Starting phenix.real_space_refine on Mon Aug 25 13:45:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkq_34858/08_2025/8hkq_34858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkq_34858/08_2025/8hkq_34858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hkq_34858/08_2025/8hkq_34858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkq_34858/08_2025/8hkq_34858.map" model { file = "/net/cci-nas-00/data/ceres_data/8hkq_34858/08_2025/8hkq_34858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkq_34858/08_2025/8hkq_34858.cif" } resolution = 2.9 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= 0.035 sd= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 11 8.98 5 Zn 4 6.06 5 S 204 5.16 5 Na 1 4.78 5 C 18572 2.51 5 N 4768 2.21 5 O 5104 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.02s 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: 28676 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 42, 'TRANS': 859} Chain breaks: 6 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 42, 'TRANS': 859} Chain breaks: 6 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 42, 'TRANS': 859} Chain breaks: 6 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7137 Classifications: {'peptide': 902} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 42, 'TRANS': 859} Chain breaks: 6 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {' K': 3, ' ZN': 1, 'LQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {' K': 2, ' NA': 1, ' ZN': 1, 'LQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {' K': 3, ' ZN': 1, 'LQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {' K': 3, ' ZN': 1, 'LQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1489 SG CYS D 308 73.247 61.132 112.428 1.00 69.48 S ATOM 4396 SG CYS D 777 53.197 83.668 14.260 1.00 73.37 S ATOM 4402 SG CYS D 778 50.227 86.150 14.478 1.00 80.19 S ATOM 4456 SG CYS D 785 53.680 87.362 13.299 1.00124.06 S ATOM 8626 SG CYS A 308 61.141 78.495 112.418 1.00 69.36 S ATOM 11533 SG CYS A 777 83.681 98.631 14.270 1.00 76.35 S ATOM 11539 SG CYS A 778 86.160 101.606 14.480 1.00 80.17 S ATOM 11593 SG CYS A 785 87.375 98.143 13.318 1.00120.40 S ATOM 15763 SG CYS C 308 90.728 73.303 112.466 1.00 70.07 S ATOM 18670 SG CYS C 777 68.176 53.235 14.281 1.00 76.42 S ATOM 18676 SG CYS C 778 65.703 50.251 14.480 1.00 82.13 S ATOM 18730 SG CYS C 785 64.478 53.719 13.338 1.00123.20 S ATOM 22900 SG CYS B 308 78.613 90.716 112.532 1.00 72.64 S ATOM 25807 SG CYS B 777 98.608 68.191 14.288 1.00 74.79 S ATOM 25813 SG CYS B 778 101.596 65.724 14.484 1.00 80.48 S ATOM 25867 SG CYS B 785 98.137 64.493 13.336 1.00122.16 S Time building chain proxies: 5.74, per 1000 atoms: 0.20 Number of scatterers: 28676 At special positions: 0 Unit cell: (152.88, 152.88, 144.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 K 11 19.00 S 204 16.00 Na 1 11.00 F 12 9.00 O 5104 8.00 N 4768 7.00 C 18572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 778 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 778 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 777 " pdb=" ZN C1302 " pdb="ZN ZN C1302 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1302 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1302 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1302 " - pdb=" SG CYS C 778 " pdb=" ZN D1302 " pdb="ZN ZN D1302 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1302 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1302 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1302 " - pdb=" SG CYS D 778 " Number of angles added : 12 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 20 sheets defined 53.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'D' and resid 110 through 136 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 173 through 198 Processing helix chain 'D' and resid 211 through 228 removed outlier: 3.688A pdb=" N GLU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.329A pdb=" N ILE D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 240 through 256 removed outlier: 4.053A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 removed outlier: 3.632A pdb=" N ILE D 273 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 357 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.674A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 421 Processing helix chain 'D' and resid 422 through 427 removed outlier: 4.643A pdb=" N GLN D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 446 through 450 removed outlier: 3.529A pdb=" N ASN D 449 " --> pdb=" O LYS D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 482 removed outlier: 3.507A pdb=" N ALA D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 499 removed outlier: 4.330A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 579 through 591 Processing helix chain 'D' and resid 633 through 644 removed outlier: 3.733A pdb=" N LYS D 644 " --> pdb=" O GLU D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 removed outlier: 3.642A pdb=" N TYR D 796 " --> pdb=" O ASP D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 822 Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 Processing helix chain 'D' and resid 865 through 873 removed outlier: 3.705A pdb=" N LEU D 869 " --> pdb=" O ASN D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.900A pdb=" N MET D 889 " --> pdb=" O GLU D 886 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER D 890 " --> pdb=" O SER D 887 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA D 891 " --> pdb=" O THR D 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 886 through 891' Processing helix chain 'D' and resid 893 through 897 Processing helix chain 'D' and resid 898 through 912 Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.324A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 930 " --> pdb=" O MET D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 952 removed outlier: 3.595A pdb=" N LEU D 940 " --> pdb=" O ASP D 936 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 952 " --> pdb=" O ARG D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 960 removed outlier: 4.157A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 960' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 972 through 982 Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1013 through 1017 Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1130 through 1143 Processing helix chain 'D' and resid 1144 through 1161 Processing helix chain 'A' and resid 111 through 137 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 173 through 198 Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.626A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 4.307A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 254 removed outlier: 4.162A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 293 removed outlier: 4.206A pdb=" N GLN A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 357 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.647A pdb=" N GLN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.712A pdb=" N GLN A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 463 through 482 removed outlier: 3.503A pdb=" N ALA A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 removed outlier: 4.261A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.740A pdb=" N LYS A 644 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.623A pdb=" N TYR A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 865 through 873 removed outlier: 3.672A pdb=" N LEU A 869 " --> pdb=" O ASN A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.883A pdb=" N MET A 889 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 890 " --> pdb=" O SER A 887 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 891 " --> pdb=" O THR A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 912 Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.327A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 