0.11), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 60 TYR 0.037 0.002 TYR A 160 PHE 0.020 0.002 PHE C 914 TRP 0.021 0.002 TRP C 902 HIS 0.013 0.001 HIS F 34 Details of bonding type rmsd covalent geometry : bond 0.00470 (46584) covalent geometry : angle 0.65884 (63392) SS BOND : bond 0.00645 ( 72) SS BOND : angle 1.99839 ( 144) hydrogen bonds : bond 0.04666 ( 1841) hydrogen bonds : angle 5.91108 ( 5031) link_NAG-ASN : bond 0.00420 ( 32) link_NAG-ASN : angle 3.48390 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7654 (pp20) REVERT: A 1157 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8185 (tp) REVERT: M 111 ILE cc_start: 0.4901 (mm) cc_final: 0.4615 (mt) REVERT: B 756 MET cc_start: 0.8671 (ttm) cc_final: 0.8446 (ttt) REVERT: Q 17 GLU cc_start: 0.1187 (pm20) cc_final: 0.0408 (pp20) REVERT: C 871 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6203 (p90) REVERT: I 95 TYR cc_start: 0.1993 (m-80) cc_final: 0.1774 (m-10) REVERT: J 127 LYS cc_start: 0.3658 (pttp) cc_final: 0.3349 (mptt) REVERT: J 184 LYS cc_start: -0.0204 (mmtt) cc_final: -0.0425 (mmtt) REVERT: J 208 LYS cc_start: 0.0814 (OUTLIER) cc_final: 0.0331 (ptmm) REVERT: O 29 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6176 (pp) outliers start: 42 outliers final: 16 residues processed: 275 average time/residue: 0.5568 time to fit residues: 199.0225 Evaluate side-chains 241 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 871 PHE Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain O residue 29 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 63 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 546 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 94 optimal weight: 0.4980 chunk 306 optimal weight: 3.9990 chunk 381 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 460 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 HIS C 261 HIS C 455 ASN C 778 GLN O 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.223489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.208931 restraints weight = 79264.747| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 1.08 r_work: 0.3909 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work: 0.3588 rms_B_bonded: 3.83 restraints_weight: 0.1250 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 46688 Z= 0.204 Angle : 0.659 13.901 63632 Z= 0.336 Chirality : 0.047 0.286 7256 Planarity : 0.005 0.076 8130 Dihedral : 5.534 56.606 6926 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.43 % Favored : 93.52 % Rotamer: Outliers : 1.42 % Allowed : 9.57 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.25 (0.11), residues: 5769 helix: 1.57 (0.19), residues: 732 sheet: 0.61 (0.12), residues: 1991 loop : -1.17 (0.11), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 60 TYR 0.033 0.002 TYR C 160 PHE 0.027 0.002 PHE B 184 TRP 0.017 0.002 TRP H 55 HIS 0.010 0.001 HIS F 34 Details of bonding type rmsd covalent geometry : bond 0.00494 (46584) covalent geometry : angle 0.64082 (63392) SS BOND : bond 0.00622 ( 72) SS BOND : angle 1.87964 ( 144) hydrogen bonds : bond 0.04579 ( 1841) hydrogen bonds : angle 5.71368 ( 5031) link_NAG-ASN : bond 0.00375 ( 32) link_NAG-ASN : angle 3.36295 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 232 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 796 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7978 (pp20) REVERT: A 836 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: A 1157 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8290 (tp) REVERT: H 99 HIS cc_start: 0.5605 (OUTLIER) cc_final: 0.5086 (t-90) REVERT: M 34 MET cc_start: 0.3270 (mpm) cc_final: 0.2955 (mpm) REVERT: M 38 ARG cc_start: 0.2911 (ttm-80) cc_final: 0.2541 (ttm-80) REVERT: B 756 MET cc_start: 0.8952 (ttm) cc_final: 0.8731 (ttt) REVERT: C 871 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6299 (p90) REVERT: C 1000 LEU cc_start: 0.8282 (mp) cc_final: 0.7948 (tp) REVERT: I 95 TYR cc_start: 0.2059 (m-80) cc_final: 0.1704 (m-10) REVERT: J 127 LYS cc_start: 0.3685 (pttp) cc_final: 0.3152 (mptt) REVERT: J 184 LYS cc_start: -0.0326 (mmtt) cc_final: -0.0538 (mmtt) REVERT: J 208 LYS cc_start: 0.0774 (OUTLIER) cc_final: 0.0328 (ptmm) REVERT: K 52 TYR cc_start: 0.5484 (m-80) cc_final: 