930 " --> pdb=" O MET A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.582A pdb=" N LEU A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 952 " --> pdb=" O ARG A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 4.199A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 972 through 982 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1130 through 1143 Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'C' and resid 111 through 136 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.545A pdb=" N TRP C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 198 Processing helix chain 'C' and resid 211 through 228 removed outlier: 3.715A pdb=" N GLU C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Proline residue: C 221 - end of helix removed outlier: 4.278A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 removed outlier: 3.505A pdb=" N ARG C 232 " --> pdb=" O PRO C 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 229 through 232' Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 254 removed outlier: 3.901A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 293 removed outlier: 4.025A pdb=" N GLN C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 357 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.668A pdb=" N GLN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 421 Processing helix chain 'C' and resid 422 through 427 removed outlier: 4.653A pdb=" N GLN C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 463 through 482 Processing helix chain 'C' and resid 493 through 499 removed outlier: 4.331A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 547 through 557 Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 579 through 591 Processing helix chain 'C' and resid 633 through 644 removed outlier: 3.721A pdb=" N LYS C 644 " --> pdb=" O GLU C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 removed outlier: 3.625A pdb=" N TYR C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 822 Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 865 through 873 removed outlier: 3.729A pdb=" N LEU C 869 " --> pdb=" O ASN C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.880A pdb=" N MET C 889 " --> pdb=" O GLU C 886 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 890 " --> pdb=" O SER C 887 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA C 891 " --> pdb=" O THR C 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 891' Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 898 through 912 Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.321A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 930 " --> pdb=" O MET C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 952 removed outlier: 3.587A pdb=" N LEU C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN C 952 " --> pdb=" O ARG C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 960 removed outlier: 4.213A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 960' Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 972 through 982 Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1013 through 1017 Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1130 through 1143 Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'B' and resid 111 through 136 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 173 through 198 Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.661A pdb=" N GLU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix removed outlier: 3.931A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 254 removed outlier: 4.050A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 293 removed outlier: 3.982A pdb=" N GLN B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 357 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.681A pdb=" N GLN B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.750A pdb=" N GLN B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.513A pdb=" N ASN B 449 " --> pdb=" O LYS B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 482 removed outlier: 3.517A pdb=" N ALA B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 4.338A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 591 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.734A pdb=" N LYS B 644 " --> pdb=" O GLU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.635A pdb=" N TYR B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 822 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 Processing helix chain 'B' and resid 865 through 873 removed outlier: 3.673A pdb=" N LEU B 869 " --> pdb=" O ASN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.965A pdb=" N MET B 889 " --> pdb=" O GLU B 886 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 890 " --> pdb=" O SER B 887 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 891 " --> pdb=" O THR B 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 898 through 912 Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.329A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B 930 " --> pdb=" O MET B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 952 removed outlier: 3.592A pdb=" N LEU B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 952 " --> pdb=" O ARG B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 4.149A pdb=" N PHE B 960 " --> pdb=" O ALA B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 960' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 972 through 982 removed outlier: 3.554A pdb=" N ASP B 976 " --> pdb=" O ILE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1130 through 1143 Processing helix chain 'B' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'D' and resid 429 through 433 removed outlier: 6.299A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N PHE D 454 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 375 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.665A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AA4, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.003A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU D 802 " --> pdb=" O ALA D 877 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN D 879 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER D 916 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU D 920 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 4.051A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.288A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N PHE A 454 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.661A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA9, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.015A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU A 802 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 879 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 920 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 4.033A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.292A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N PHE C 454 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.653A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB5, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.000A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 879 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 920 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 4.148A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.304A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N PHE B 454 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 375 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.661A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AC1, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.005A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 879 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 4.035A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) 1376 hydrogen bonds defined for protein. 3876 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: 6.75 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.52 - 0.82: 1 0.82 - 1.12: 0 1.12 - 1.42: 12107 1.42 - 1.71: 16935 1.71 - 2.01: 297 Bond restraints: 29340 Sorted by residual: bond pdb=" CG PRO C 229 " pdb=" CD PRO C 229 " ideal model delta sigma weight residual 1.503 0.520 0.983 3.40e-02 8.65e+02 8.36e+02 bond pdb=" CB PRO C 229 " pdb=" CG PRO C 229 " ideal model delta sigma weight residual 1.492 2.013 -0.521 5.00e-02 4.00e+02 1.09e+02 bond pdb=" C27 LQ9 C1301 " pdb=" N12 LQ9 C1301 " ideal model delta sigma weight residual 1.326 1.494 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" C27 LQ9 A1301 " pdb=" N12 LQ9 A1301 " ideal model delta sigma weight residual 1.326 1.493 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" C27 LQ9 D1301 " pdb=" N12 LQ9 D1301 " ideal model delta sigma weight residual 1.326 1.493 -0.167 2.00e-02 2.50e+03 6.93e+01 ... (remaining 29335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.70: 39880 11.70 - 23.40: 2 23.40 - 35.10: 1 35.10 - 46.81: 0 46.81 - 58.51: 1 Bond angle restraints: 39884 Sorted by residual: angle pdb=" N PRO C 229 " pdb=" CD PRO C 229 " pdb=" CG PRO C 229 " ideal model delta sigma weight residual 103.20 44.69 58.51 1.50e+00 4.44e-01 1.52e+03 angle pdb=" CA PRO C 229 " pdb=" CB PRO C 229 " pdb=" CG PRO C 229 " ideal model delta sigma weight residual 104.50 73.07 31.43 1.90e+00 2.77e-01 2.74e+02 angle pdb=" N PRO C 229 " pdb=" CA PRO C 229 " pdb=" CB PRO C 229 " ideal model delta sigma weight residual 103.08 93.54 9.54 9.70e-01 1.06e+00 9.68e+01 angle pdb=" CB PRO C 229 " pdb=" CG PRO C 229 " pdb=" CD PRO C 229 " ideal model delta sigma weight residual 106.10 83.98 22.12 3.20e+00 9.77e-02 4.78e+01 angle pdb=" CA PRO C 229 " pdb=" N PRO C 229 " pdb=" CD PRO C 229 " ideal model delta sigma weight residual 112.00 103.86 8.14 1.40e+00 5.10e-01 3.38e+01 ... (remaining 39879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 15872 21.23 - 42.46: 1401 42.46 - 63.68: 216 63.68 - 84.91: 36 84.91 - 106.14: 7 Dihedral angle restraints: 17532 sinusoidal: 6880 harmonic: 10652 Sorted by residual: dihedral pdb=" CA CYS B 148 " pdb=" C CYS B 148 " pdb=" N PRO B 149 " pdb=" CA PRO B 149 " ideal model delta harmonic sigma weight residual 180.00 146.11 33.89 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA CYS C 148 " pdb=" C CYS C 148 " pdb=" N PRO C 149 " pdb=" CA PRO C 149 " ideal model delta harmonic sigma weight residual 180.00 146.43 33.57 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" CA CYS A 148 " pdb=" C CYS A 148 " pdb=" N PRO A 149 " pdb=" CA PRO A 149 " ideal model delta harmonic sigma weight residual 180.00 147.80 32.20 0 5.00e+00 4.00e-02 4.15e+01 ... (remaining 17529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3576 0.046 - 0.093: 729 0.093 - 0.139: 233 0.139 - 0.185: 15 0.185 - 0.232: 3 Chirality restraints: 4556 Sorted by residual: chirality pdb=" CA SER C 313 " pdb=" N SER C 313 " pdb=" C SER C 313 " pdb=" CB SER C 313 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA MET A 192 " pdb=" N MET A 192 " pdb=" C MET A 192 " pdb=" CB MET A 192 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C13 LQ9 D1301 " pdb=" C15 LQ9 D1301 " pdb=" C17 LQ9 D1301 " pdb=" N07 LQ9 D1301 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 4553 not shown) Planarity restraints: 5008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 325 " 0.064 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO B 326 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 325 " 0.017 2.00e-02 2.50e+03 1.77e-02 7.84e+00 pdb=" CG TRP C 325 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP C 325 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 325 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 325 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 325 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 325 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 325 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 325 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 325 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 148 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.87e+00 pdb=" N PRO C 149 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.037 5.00e-02 4.00e+02 ... (remaining 5005 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.25: 16 2.25 - 2.98: 13788 2.98 - 3.70: 50855 3.70 - 4.42: 83020 4.42 - 5.14: 139304 Nonbonded interactions: 286983 Sorted by model distance: nonbonded pdb=" CG MET D 334 " pdb=" F02 LQ9 D1301 " model vdw 1.532 3.390 nonbonded pdb=" CG MET A 334 " pdb=" F02 LQ9 A1301 " model vdw 1.640 3.390 nonbonded pdb=" CG MET B 334 " pdb=" F02 LQ9 B1301 " model vdw 1.900 3.390 nonbonded pdb=" OG SER C 426 " pdb=" OE1 GLN C 427 " model vdw 2.096 3.040 nonbonded pdb=" O VAL D 183 " pdb=" OG SER D 187 " model vdw 2.125 3.040 ... (remaining 286978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 110 through 1302 or resid 1304 through 1305)) selection = (chain 'B' and (resid 110 through 1302 or resid 1304 through 1305)) selection = (chain 'C' and (resid 110 through 1302 or resid 1304 through 1305)) selection = (chain 'D' and (resid 110 through 1302 or resid 1304 through 1305)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 31.130 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.070 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 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 0.983 29356 Z= 0.317 Angle : 0.762 58.508 39896 Z= 0.407 Chirality : 0.041 0.232 4556 Planarity : 0.004 0.093 5008 Dihedral : 16.067 106.141 10620 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.19 % Allowed : 22.22 % Favored : 77.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3552 helix: 0.65 (0.13), residues: 1720 sheet: -0.38 (0.28), residues: 308 loop : -0.30 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 600 TYR 0.019 0.001 TYR D 553 PHE 0.030 0.001 PHE B 268 TRP 0.048 0.002 TRP C 325 HIS 0.005 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00840 (29340) covalent geometry : angle 0.76163 (39884) hydrogen bonds : bond 0.15336 ( 1376) hydrogen bonds : angle 5.22912 ( 3876) metal coordination : bond 0.00173 ( 16) metal coordination : angle 0.77524 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 508 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7004 (tpt) cc_final: 0.6790 (tpp) REVERT: D 387 MET cc_start: 0.8327 (mmm) cc_final: 0.7888 (mmp) REVERT: C 174 MET cc_start: 0.5294 (mmm) cc_final: 0.4987 (pmm) outliers start: 6 outliers final: 4 residues processed: 513 average time/residue: 0.6470 time to fit residues: 394.5956 Evaluate side-chains 302 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 298 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain B residue 212 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 ASN D 218 ASN D 254 ASN D 369 GLN D 400 GLN D 469 HIS D 470 GLN D 505 HIS D 800 ASN D 816 ASN D1136 GLN ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 254 ASN A 400 GLN A 415 GLN A 469 HIS A 470 GLN A 548 GLN ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A 816 ASN A 879 ASN A1159 HIS C 251 ASN C 254 ASN C 400 GLN C 469 HIS C 470 GLN C 505 HIS C 540 GLN C 632 ASN C 800 ASN C 816 ASN C1155 ASN C1159 HIS B 254 ASN B 400 GLN B 469 HIS B 470 GLN B 484 ASN B 505 HIS B 632 ASN B 800 ASN B 816 ASN B 845 HIS B1136 GLN B1155 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.109879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.088411 restraints weight = 74552.475| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.80 r_work: 0.3431 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29356 Z= 0.143 Angle : 0.667 14.385 39896 Z= 0.326 Chirality : 0.043 0.183 4556 Planarity : 0.005 0.080 5008 