0.5011 (m-80) REVERT: O 29 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6409 (pp) outliers start: 72 outliers final: 32 residues processed: 281 average time/residue: 0.6102 time to fit residues: 226.1873 Evaluate side-chains 248 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 871 PHE Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain O residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 120 optimal weight: 6.9990 chunk 77 optimal weight: 0.0980 chunk 345 optimal weight: 40.0000 chunk 414 optimal weight: 8.9990 chunk 309 optimal weight: 30.0000 chunk 218 optimal weight: 0.6980 chunk 409 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 147 optimal weight: 30.0000 chunk 553 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS ** P 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS C 455 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.223164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.208507 restraints weight = 79196.696| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 1.08 r_work: 0.3921 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work: 0.3574 rms_B_bonded: 4.53 restraints_weight: 0.1250 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 46688 Z= 0.235 Angle : 0.675 14.515 63632 Z= 0.343 Chirality : 0.048 0.274 7256 Planarity : 0.005 0.080 8130 Dihedral : 5.538 57.756 6926 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 1.75 % Allowed : 11.61 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.30 (0.11), residues: 5769 helix: 1.46 (0.19), residues: 738 sheet: 0.56 (0.12), residues: 1969 loop : -1.16 (0.11), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 60 TYR 0.035 0.002 TYR C 160 PHE 0.022 0.002 PHE C 914 TRP 0.017 0.002 TRP M 36 HIS 0.016 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00573 (46584) covalent geometry : angle 0.65547 (63392) SS BOND : bond 0.00662 ( 72) SS BOND : angle 1.96752 ( 144) hydrogen bonds : bond 0.04734 ( 1841) hydrogen bonds : angle 5.67794 ( 5031) link_NAG-ASN : bond 0.00374 ( 32) link_NAG-ASN : angle 3.53231 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 223 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 836 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: A 1157 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8204 (tp) REVERT: H 99 HIS cc_start: 0.5484 (OUTLIER) cc_final: 0.5046 (t-90) REVERT: M 38 ARG cc_start: 0.2646 (ttm-80) cc_final: 0.2278 (ttm-80) REVERT: M 94 TYR cc_start: 0.3128 (OUTLIER) cc_final: 0.1612 (m-10) REVERT: B 756 MET cc_start: 0.8821 (ttm) cc_final: 0.8604 (ttt) REVERT: C 871 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6429 (p90) REVERT: C 966 ASP cc_start: 0.8211 (m-30) cc_final: 0.7962 (m-30) REVERT: C 1000 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7967 (tp) REVERT: I 95 TYR cc_start: 0.2017 (m-80) cc_final: 0.1694 (m-10) REVERT: J 108 LYS cc_start: 0.4544 (mmmt) cc_final: 0.4296 (mmtt) REVERT: J 127 LYS cc_start: 0.3513 (pttp) cc_final: 0.3165 (mptt) REVERT: J 208 LYS cc_start: 0.1047 (OUTLIER) cc_final: 0.0390 (ptmm) REVERT: K 52 TYR cc_start: 0.5622 (m-80) cc_final: 0.5210 (m-80) REVERT: O 29 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6294 (pp) outliers start: 89 outliers final: 40 residues processed: 290 average time/residue: 0.5526 time to fit residues: 215.5866 Evaluate side-chains 258 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 754 CYS Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain M residue 94 TYR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain O residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 327 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 416 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 519 optimal weight: 40.0000 chunk 40 optimal weight: 8.9990 chunk 468 optimal weight: 0.8980 chunk 200 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 147 optimal weight: 30.