Dihedral : 7.329 87.604 3992 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.98 % Allowed : 21.63 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.14), residues: 3552 helix: 0.79 (0.13), residues: 1716 sheet: -0.48 (0.28), residues: 344 loop : -0.02 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 565 TYR 0.022 0.002 TYR B 351 PHE 0.050 0.002 PHE C 212 TRP 0.035 0.001 TRP A 243 HIS 0.008 0.001 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00324 (29340) covalent geometry : angle 0.66683 (39884) hydrogen bonds : bond 0.03965 ( 1376) hydrogen bonds : angle 4.37046 ( 3876) metal coordination : bond 0.00522 ( 16) metal coordination : angle 1.36454 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 395 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7534 (tpt) cc_final: 0.7267 (tpp) REVERT: D 388 ASP cc_start: 0.7411 (t0) cc_final: 0.7095 (t0) REVERT: D 545 SER cc_start: 0.6649 (OUTLIER) cc_final: 0.6429 (p) REVERT: D 566 MET cc_start: 0.7371 (tmm) cc_final: 0.6913 (tmm) REVERT: A 188 PHE cc_start: 0.7771 (t80) cc_final: 0.7328 (t80) REVERT: A 972 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6406 (mm) REVERT: A 1157 MET cc_start: 0.6549 (mtp) cc_final: 0.6303 (mtp) REVERT: C 174 MET cc_start: 0.6584 (mmm) cc_final: 0.5690 (pmm) REVERT: C 908 MET cc_start: 0.7148 (mmt) cc_final: 0.6838 (tpp) REVERT: B 204 TRP cc_start: 0.5292 (t-100) cc_final: 0.5026 (t60) REVERT: B 222 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7835 (t80) REVERT: B 805 VAL cc_start: 0.5818 (OUTLIER) cc_final: 0.5284 (p) REVERT: B 1011 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7040 (tppt) outliers start: 123 outliers final: 22 residues processed: 475 average time/residue: 0.5279 time to fit residues: 306.8768 Evaluate side-chains 332 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 305 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 387 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1011 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 244 optimal weight: 4.9990 chunk 358 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 178 optimal weight: 0.0970 chunk 108 optimal weight: 5.9990 chunk 215 optimal weight: 0.0060 chunk 288 optimal weight: 20.0000 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 879 ASN ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A1159 HIS ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 879 ASN C1159 HIS B 218 ASN B 460 ASN ** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS B 879 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.109680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.088559 restraints weight = 73752.625| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.55 r_work: 0.3431 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29356 Z= 0.119 Angle : 0.611 10.823 39896 Z= 0.294 Chirality : 0.042 0.153 4556 Planarity : 0.004 0.083 5008 Dihedral : 7.105 88.096 3986 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.95 % Allowed : 24.26 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.14), residues: 3552 helix: 0.92 (0.13), residues: 1744 sheet: -0.44 (0.28), residues: 340 loop : -0.00 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 600 TYR 0.028 0.001 TYR C 938 PHE 0.028 0.001 PHE D 585 TRP 0.028 0.001 TRP C 325 HIS 0.012 0.001 HIS B 845 Details of bonding type rmsd covalent geometry : bond 0.00261 (29340) covalent geometry : angle 0.61086 (39884) hydrogen bonds : bond 0.03668 ( 1376) hydrogen bonds : angle 4.22901 ( 3876) metal coordination : bond 0.00303 ( 16) metal coordination : angle 1.38915 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 359 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7536 (tpt) cc_final: 0.7253 (tpp) REVERT: D 388 ASP cc_start: 0.7548 (t0) cc_final: 0.7193 (t0) REVERT: D 566 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7123 (tmm) REVERT: A 188 PHE cc_start: 0.7760 (t80) cc_final: 0.7093 (t80) REVERT: A 222 PHE cc_start: 0.8215 (m-80) cc_final: 0.7985 (t80) REVERT: A 356 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7278 (ppp80) REVERT: A 545 SER cc_start: 0.6108 (OUTLIER) cc_final: 0.5808 (p) REVERT: A 565 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6289 (ttp80) REVERT: A 942 LEU cc_start: 0.7022 (mt) cc_final: 0.6715 (mt) REVERT: A 972 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6507 (mm) REVERT: A 1157 MET cc_start: 0.6739 (mtp) cc_final: 0.6312 (mtp) REVERT: C 174 MET cc_start: 0.6797 (mmm) cc_final: 0.5809 (pmm) REVERT: C 216 MET cc_start: 0.7948 (mmt) cc_final: 0.7725 (mmt) REVERT: C 908 MET cc_start: 0.7274 (mmp) cc_final: 0.6981 (tpp) REVERT: B 188 PHE cc_start: 0.8287 (t80) cc_final: 0.7921 (t80) REVERT: B 204 TRP cc_start: 0.5352 (t-100) cc_final: 0.5043 (t60) REVERT: B 216 MET cc_start: 0.8003 (ttp) cc_final: 0.7272 (tpp) REVERT: B 222 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7952 (t80) REVERT: B 283 PHE cc_start: 0.6956 (t80) cc_final: 0.6584 (t80) REVERT: B 388 ASP cc_start: 0.7234 (t0) cc_final: 0.6942 (t0) REVERT: B 389 PHE cc_start: 0.7222 (t80) cc_final: 0.6786 (t80) REVERT: B 545 SER cc_start: 0.6575 (OUTLIER) cc_final: 0.6320 (p) REVERT: B 788 ASN cc_start: 0.6722 (m-40) cc_final: 0.6414 (m-40) REVERT: B 896 MET cc_start: 0.8182 (mmm) cc_final: 0.7748 (mmm) REVERT: B 1011 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7107 (tppt) outliers start: 91 outliers final: 20 residues processed: 417 average time/residue: 0.5378 time to fit residues: 274.5159 Evaluate side-chains 325 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 316 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 337 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 632 ASN D 981 GLN ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS A 981 GLN A1159 HIS ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN C 460 ASN C 490 GLN C1159 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.101629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.079284 restraints weight = 74443.056| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.71 r_work: 0.3118 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.149 29356 Z= 0.514 Angle : 0.904 12.511 39896 Z= 0.450 Chirality : 0.057 0.355 4556 Planarity : 0.006 0.088 5008 Dihedral : 7.487 89.741 3986 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.89 % Allowed : 23.58 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.14), residues: 3552 helix: 0.20 (0.12), residues: 1724 sheet: -0.97 (0.27), residues: 340 loop : -0.30 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1020 TYR 0.045 0.003 TYR B1006 PHE 0.064 0.004 PHE A 776 TRP 0.028 0.002 TRP C 325 HIS 0.012 0.002 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.01265 (29340) covalent geometry : angle 0.90211 (39884) hydrogen bonds : bond 0.05152 ( 1376) hydrogen bonds : angle 4.80066 ( 3876) metal coordination : bond 0.00999 ( 16) metal coordination : angle 3.03188 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 400 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 216 MET cc_start: 0.7557 (tpt) cc_final: 0.7327 (tpp) REVERT: D 418 ARG cc_start: 0.8527 (mtm-85) cc_final: 0.8164 (mtt90) REVERT: A 127 CYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8361 (m) REVERT: A 163 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7096 (p0) REVERT: A 231 LEU cc_start: 0.8237 (mm) cc_final: 0.7939 (tp) REVERT: A 305 PHE cc_start: 0.8892 (t80) cc_final: 0.8666 (t80) REVERT: A 334 MET cc_start: 0.8537 (mmm) cc_final: 0.8268 (tpt) REVERT: A 356 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7676 (ppp80) REVERT: A 447 MET cc_start: 0.8598 (mmm) cc_final: 0.8297 (tpt) REVERT: A 473 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8661 (mp) REVERT: A 516 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8138 (mtm) REVERT: A 538 ARG cc_start: 0.8788 (mtp85) cc_final: 0.8535 (mtp-110) REVERT: A 566 MET cc_start: 0.7964 (tpp) cc_final: 0.7317 (tpt) REVERT: A 576 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: A 799 LYS cc_start: 0.8564 (pttp) cc_final: 0.8348 (ptmm) REVERT: A 841 LYS cc_start: 0.8532 (tmmt) cc_final: 0.8249 (tmmm) REVERT: A 1019 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6975 (tt) REVERT: A 1138 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7267 (mm) REVERT: C 213 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7428 (t) REVERT: C 216 MET cc_start: 0.8196 (mmt) cc_final: 0.7804 (mmt) REVERT: C 351 TYR cc_start: 0.7948 (t80) cc_final: 0.7261 (t80) REVERT: C 447 MET cc_start: 0.8186 (mmm) cc_final: 0.7714 (tpp) REVERT: C 615 ILE cc_start: 0.8207 (tp) cc_final: 0.8005 (tp) REVERT: C 631 GLU cc_start: 0.8004 (mp0) cc_final: 0.7679 (mp0) REVERT: C 930 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7120 (tpt) REVERT: C 975 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 188 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7750 (t80) REVERT: B 204 TRP cc_start: 0.5643 (t-100) cc_final: 0.5308 (t60) REVERT: B 216 MET cc_start: 0.8003 (ttp) cc_final: 0.7412 (tpp) REVERT: B 222 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8311 (t80) REVERT: B 538 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8366 (mtp85) REVERT: B 566 MET cc_start: 0.8203 (tpp) cc_final: 0.7925 (tpt) REVERT: B 828 ARG cc_start: 0.8088 (ptp90) cc_final: 0.7807 (ttp80) REVERT: B 829 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8321 (ptpp) REVERT: B 855 MET cc_start: 0.8792 (mtm) cc_final: 0.8450 (mtm) REVERT: B 1011 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8566 (ttmt) REVERT: B 1138 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7409 (mm) REVERT: B 1204 LEU cc_start: 0.8323 (mt) cc_final: 0.8025 (mt) outliers start: 151 outliers final: 57 residues processed: 503 average time/residue: 0.6193 time to fit residues: 372.1019 Evaluate side-chains 417 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 344 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 370 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 383 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 930 MET Chi-restraints excluded: chain C residue 975 LEU Chi-restraints excluded: chain C residue 1021 THR Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1196 VAL Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 627 ILE Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 829 LYS Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 275 optimal weight: 0.0050 chunk 246 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 319 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 251 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 HIS ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A1159 HIS C 247 HIS C1159 HIS B 119 ASN B 460 ASN B 845 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.104255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081662 restraints weight = 72934.393| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.80 r_work: 0.3200 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29356 Z= 0.126 Angle : 0.642 10.989 39896 Z= 0.311 Chirality : 0.043 0.213 4556 Planarity : 0.004 0.085 5008 Dihedral : 6.621 79.261 3984 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.30 % Allowed : 25.87 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.14), residues: 3552 helix: 0.69 (0.13), residues: 1736 sheet: -1.15 (0.27), residues: 340 loop : -0.10 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 565 TYR 0.024 0.002 TYR B 351 PHE 0.058 0.002 PHE A 235 TRP 0.029 0.001 TRP C 325 HIS 0.025 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00284 (29340) covalent geometry : angle 0.64199 (39884) hydrogen bonds : bond 0.03706 ( 1376) hydrogen bonds : angle 4.38360 ( 3876) metal coordination : bond 0.00424 ( 16) metal coordination : angle 1.55951 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 352 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 155 PHE cc_start: 0.7961 (t80) cc_final: 0.7675 (t80) REVERT: D 216 MET cc_start: 0.7572 (tpt) cc_final: 0.7311 (tpp) REVERT: D 418 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8263 (mtt90) REVERT: D 447 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7864 (mmt) REVERT: D 1162 LEU cc_start: 0.8465 (mp) cc_final: 0.7987 (mm) REVERT: A 163 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.6920 (p0) REVERT: A 231 LEU cc_start: 0.8136 (mm) cc_final: 0.7850 (tp) REVERT: A 340 VAL cc_start: 0.8967 (p) cc_final: 0.8702 (m) REVERT: A 447 MET cc_start: 0.8664 (mmm) cc_final: 0.8429 (tpt) REVERT: A 538 ARG cc_start: 0.8718 (mtp85) cc_final: 0.8432 (mtp-110) REVERT: A 799 LYS cc_start: 0.8537 (pttp) cc_final: 0.8213 (ptmm) REVERT: A 828 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7965 (ttm-80) REVERT: A 841 LYS cc_start: 0.8608 (tmmt) cc_final: 0.8360 (tmmm) REVERT: C 216 MET cc_start: 0.8240 (mmt) cc_final: 0.7801 (mmt) REVERT: C 279 LEU cc_start: 0.8691 (tm) cc_final: 0.8461 (tt) REVERT: C 631 GLU cc_start: 0.7955 (mp0) cc_final: 0.7700 (mp0) REVERT: C 844 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.7050 (t-90) REVERT: C 930 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6747 (tpt) REVERT: B 188 PHE cc_start: 0.8376 (t80) cc_final: 0.7767 (t80) REVERT: B 204 TRP cc_start: 0.5502 (t-100) cc_final: 0.5205 (t60) REVERT: B 216 MET cc_start: 0.7894 (ttp) cc_final: 0.7327 (tpp) REVERT: B 220 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7844 (pt) REVERT: B 222 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8168 (t80) REVERT: B 283 PHE cc_start: 0.8134 (t80) cc_final: 0.7880 (t80) REVERT: B 473 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8392 (mp) REVERT: B 538 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8362 (mtp85) REVERT: B 566 MET cc_start: 0.8002 (tpp) cc_final: 0.7794 (tpt) REVERT: B 1011 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8574 (ttmt) REVERT: B 1138 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7491 (mm) REVERT: B 1204 LEU cc_start: 0.8261 (mt) cc_final: 0.7967 (mt) outliers start: 102 outliers final: 39 residues processed: 415 average time/residue: 0.6284 time to fit residues: 310.5386 Evaluate side-chains 370 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 930 MET Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 27 optimal weight: 0.0970 chunk 219 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 308 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 981 GLN C1159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.104759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.081537 restraints weight = 72789.570| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.70 r_work: 0.3206 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29356 Z= 0.133 Angle : 0.632 10.803 39896 Z= 0.303 Chirality : 0.042 0.237 4556 Planarity : 0.004 0.075 5008 Dihedral : 6.029 65.530 3984 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.53 % Allowed : 25.68 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.14), residues: 3552 helix: 0.97 (0.13), residues: 1708 sheet: -0.95 (0.27), residues: 344 loop : 0.17 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 948 TYR 0.026 0.001 TYR C 351 PHE 0.036 0.002 PHE B 212 TRP 0.026 0.001 TRP C 325 HIS 0.024 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00310 (29340) covalent geometry : angle 0.63151 (39884) hydrogen bonds : bond 0.03543 ( 1376) hydrogen bonds : angle 4.20955 ( 3876) metal coordination : bond 0.00557 ( 16) metal coordination : angle 1.28148 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 344 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 155 PHE cc_start: 0.7942 (t80) cc_final: 0.7671 (t80) REVERT: D 418 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8281 (mtt90) REVERT: D 447 MET