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN ** Q 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN J 199 HIS O 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.224079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.209680 restraints weight = 79624.384| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 1.09 r_work: 0.3934 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work: 0.3600 rms_B_bonded: 4.22 restraints_weight: 0.1250 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 46688 Z= 0.135 Angle : 0.609 13.473 63632 Z= 0.310 Chirality : 0.045 0.280 7256 Planarity : 0.005 0.081 8130 Dihedral : 5.187 58.069 6926 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.58 % Favored : 94.37 % Rotamer: Outliers : 1.79 % Allowed : 12.62 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.13 (0.11), residues: 5769 helix: 1.79 (0.19), residues: 737 sheet: 0.59 (0.12), residues: 1992 loop : -1.05 (0.11), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 174 TYR 0.029 0.001 TYR C 160 PHE 0.024 0.001 PHE H 100 TRP 0.020 0.001 TRP M 36 HIS 0.005 0.001 HIS F 34 Details of bonding type rmsd covalent geometry : bond 0.00314 (46584) covalent geometry : angle 0.59262 (63392) SS BOND : bond 0.00493 ( 72) SS BOND : angle 1.69685 ( 144) hydrogen bonds : bond 0.03911 ( 1841) hydrogen bonds : angle 5.47900 ( 5031) link_NAG-ASN : bond 0.00317 ( 32) link_NAG-ASN : angle 3.11635 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 238 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 836 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: A 1157 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8227 (tp) REVERT: H 99 HIS cc_start: 0.5573 (OUTLIER) cc_final: 0.5136 (t-90) REVERT: M 111 ILE cc_start: 0.4891 (mm) cc_final: 0.4600 (mt) REVERT: B 756 MET cc_start: 0.8916 (ttm) cc_final: 0.8710 (ttt) REVERT: F 4 MET cc_start: 0.3100 (tpp) cc_final: 0.2819 (tpp) REVERT: C 450 ILE cc_start: 0.8307 (mp) cc_final: 0.8093 (pt) REVERT: C 871 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6405 (p90) REVERT: C 1000 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7896 (tp) REVERT: I 95 TYR cc_start: 0.2026 (m-80) cc_final: 0.1669 (m-10) REVERT: J 208 LYS cc_start: 0.0828 (OUTLIER) cc_final: 0.0177 (ptmm) REVERT: K 52 TYR cc_start: 0.5603 (m-80) cc_final: 0.5108 (m-80) REVERT: K 82 MET cc_start: 0.1863 (OUTLIER) cc_final: 0.0393 (mmm) REVERT: O 29 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6525 (pp) outliers start: 91 outliers final: 34 residues processed: 306 average time/residue: 0.3340 time to fit residues: 139.4125 Evaluate side-chains 250 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 754 CYS Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 871 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain O residue 29 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 415 optimal weight: 10.0000 chunk 244 optimal weight: 0.0770 chunk 474 optimal weight: 4.9990 chunk 372 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 225 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 505 optimal weight: 50.0000 chunk 155 optimal weight: 6.9990 overall best weight: 3.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 333 ASN ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 ASN N 27 GLN N 32 HIS ** Q 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN C 68 GLN C 82 HIS C 261 HIS C 455 ASN O 37 GLN O 168 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.217072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.201961 restraints weight = 78256.932| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 1.07 r_work: 0.3831 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work: 0.3466 rms_B_bonded: 3.93 restraints_weight: 0.1250 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.156 46688 Z= 0.310 Angle : 0.733 19.411 63632 Z= 0.371 Chirality : 0.051 0.801 7256 Planarity : 0.006 0.084 8130 Dihedral : 5.659 59.196 6926 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.96 % Rotamer: Outliers : 2.30 % Allowed : 13.62 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.38 (0.11), residues: 5769 helix: 1.35 (0.19), residues: 737 sheet: 0.47 (0.12), residues: 1991 loop : -1.19 (0.11), residues: 3041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 921 TYR 0.036 0.002 TYR A 160 PHE 0.027 0.002 PHE C 914 TRP 0.022 0.002 TRP F 35 HIS 0.008 0.001 HIS B1080 Details of bonding type rmsd covalent geometry : bond 0.00761 (46584) covalent geometry : angle 0.71050 (63392) SS BOND : bond 0.00808 ( 72) SS BOND : angle 2.08561 ( 144) hydrogen bonds : bond 0.05244 ( 1841) hydrogen bonds : angle 5.67331 ( 5031) link_NAG-ASN : bond 0.00479 ( 32) link_NAG-ASN : angle 4.00717 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 214 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 HIS cc_start: 0.5237 (OUTLIER) cc_final: 0.5034 (m-70) REVERT: A 585 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 836 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: A 1157 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8260 (tp) REVERT: H 99 HIS cc_start: 0.5789 (OUTLIER) cc_final: 0.5333 (t-90) REVERT: E 34 MET cc_start: 0.4054 (mmm) cc_final: 0.3720 (tpp) REVERT: F 211 PHE cc_start: -0.0547 (OUTLIER) cc_final: -0.0807 (p90) REVERT: C 778 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7906 (pp30) REVERT: C 871 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6290 (p90) REVERT: C 1000 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7907 (tp) REVERT: I 95 TYR cc_start: 0.2070 (m-80) cc_final: 0.1653 (m-10) REVERT: J 208 LYS cc_start: 0.0791 (OUTLIER) cc_final: 0.0171 (ptmm) REVERT: K 52 TYR cc_start: 0.5757 (m-80) cc_final: 0.5192 (m-80) REVERT: K 82 MET cc_start: 0.1833 (OUTLIER) cc_final: 0.0519 (mmm) outliers start: 117 outliers final: 54 residues processed: 306 average time/residue: 0.3227 time to fit residues: 135.8522 Evaluate side-chains 265 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 754 CYS Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 1061 LYS Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain P residue 110 TYR Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 778 GLN Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 22 optimal weight: 5.9990 chunk 323 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 384 optimal weight: 6.9990 chunk 450 optimal weight: 0.9980 chunk 148 optimal weight: 0.0980 chunk 474 optimal weight: 3.9990 chunk 490 optimal weight: 7.9990 chunk 440 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 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 162 HIS ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 778 GLN O 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.224196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.209395 restraints weight = 78764.780| |-----------------------------------------------------------------------------| r_work (start): 0.4623 rms_B_bonded: 1.09 r_work: 0.3876 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work: 0.3485 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 46688 Z= 0.137 Angle : 0.636 17.144 63632 Z= 0.320 Chirality : 0.046 0.737 7256 Planarity : 0.005 0.085 8130 Dihedral : 5.328 59.411 6926 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 1.87 % Allowed : 14.49 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.14 (0.11), residues: 5769 helix: 1.81 (0.19), residues: 733 sheet: 0.61 (0.12), residues: 1973 loop : -1.08 (0.11), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 174 TYR 0.051 0.001 TYR A 160 PHE 0.026 0.001 PHE N 71 TRP 0.032 0.001 TRP H 169 HIS 0.016 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00321 (46584) covalent geometry : angle 0.61452 (63392) SS BOND : bond 0.00563 ( 72) SS BOND : angle 1.95064 ( 144) hydrogen bonds : bond 0.03929 ( 1841) hydrogen bonds : angle 5.43815 ( 5031) link_NAG-ASN : bond 0.00644 ( 32) link_NAG-ASN : angle 3.60622 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 208 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.8318 (m-10) cc_final: 0.8077 (m-80) REVERT: A 836 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: A 1157 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8220 (tp) REVERT: H 99 HIS cc_start: 0.5839 (OUTLIER) cc_final: 0.5416 (t-90) REVERT: P 100 PHE cc_start: 0.3608 (t80) cc_final: 0.3362 (t80) REVERT: E 34 MET cc_start: 0.3975 (mmm) cc_final: 0.3621 (tpp) REVERT: F 4 MET cc_start: 0.3120 (tpp) cc_final: 0.2882 (tpp) REVERT: C 450 ILE cc_start: 0.8359 (mp) cc_final: 0.8099 (pt) REVERT: C 871 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6361 (p90) REVERT: C 1000 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7912 (tp) REVERT: I 95 TYR cc_start: 0.1926 (m-80) cc_final: 0.1540 (m-10) REVERT: J 208 LYS cc_start: 0.0854 (OUTLIER) cc_final: 0.0326 (ptmm) REVERT: K 52 TYR cc_start: 0.5831 (m-80) cc_final: 0.5369 (m-80) outliers start: 95 outliers final: 46 residues processed: 285 average time/residue: 0.2943 time to fit residues: 116.1155 Evaluate side-chains 256 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 754 CYS Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 110 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain K residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 455 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 365 optimal weight: 50.0000 chunk 316 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 395 optimal weight: 3.9990 chunk 564 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN C 261 HIS C 455 ASN C 778 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.221271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.206370 restraints weight = 78386.557| |-----------------------------------------------------------------------------| r_work (start): 0.4600 rms_B_bonded: 1.08 r_work: 0.3851 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work: 0.3509 rms_B_bonded: 4.17 restraints_weight: 0.1250 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.007 0.140 46688 Z= 0.267 Angle : 0.701 15.507 63632 Z= 0.355 Chirality : 0.050 0.766 7256 Planarity : 0.005 0.085 8130 Dihedral : 5.534 60.075 6926 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.97 % Favored : 93.00 % Rotamer: Outliers : 2.07 % Allowed : 14.60 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.32 (0.11), residues: 5769 helix: 1.51 (0.19), residues: 734 sheet: 0.49 (0.12), residues: 1995 loop : -1.16 (0.11), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 921 TYR 0.033 0.002 TYR A 160 PHE 0.024 0.002 PHE C 914 TRP 0.032 0.002 TRP I 55 HIS 0.007 0.001 HIS B1080 Details of bonding type rmsd covalent geometry : bond 0.00653 (46584) covalent geometry : angle 0.67926 (63392) SS BOND : bond 0.00745 ( 72) SS BOND : angle 2.11203 ( 144) hydrogen bonds : bond 0.04900 ( 1841) hydrogen bonds : angle 5.56384 ( 5031) link_NAG-ASN : bond 0.00535 ( 32) link_NAG-ASN : angle 3.75395 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 207 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 836 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: H 55 TRP cc_start: 0.6783 (OUTLIER) cc_final: 0.6401 (p-90) REVERT: H 99 HIS cc_start: 0.5704 (OUTLIER) cc_final: 0.5251 (t-90) REVERT: E 34 MET cc_start: 0.4033 (mmm) cc_final: 0.3503 (mmm) REVERT: F 4 MET cc_start: 0.2952 (tpp) cc_final: 0.2638 (tpp) REVERT: C 871 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6222 (p90) REVERT: C 1000 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7946 (tp) REVERT: I 27 PHE cc_start: 0.3833 (OUTLIER) cc_final: 0.3562 (p90) REVERT: I 95 TYR cc_start: 0.1894 (m-80) cc_final: 0.1570 (m-10) REVERT: J 208 LYS cc_start: 0.0987 (OUTLIER) cc_final: 0.0645 (ptmm) REVERT: K 52 TYR cc_start: 0.5662 (m-80) cc_final: 0.5153 (m-80) REVERT: O 29 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6482 (pp) outliers start: 105 outliers final: 58 residues processed: 289 average time/residue: 0.2948 time to fit residues: 117.3115 Evaluate side-chains 266 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 200 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 754 CYS Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 55 TRP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 1061 LYS Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1110 VAL Chi-restraints excluded: chain B residue 1152 THR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 110 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain I residue 27 PHE Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain O residue 29 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 367 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 317 optimal weight: 50.0000 chunk 68 optimal weight: 0.6980 chunk 448 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 217 optimal weight: 0.5980 chunk 435 optimal weight: 0.6980 chunk 274 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN B 137 ASN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 199 HIS C 68 GLN C 261 HIS ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 