cc_start: 0.8406 (mmm) cc_final: 0.7989 (mmt) REVERT: D 896 MET cc_start: 0.8752 (mmt) cc_final: 0.8544 (mmm) REVERT: D 936 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: D 1017 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8455 (mm) REVERT: D 1162 LEU cc_start: 0.8476 (mp) cc_final: 0.8001 (mm) REVERT: A 127 CYS cc_start: 0.8634 (t) cc_final: 0.8369 (m) REVERT: A 163 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7014 (p0) REVERT: A 168 LEU cc_start: 0.7619 (mp) cc_final: 0.7270 (pt) REVERT: A 231 LEU cc_start: 0.8128 (mm) cc_final: 0.7822 (tp) REVERT: A 334 MET cc_start: 0.8649 (mmm) cc_final: 0.8440 (tpt) REVERT: A 356 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7751 (ppp80) REVERT: A 447 MET cc_start: 0.8659 (mmm) cc_final: 0.8410 (tpt) REVERT: A 473 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 538 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8435 (mtp-110) REVERT: A 566 MET cc_start: 0.7968 (tpp) cc_final: 0.7545 (tpp) REVERT: A 799 LYS cc_start: 0.8583 (pttp) cc_final: 0.8274 (ptmm) REVERT: A 841 LYS cc_start: 0.8689 (tmmt) cc_final: 0.8459 (tmmm) REVERT: A 1146 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7405 (tpm170) REVERT: C 213 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7392 (t) REVERT: C 216 MET cc_start: 0.8248 (mmp) cc_final: 0.7797 (mmt) REVERT: C 217 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8533 (mp) REVERT: C 279 LEU cc_start: 0.8737 (tm) cc_final: 0.8518 (tt) REVERT: C 398 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7964 (ptm-80) REVERT: C 447 MET cc_start: 0.8338 (mmm) cc_final: 0.8053 (mmm) REVERT: C 773 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8323 (ptmt) REVERT: C 844 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7132 (t-90) REVERT: B 188 PHE cc_start: 0.8466 (t80) cc_final: 0.7872 (t80) REVERT: B 204 TRP cc_start: 0.5580 (t-100) cc_final: 0.5276 (t60) REVERT: B 216 MET cc_start: 0.7914 (ttp) cc_final: 0.7262 (tpp) REVERT: B 220 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7876 (pt) REVERT: B 222 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8214 (t80) REVERT: B 447 MET cc_start: 0.8459 (mmm) cc_final: 0.7693 (tpp) REVERT: B 473 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 538 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8301 (mtp85) REVERT: B 552 MET cc_start: 0.8069 (mtp) cc_final: 0.7864 (mtp) REVERT: B 566 MET cc_start: 0.8090 (tpp) cc_final: 0.7847 (tpt) REVERT: B 1011 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8602 (ttmt) REVERT: B 1138 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7517 (mm) outliers start: 109 outliers final: 45 residues processed: 423 average time/residue: 0.6071 time to fit residues: 307.6346 Evaluate side-chains 388 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 328 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 936 ASP Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain D residue 981 GLN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 398 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 844 HIS Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 844 HIS Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 182 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 329 optimal weight: 0.9990 chunk 187 optimal weight: 20.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 981 GLN ** D1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 845 HIS ** A 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 HIS C1159 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.103831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081076 restraints weight = 72644.031| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.71 r_work: 0.3178 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.7781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29356 Z= 0.176 Angle : 0.663 12.312 39896 Z= 0.316 Chirality : 0.044 0.260 4556 Planarity : 0.004 0.079 5008 Dihedral : 5.938 61.071 3984 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.85 % Allowed : 26.17 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.14), residues: 3552 helix: 0.89 (0.13), residues: 1728 sheet: -0.92 (0.27), residues: 344 loop : 0.25 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 418 TYR 0.025 0.002 TYR D 351 PHE 0.043 0.002 PHE B 235 TRP 0.026 0.001 TRP C 325 HIS 0.035 0.002 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00426 (29340) covalent geometry : angle 0.66300 (39884) hydrogen bonds : bond 0.03702 ( 1376) hydrogen bonds : angle 4.23530 ( 3876) metal coordination : bond 0.00658 ( 16) metal coordination : angle 1.23447 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 339 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8586 (t) REVERT: D 155 PHE cc_start: 0.7866 (t80) cc_final: 0.7590 (t80) REVERT: D 418 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8210 (mtt90) REVERT: D 447 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8030 (mmt) REVERT: D 936 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: D 1017 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8441 (mm) REVERT: D 1136 GLN cc_start: 0.7154 (tm-30) cc_final: 0.6658 (pp30) REVERT: A 163 ASN cc_start: 0.8144 (OUTLIER) cc_final: 0.7083 (p0) REVERT: A 231 LEU cc_start: 0.8167 (mm) cc_final: 0.7913 (tp) REVERT: A 447 MET cc_start: 0.8704 (mmm) cc_final: 0.8452 (tpt) REVERT: A 473 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8629 (mp) REVERT: A 538 ARG cc_start: 0.8653 (mtp85) cc_final: 0.8415 (mtp-110) REVERT: A 566 MET cc_start: 0.8025 (tpp) cc_final: 0.7483 (tpt) REVERT: A 799 LYS cc_start: 0.8610 (pttp) cc_final: 0.8300 (ptmm) REVERT: A 828 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7912 (ttm-80) REVERT: A 841 LYS cc_start: 0.8722 (tmmt) cc_final: 0.8480 (tmmm) REVERT: A 1146 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7560 (tpm-80) REVERT: C 213 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7425 (t) REVERT: C 216 MET cc_start: 0.8308 (mmp) cc_final: 0.7868 (mmt) REVERT: C 279 LEU cc_start: 0.8756 (tm) cc_final: 0.8523 (tt) REVERT: C 352 LEU cc_start: 0.7966 (pp) cc_final: 0.7628 (mt) REVERT: C 773 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8375 (ptmt) REVERT: C 930 MET cc_start: 0.7289 (tpt) cc_final: 0.6591 (tpt) REVERT: C 969 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8315 (p) REVERT: B 188 PHE cc_start: 0.8458 (t80) cc_final: 0.7880 (t80) REVERT: B 204 TRP cc_start: 0.5588 (t-100) cc_final: 0.5278 (t60) REVERT: B 216 MET cc_start: 0.7884 (ttp) cc_final: 0.7533 (tpp) REVERT: B 222 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8271 (t80) REVERT: B 235 PHE cc_start: 0.7977 (t80) cc_final: 0.7667 (t80) REVERT: B 283 PHE cc_start: 0.8158 (t80) cc_final: 0.7935 (t80) REVERT: B 352 LEU cc_start: 0.8387 (tt) cc_final: 0.8133 (mp) REVERT: B 552 MET cc_start: 0.8079 (mtp) cc_final: 0.7838 (mtp) REVERT: B 566 MET cc_start: 0.8129 (tpp) cc_final: 0.7885 (tpt) REVERT: B 1011 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8643 (ttmt) REVERT: B 1138 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7601 (mm) REVERT: B 1141 TYR cc_start: 0.8037 (t80) cc_final: 0.7718 (t80) REVERT: B 1174 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.5512 (mp10) REVERT: B 1204 LEU cc_start: 0.8394 (mt) cc_final: 0.8061 (mp) outliers start: 119 outliers final: 46 residues processed: 424 average time/residue: 0.5996 time to fit residues: 305.2046 Evaluate side-chains 385 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 325 TRP Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 936 ASP Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain D residue 1162 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 828 ARG Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 844 HIS Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1174 GLN Chi-restraints excluded: chain B residue 1187 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 319 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 297 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 268 optimal weight: 0.4980 chunk 64 optimal weight: 0.0270 chunk 186 optimal weight: 5.9990 chunk 334 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN D1159 HIS A 981 GLN A1159 HIS C 291 HIS C1159 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.104828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.081363 restraints weight = 72343.848| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.77 r_work: 0.3201 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.7885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29356 Z= 0.116 Angle : 0.649 12.251 39896 Z= 0.305 Chirality : 0.042 0.255 4556 Planarity : 0.004 0.069 5008 Dihedral : 5.625 55.733 3984 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.75 % Allowed : 27.53 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.14), residues: 3552 helix: 1.05 (0.13), residues: 1716 sheet: -0.84 (0.27), residues: 344 loop : 0.28 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B1142 TYR 0.025 0.001 TYR B 351 PHE 0.041 0.002 PHE B 235 TRP 0.026 0.001 TRP C 325 HIS 0.035 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00266 (29340) covalent geometry : angle 0.64904 (39884) hydrogen bonds : bond 0.03402 ( 1376) hydrogen bonds : angle 4.16527 ( 3876) metal coordination : bond 0.00436 ( 16) metal coordination : angle 1.17891 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 331 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 126 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8588 (t) REVERT: D 155 PHE cc_start: 0.7849 (t80) cc_final: 0.7595 (t80) REVERT: D 306 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7631 (t80) REVERT: D 896 MET cc_start: 0.8724 (mmt) cc_final: 0.8429 (mmm) REVERT: D 936 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: D 959 MET cc_start: 0.8692 (ptm) cc_final: 0.8259 (ttp) REVERT: D 1017 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8426 (mm) REVERT: D 1136 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6646 (pp30) REVERT: A 163 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7850 (p0) REVERT: A 168 LEU cc_start: 0.7741 (mp) cc_final: 0.7472 (pt) REVERT: A 231 LEU cc_start: 0.8121 (mm) cc_final: 0.7902 (tp) REVERT: A 447 MET cc_start: 0.8655 (mmm) cc_final: 0.8428 (tpt) REVERT: A 538 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8392 (mtp-110) REVERT: A 566 MET cc_start: 0.7957 (tpp) cc_final: 0.7419 (tpt) REVERT: A 799 LYS cc_start: 0.8667 (pttp) cc_final: 0.8309 (ptmm) REVERT: A 841 LYS cc_start: 0.8751 (tmmt) cc_final: 0.8508 (tmmm) REVERT: A 972 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7216 (mm) REVERT: A 1138 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7158 (mm) REVERT: A 1146 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7540 (tpm-80) REVERT: C 216 MET cc_start: 0.8250 (mmp) cc_final: 0.7838 (mmt) REVERT: C 279 LEU cc_start: 0.8797 (tm) cc_final: 0.8571 (tt) REVERT: C 352 LEU cc_start: 0.7912 (pp) cc_final: 0.7591 (mt) REVERT: C 773 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8380 (ptmt) REVERT: B 188 PHE cc_start: 0.8414 (t80) cc_final: 0.7839 (t80) REVERT: B 204 TRP cc_start: 0.5596 (t-100) cc_final: 0.5283 (t60) REVERT: B 216 MET cc_start: 0.7791 (ttp) cc_final: 0.7339 (tpp) REVERT: B 235 PHE cc_start: 0.7770 (t80) cc_final: 0.7570 (t80) REVERT: B 283 PHE cc_start: 0.8195 (t80) cc_final: 0.7943 (t80) REVERT: B 352 LEU cc_start: 0.8365 (tt) cc_final: 0.8125 (mp) REVERT: B 473 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8365 (mp) REVERT: B 566 MET cc_start: 0.8029 (tpp) cc_final: 0.7760 (tpt) REVERT: B 1011 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8662 (ttmt) REVERT: B 1138 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7575 (mm) REVERT: B 1204 LEU cc_start: 0.8364 (mt) cc_final: 0.7981 (mp) outliers start: 85 outliers final: 45 residues processed: 393 average time/residue: 0.6105 time to fit residues: 287.2286 Evaluate side-chains 374 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 936 ASP Chi-restraints excluded: chain D residue 1010 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 981 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1146 ARG Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 855 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 844 HIS Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1014 GLU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain B residue 1187 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 265 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 328 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 351 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1159 HIS A1159 HIS C 291 HIS B 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.104640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.081378 restraints weight = 73048.406| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.77 r_work: 0.3202 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.7973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29356 Z= 0.125 Angle : 0.662 16.979 39896 Z= 0.309 Chirality : 0.043 0.293 4556 Planarity : 0.004 0.075 5008 Dihedral : 5.402 52.063 3984 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.59 % Allowed : 27.53 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.14), residues: 3552 helix: 1.08 (0.13), residues: 1716 sheet: -0.75 (0.28), residues: 344 loop : 0.32 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 418 TYR 0.017 0.001 TYR C 553 PHE 0.035 0.002 PHE A 235 TRP 0.025 0.001 TRP C 325 HIS 0.034 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00290 (29340) covalent geometry : angle 0.66195 (39884) hydrogen bonds : bond 0.03394 ( 1376) hydrogen bonds : angle 4.12615 ( 3876) metal coordination : bond 0.00482 ( 16) metal coordination : angle 1.19128 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 331 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 155 PHE cc_start: 0.7838 (t80) cc_final: 0.7555 (t80) REVERT: D 306 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7568 (t80) REVERT: D 896 MET cc_start: 0.8749 (mmt) cc_final: 0.8426 (mmm) REVERT: D 936 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: D 959 MET cc_start: 0.8694 (ptm) cc_final: 0.8319 (ttp) REVERT: D 1017 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8441 (mm) REVERT: D 1136 GLN cc_start: 0.7227 (tm-30) cc_final: 0.6711 (pp30) REVERT: A 163 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7849 (p0) REVERT: A 168 LEU cc_start: 0.7742 (mp) cc_final: 0.7491 (pt) REVERT: A 231 LEU cc_start: 0.8025 (mm) cc_final: 0.7797 (tp) REVERT: A 447 MET cc_start: 0.8637 (mmm) cc_final: 0.8392 (tpt) REVERT: A 473 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8535 (mp) REVERT: A 516 MET cc_start: 0.8340 (mtp) cc_final: 0.8073 (mtm) REVERT: A 538 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8335 (mtp-110) REVERT: A 566 MET cc_start: 0.7964 (tpp) cc_final: 0.7457 (tpt) REVERT: A 799 LYS cc_start: 0.8672 (pttp) cc_final: 0.8314 (ptmm) REVERT: A 841 LYS cc_start: 0.8771 (tmmt) cc_final: 0.8537 (tmmm) REVERT: A 972 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7195 (mm) REVERT: A 974 MET cc_start: 0.7886 (ppp) cc_final: 0.7474 (ptm) REVERT: A 1138 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7233 (mm) REVERT: C 119 ASN cc_start: 0.7608 (t0) cc_final: 0.7234 (m-40) REVERT: C 216 MET cc_start: 0.8176 (mmp) cc_final: 0.7760 (mmt) REVERT: C 279 LEU cc_start: 0.8813 (tm) cc_final: 0.8587 (tt) REVERT: C 352 LEU cc_start: 0.7916 (pp) cc_final: 0.7628 (mt) REVERT: C 773 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8396 (ptmt) REVERT: C 969 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8156 (p) REVERT: C 1159 HIS cc_start: 0.8150 (t-90) cc_final: 0.7862 (t-170) REVERT: B 188 PHE cc_start: 0.8497 (t80) cc_final: 0.7914 (t80) REVERT: B 204 TRP cc_start: 0.5642 (t-100) cc_final: 0.5307 (t60) REVERT: B 216 MET cc_start: 0.7977 (ttp) cc_final: 0.7702 (tpp) REVERT: B 283 PHE cc_start: 0.8201 (t80) cc_final: 0.7908 (t80) REVERT: B 334 MET cc_start: 0.7805 (tpp) cc_final: 0.7578 (ttp) REVERT: B 473 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8380 (mp) REVERT: B 538 ARG cc_start: 0.8279 (mtp85) cc_final: 0.8025 (mtp-110) REVERT: B 566 MET cc_start: 0.8037 (tpp) cc_final: 0.7768 (tpt) REVERT: B 1011 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8665 (ttmt) REVERT: B 1138 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7572 (mm) REVERT: B 1174 GLN cc_start: 0.6376 (OUTLIER) cc_final: 0.5597 (mp10) REVERT: B 1204 LEU cc_start: 0.8370 (mt) cc_final: 0.8030 (mp) outliers start: 80 outliers final: 42 residues processed: 386 average time/residue: 0.6168 time to fit residues: 285.5156 Evaluate side-chains 376 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 322 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 855 MET Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 936 ASP Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 829 LYS Chi-restraints excluded: chain B residue 844 HIS Chi-restraints excluded: chain B residue 1010 MET Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1174 GLN Chi-restraints excluded: chain B residue 1187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 98 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 355 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN D1159 HIS A1159 HIS C 291 HIS B 415 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.103432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.080821 restraints weight = 72707.030| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.63 r_work: 0.3186 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.8230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29356 Z= 0.169 Angle : 0.692 15.371 39896 Z= 0.325 Chirality : 0.044 0.289 4556 Planarity : 0.004 0.066 5008 Dihedral : 5.469 53.222 3984 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.17 % Allowed : 28.08 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.14), residues: 3552 helix: 1.00 (0.13), residues: 1724 sheet: -0.74 (0.28), residues: 344 loop : 0.38 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 418 TYR 0.025 0.002 TYR B 351 PHE 0.043 0.002 PHE B 235 TRP 0.024 0.001 TRP C 325 HIS 0.035 0.002 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00409 (29340) covalent geometry : angle 0.69215 (39884) hydrogen bonds : bond 0.03652 ( 1376) hydrogen bonds : angle 4.18146 ( 3876) metal coordination : bond 0.00579 ( 16) metal coordination : angle 1.21770 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 335 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 155 PHE cc_start: 0.7848 (t80) cc_final: 0.7608 (t80) REVERT: D 274 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8779 (tp) REVERT: D 306 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.7626 (t80) REVERT: D 936 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: D 959 MET cc_start: 0.8747 (ptm) cc_final: 0.8484 (ttp) REVERT: D 1017 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8509 (mm) REVERT: D 1020 ARG cc_start: 0.8528 (mtm110) cc_final: 0.8123 (mtm-85) REVERT: D 1136 GLN cc_start: 0.7339 (tm-30) cc_final: 0.6752 (pp30) REVERT: A 163 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7926 (p0) REVERT: A 168 LEU cc_start: 0.7750 (mp) cc_final: 0.7493 (pt) REVERT: A 176 LEU cc_start: 0.8437 (mt) cc_final: 0.8182 (mm) REVERT: A 231 LEU cc_start: 0.8133 (mm) cc_final: 0.7895 (tp) REVERT: A 447 MET cc_start: 0.8647 (mmm) cc_final: 0.8416 (tpt) REVERT: A 473 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 516 MET cc_start: 0.8395 (mtp) cc_final: 0.8143 (mtm) REVERT: A 538 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8354 (mtp-110) REVERT: A 566 MET cc_start: 0.8014 (tpp) cc_final: 0.7540 (tpt) REVERT: A 799 LYS cc_start: 0.8669 (pttp) cc_final: 0.8347 (ptmm) REVERT: A 959 MET cc_start: 0.8236 (ptm) cc_final: 0.8003 (ttm) REVERT: A 972 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7282 (mm) REVERT: A 974 MET cc_start: 0.7942 (ppp) cc_final: 0.7525 (ptm) REVERT: C 135 LEU cc_start: 0.8738 (tp) cc_final: 0.8528 (tp) REVERT: C 216 MET cc_start: 0.8129 (mmp) cc_final: 0.7717 (mmt) REVERT: C 268 PHE cc_start: 0.8293 (t80) cc_final: 0.8079 (t80) REVERT: C 279 LEU cc_start: 0.8815 (tm) cc_final: 0.8596 (tt) REVERT: C 352 LEU cc_start: 0.7992 (pp) cc_final: 0.7703 (mt) REVERT: C 418 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8426 (mtt180) REVERT: C 773 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8412 (ptmt) REVERT: C 969 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8285 (p) REVERT: B 188 PHE cc_start: 0.8454 (t80) cc_final: 0.7808 (t80) REVERT: B 204 TRP cc_start: 0.5658 (t-100) cc_final: 0.5344 (t60) REVERT: B 216 MET cc_start: 0.7949 (ttp) cc_final: 0.7683 (tpp) REVERT: B 1011 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8691 (ttmt) REVERT: B 1138 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7671 (mm) REVERT: B 1174 GLN cc_start: 0.6460 (OUTLIER) cc_final: 0.5664 (mp10) outliers start: 67 outliers final: 44 residues processed: 385 average time/residue: 0.6202 time to fit residues: 285.4538 Evaluate side-chains 376 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 321 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 855 MET Chi-restraints excluded: chain D residue 883 VAL Chi-restraints excluded: chain D residue 936 ASP Chi-restraints excluded: chain D residue 974 MET Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1159 HIS Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1043 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 829 LYS Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 1011 LYS Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1133 ILE Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1140 LEU Chi-restraints excluded: chain B residue 1174 GLN Chi-restraints excluded: chain B residue 1187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 359 optimal weight: 0.8980 chunk 252 optimal weight: 6.9990 chunk 203 optimal weight: 0.0980 chunk 352 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 296 optimal weight: 0.9990 chunk 330 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 241 ASN D1159 HIS A 180 GLN ** A 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1159 HIS B 415 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.104741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082556 restraints weight = 72213.602| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.83 r_work: 0.3204 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.8280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29356 Z= 0.121 Angle : 0.675 15.350 39896 Z= 0.316 Chirality : 0.043 0.319 4556 Planarity : 0.004 0.073 5008 Dihedral : 5.300 49.789 3984 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.01 % Allowed : 28.27 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.14), residues: 3552 helix: 1.09 (0.13), residues: 1716 sheet: -0.74 (0.28), residues: 344 loop : 0.37 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 948 TYR 0.021 0.001 TYR C 553 PHE 0.046 0.002 PHE A 235 TRP 0.025 0.001 TRP C 325 HIS 0.049 0.002 HIS C 291 Details of bonding type rmsd covalent geometry : bond 0.00278 (29340) covalent geometry : angle 0.67474 (39884) hydrogen bonds : bond 0.03422 ( 1376) hydrogen bonds : angle 4.14396 ( 3876) metal coordination : bond 0.00412 ( 16) metal coordination : angle 1.18004 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9561.36 seconds wall clock time: 164 minutes 24.39 seconds (9864.39 seconds total)