691 GLN C 778 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.222888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.208334 restraints weight = 78793.735| |-----------------------------------------------------------------------------| r_work (start): 0.4627 rms_B_bonded: 1.09 r_work: 0.3908 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work: 0.3519 rms_B_bonded: 4.56 restraints_weight: 0.1250 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 46688 Z= 0.120 Angle : 0.615 12.827 63632 Z= 0.311 Chirality : 0.045 0.635 7256 Planarity : 0.005 0.087 8130 Dihedral : 5.122 59.152 6926 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 1.38 % Allowed : 15.43 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.11 (0.11), residues: 5769 helix: 1.85 (0.19), residues: 741 sheet: 0.62 (0.12), residues: 1973 loop : -1.06 (0.11), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 55 TYR 0.031 0.001 TYR J 50 PHE 0.017 0.001 PHE F 211 TRP 0.028 0.001 TRP F 35 HIS 0.011 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00274 (46584) covalent geometry : angle 0.59820 (63392) SS BOND : bond 0.00563 ( 72) SS BOND : angle 1.74509 ( 144) hydrogen bonds : bond 0.03690 ( 1841) hydrogen bonds : angle 5.33755 ( 5031) link_NAG-ASN : bond 0.00554 ( 32) link_NAG-ASN : angle 3.17974 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.8263 (m-10) cc_final: 0.8025 (m-80) REVERT: A 836 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: H 99 HIS cc_start: 0.5857 (OUTLIER) cc_final: 0.5409 (t-90) REVERT: M 79 TYR cc_start: 0.5005 (m-10) cc_final: 0.4703 (t80) REVERT: M 111 ILE cc_start: 0.4920 (mm) cc_final: 0.4643 (mt) REVERT: E 34 MET cc_start: 0.4036 (mmm) cc_final: 0.3594 (mmm) REVERT: F 4 MET cc_start: 0.3076 (tpp) cc_final: 0.2718 (tpp) REVERT: C 450 ILE cc_start: 0.8341 (mp) cc_final: 0.8099 (pt) REVERT: C 871 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6319 (p90) REVERT: C 1000 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7906 (tp) REVERT: I 95 TYR cc_start: 0.1915 (m-80) cc_final: 0.1546 (m-10) REVERT: J 208 LYS cc_start: 0.0928 (OUTLIER) cc_final: 0.0674 (ptmm) REVERT: K 52 TYR cc_start: 0.5752 (m-80) cc_final: 0.5222 (m-80) REVERT: O 29 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6558 (pp) outliers start: 70 outliers final: 44 residues processed: 270 average time/residue: 0.3393 time to fit residues: 125.4367 Evaluate side-chains 248 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 754 CYS Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 1061 LYS Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 110 TYR Chi-restraints excluded: chain P residue 213 VAL Chi-restraints excluded: chain Q residue 164 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain O residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 529 optimal weight: 30.0000 chunk 207 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 262 optimal weight: 0.6980 chunk 410 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 358 optimal weight: 0.0470 chunk 86 optimal weight: 4.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 27 GLN B 204 ASN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 778 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.223420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.208933 restraints weight = 79307.031| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 1.10 r_work: 0.3892 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work: 0.3509 rms_B_bonded: 4.55 restraints_weight: 0.1250 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 46688 Z= 0.117 Angle : 0.607 13.437 63632 Z= 0.306 Chirality : 0.045 0.628 7256 Planarity : 0.005 0.088 8130 Dihedral : 4.906 57.982 6926 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.26 % Rotamer: Outliers : 1.30 % Allowed : 15.61 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.00 (0.11), residues: 5769 helix: 2.01 (0.20), residues: 741 sheet: 0.72 (0.12), residues: 1970 loop : -1.03 (0.11), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 206 TYR 0.030 0.001 TYR J 50 PHE 0.029 0.001 PHE H 100 TRP 0.029 0.001 TRP F 35 HIS 0.006 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00268 (46584) covalent geometry : angle 0.59114 (63392) SS BOND : bond 0.00526 ( 72) SS BOND : angle 1.70557 ( 144) hydrogen bonds : bond 0.03560 ( 1841) hydrogen bonds : angle 5.23233 ( 5031) link_NAG-ASN : bond 0.00510 ( 32) link_NAG-ASN : angle 3.01224 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11538 Ramachandran restraints generated. 5769 Oldfield, 0 Emsley, 5769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 209 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 THR cc_start: 0.8499 (p) cc_final: 0.8197 (t) REVERT: A 836 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: H 99 HIS cc_start: 0.5934 (OUTLIER) cc_final: 0.5505 (t-90) REVERT: M 79 TYR cc_start: 0.5106 (m-10) cc_final: 0.4833 (t80) REVERT: M 93 TYR cc_start: 0.3696 (m-80) cc_final: 0.3095 (m-10) REVERT: E 34 MET cc_start: 0.4113 (mmm) cc_final: 0.3629 (mmm) REVERT: F 4 MET cc_start: 0.3033 (tpp) cc_final: 0.2727 (tpp) REVERT: C 450 ILE cc_start: 0.8354 (mp) cc_final: 0.8083 (pt) REVERT: C 871 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6230 (p90) REVERT: C 1000 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7867 (tp) REVERT: I 95 TYR cc_start: 0.1826 (m-80) cc_final: 0.1487 (m-10) REVERT: J 208 LYS cc_start: 0.0761 (OUTLIER) cc_final: 0.0559 (ptmm) REVERT: K 52 TYR cc_start: 0.5759 (m-80) cc_final: 0.5280 (m-80) REVERT: K 102 PHE cc_start: 0.5166 (t80) cc_final: 0.4955 (t80) REVERT: O 29 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6522 (pp) outliers start: 66 outliers final: 47 residues processed: 261 average time/residue: 0.2862 time to fit residues: 103.7932 Evaluate side-chains 250 residues out of total 5081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain N residue 106 VAL Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 287 GLN Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 1061 LYS Chi-restraints excluded: chain B residue 1108 GLU Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 110 TYR Chi-restraints excluded: chain P residue 213 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 261 HIS Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 541 CYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 871 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1014 THR Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain O residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 94 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 234 optimal weight: 30.0000 chunk 221 optimal weight: 10.0000 chunk 478 optimal weight: 0.9990 chunk 399 optimal weight: 0.9990 chunk 386 optimal weight: 5.9990 chunk 267 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN B 204 ASN ** B 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 261 HIS ** C 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN C 778 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.222539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.207873 restraints weight = 78766.096| |-----------------------------------------------------------------------------| r_work (start): 0.4620 rms_B_bonded: 1.09 r_work: 0.3875 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work: 0.3555 rms_B_bonded: 3.83 restraints_weight: 0.1250 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 46688 Z= 0.162 Angle : 0.631 14.073 63632 Z= 0.319 Chirality : 0.046 0.690 7256 Planarity : 0.005 0.087 8130 Dihedral : 4.985 57.434 6926 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 1.46 % Allowed : 15.51 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.41 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.04 (0.11), residues: 5769 helix: 1.95 (0.19), residues: 741 sheet: 0.70 (0.12), residues: 1971 loop : -1.06 (0.11), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 206 TYR 0.037 0.002 TYR H 111 PHE 0.024 0.001 PHE N 71 TRP 0.036 0.001 TRP F 35 HIS 0.005 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00388 (46584) covalent geometry : angle 0.61488 (63392) SS BOND : bond 0.00561 ( 72) SS BOND : angle 1.76808 ( 144) hydrogen bonds : bond 0.03997 ( 1841) hydrogen bonds : angle 5.27472 ( 5031) link_NAG-ASN : bond 0.00495 ( 32) link_NAG-ASN : angle 3.13941 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19059.00 seconds wall clock time: 323 minutes 31.71 seconds (19411.71 seconds total)